# Executive Summary

# Maternal Preconception Study

## Pup Milestones

# Introduction

The results of the analysis are presented using the following structure:

1. Searchable High‑Level Summary: Provides a brief overview of the key findings from our analysis with a table of effects
2. Visualisation, Descriptive Statistics and Diagnostics by Variable: Exploratory data analysis and model diagnostics for each behavioral measure
3. Searchable ROPE Analysis Table: Model diagnostics to check the fit of the models

# Effects of Interest

- No meaningful effects found

# Searchable High‑Level Summary

### Enter search terms in the column headers to filter the table below

Note: TD in the Higher column indicates a Trend Difference for the continuous variable.

# Visualisation, Descriptive Statistics and Diagnostics by Variable

### Bar Plot

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### Density Plot

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attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.minor.x NULL

$panel.grid.minor.y list() attr(,“class”) [1] “element_blank” “element”

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: TRUE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b9010b4900>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Fur (PND)”

\(labels\)y [1] “”

\(labels\)fill [1] “group_interaction”

\(labels\)colour [1] “group_interaction”

\(labels\)label [1] “label_text”

\(labels\)height [1] “density” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

Fur Appearance by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 8.6 | 0.5 | 8.0 | 9.0 | 0.0 |
CR25 | 12.0 | 8.7 | 0.8 | 8.0 | 10.0 | 0.0 |
CRA | 10.0 | 8.7 | 0.8 | 8.0 | 10.0 | 0.0 |
CRV | 12.0 | 8.7 | 0.7 | 8.0 | 10.0 | 0.0 |
Warning symbols: * = >40% zeros in this group, ! = >20% zeros in entire sample Either flag triggers the use of a binary choice model.

### Summary Table

Model Summary
Family: poisson
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 2.143 | 0.097 | 1.947 | 2.327 | Fixed Effects
DietCR25 | 0.010 | 0.136 | −0.254 | 0.276 | Fixed Effects
DietCRA | 0.013 | 0.143 | −0.268 | 0.298 | Fixed Effects
DietCRV | 0.010 | 0.137 | −0.254 | 0.280 | Fixed Effects

### Posterior Check

$data # A tibble: 506 × 7 y_id y_name rep_id rep_label is_y is_y_label value 1 1 1 1 italic(y)[rep] ( 1 ) FALSE italic(y)[rep] 5 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 2 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 9 4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 11 5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 6 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 13 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 10 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 7 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 10 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 3 # ℹ 496 more rows

\(layers\)layers[[1]] mapping: group = ~.data$rep_id, colour = yrep geom_line: na.rm = FALSE, orientation = NA stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$layers[[2]] mapping: colour = y geom_line: na.rm = FALSE, orientation = NA, lineend = round stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^.data$value env: 0x000002b8f4213b28

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 1

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y NULL

$axis.ticks.y.left NULL

$axis.ticks.y.right NULL

$axis.ticks.theta NULL

$axis.ticks.r NULL

$axis.minor.ticks.x.top NULL

$axis.minor.ticks.x.bottom NULL

$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

$axis.line.x.bottom NULL

$axis.line.y NULL

$axis.line.y.left NULL

$axis.line.y.right NULL

$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

$legend.key.width NULL

$legend.key.spacing [1] 5.5points

$legend.key.spacing.x NULL

$legend.key.spacing.y NULL

$legend.frame NULL

$legend.ticks NULL

$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “right”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: FALSE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b8f4213b28>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$title [1] “Posterior Predictive Check”

\(labels\)x NULL

\(labels\)y NULL

\(labels\)group [1] “rep_id”

\(labels\)colour [1] “colour”

\(labels\)fill [1] “fill” attr(,“fallback”) [1] TRUE

\(labels\)weight [1] “weight” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.00 | [-0.27, 0.27] | 50.50 | 3.70
Diet: Control vs CRA
Diet: Control vs CRA | -0.01 | [-0.29, 0.28] | 52.90 | 3.50
Diet: Control vs CRV
Diet: Control vs CRV | -0.01 | [-0.27, 0.25] | 52.00 | 4.50
Diet: CR25 vs CRA
Diet: CR25 vs CRA | 0.00 | [-0.28, 0.28] | 50.75 | 3.75
Diet: CR25 vs CRV
Diet: CR25 vs CRV | 0.00 | [-0.27, 0.27] | 50.15 | 4.75
Diet: CRA vs CRV
Diet: CRA vs CRV | 0.00 | [-0.31, 0.26] | 50.80 | 4.20

No continuous ROPE effects available.

### Bar Plot

$data list() attr(,“class”) [1] “waiver”

\(layers\)layers[[1]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, fill = ~group_interaction, group = ~y_group geom_boxplot: outliers = TRUE, outlier.colour = NULL, outlier.fill = NULL, outlier.shape = NA, outlier.size = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, na.rm = FALSE, orientation = y, width = 0.5, fatten = 8.2 stat_boxplot: na.rm = FALSE, orientation = y, width = 0.5 position_dodge2

$layers[[2]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, group = ~y_group geom_point: na.rm = FALSE stat_identity: na.rm = FALSE position_beeswarm

$layers[[3]] mapping: x = ~label_x, y = ~y_group, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

$mapping named list() attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 14

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

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$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b9002c0510>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

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### Density Plot

$data # A tibble: 46 × 5 ID Diet value group_interaction color
1 356 Control 5 Control #2E2E2E 2 344 CR25 3 CR25 #E69F00 3 350 CR25 4 CR25 #E69F00 4 349 CRV 3 CRV #009E73 5 357 Control 6 Control #2E2E2E 6 360 Control 5 Control #2E2E2E 7 334 CRA 5 CRA #56B4E9 8 331 CRV 3 CRV #009E73 9 345 CR25 3 CR25 #E69F00 10 365 CR25 4 CR25 #E69F00 # ℹ 36 more rows

\(layers\)layers[[1]] mapping: colour = ~group_interaction, fill = ~group_interaction geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE stat_density_ridges: na.rm = FALSE, jittered_points = TRUE, quantile_lines = TRUE, quantiles = 2 position_points_sina

$layers[[2]] mapping: x = ~label_x_position, y = ~group_interaction, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

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\(mapping\)x expr: ^value env: 0x000002b901f7cc40

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$fill expr: ^group_interaction env: 0x000002b901f7cc40

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$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: TRUE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b901f7cc40>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Pinnea Detachment (PND)”

\(labels\)y [1] “”

\(labels\)fill [1] “group_interaction”

\(labels\)colour [1] “group_interaction”

\(labels\)label [1] “label_text”

\(labels\)height [1] “density” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

Pinnea Detachment by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 4.5 | 1.2 | 3.0 | 6.0 | 0.0 |
CR25 | 12.0 | 4.0 | 1.2 | 3.0 | 7.0 | 0.0 |
CRA | 10.0 | 5.0 | 1.7 | 3.0 | 8.0 | 0.0 |
CRV | 12.0 | 4.1 | 1.0 | 3.0 | 6.0 | 0.0 |
Warning symbols: * = >40% zeros in this group, ! = >20% zeros in entire sample Either flag triggers the use of a binary choice model.

### Summary Table

Model Summary
Family: poisson
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 1.492 | 0.133 | 1.219 | 1.741 | Fixed Effects
DietCR25 | −0.116 | 0.193 | −0.496 | 0.262 | Fixed Effects
DietCRA | 0.106 | 0.191 | −0.276 | 0.481 | Fixed Effects
DietCRV | −0.094 | 0.191 | −0.468 | 0.279 | Fixed Effects

### Posterior Check

$data # A tibble: 506 × 7 y_id y_name rep_id rep_label is_y is_y_label value 1 1 1 1 italic(y)[rep] ( 1 ) FALSE italic(y)[rep] 2 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 5 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 7 4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 1 5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 5 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 3 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 6 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 4 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 7 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 4 # ℹ 496 more rows

\(layers\)layers[[1]] mapping: group = ~.data$rep_id, colour = yrep geom_line: na.rm = FALSE, orientation = NA stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$layers[[2]] mapping: colour = y geom_line: na.rm = FALSE, orientation = NA, lineend = round stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^.data$value env: 0x000002b95567f0b0

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

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$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

$colour NULL

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$hjust [1] 1

$vjust NULL

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$lineheight NULL

$margin [1] 0points 2.2points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

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$hjust [1] 0

$vjust NULL

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$margin [1] 0points 0points 0points 2.2points

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$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

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$hjust [1] 0.5

$vjust NULL

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$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y NULL

$axis.ticks.y.left NULL

$axis.ticks.y.right NULL

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$axis.minor.ticks.y.left NULL

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$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

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$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

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$legend.key.spacing.x NULL

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$legend.frame NULL

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$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

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$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “right”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

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$vjust [1] 1

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$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

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$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

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$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: FALSE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b95567f0b0>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$title [1] “Posterior Predictive Check”

\(labels\)x NULL

\(labels\)y NULL

\(labels\)group [1] “rep_id”

\(labels\)colour [1] “colour”

\(labels\)fill [1] “fill” attr(,“fallback”) [1] TRUE

\(labels\)weight [1] “weight” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.12 | [-0.27, 0.48] | 73.20 | 10.75
Diet: Control vs CRA
Diet: Control vs CRA | -0.11 | [-0.47, 0.27] | 71.10 | 9.55
Diet: Control vs CRV
Diet: Control vs CRV | 0.09 | [-0.27, 0.47] | 70.05 | 10.65
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.22 | [-0.63, 0.18] | 87.85 | 6.10
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.02 | [-0.42, 0.34] | 54.25 | 10.60
Diet: CRA vs CRV
Diet: CRA vs CRV | 0.21 | [-0.15, 0.61] | 85.05 | 6.70

No continuous ROPE effects available.

### Bar Plot

$data list() attr(,“class”) [1] “waiver”

\(layers\)layers[[1]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, fill = ~group_interaction, group = ~y_group geom_boxplot: outliers = TRUE, outlier.colour = NULL, outlier.fill = NULL, outlier.shape = NA, outlier.size = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, na.rm = FALSE, orientation = y, width = 0.5, fatten = 8.2 stat_boxplot: na.rm = FALSE, orientation = y, width = 0.5 position_dodge2

$layers[[2]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, group = ~y_group geom_point: na.rm = FALSE stat_identity: na.rm = FALSE position_beeswarm

$layers[[3]] mapping: x = ~label_x, y = ~y_group, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

$mapping named list() attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 14

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

$axis.title.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 3.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 3.5points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 3.5points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 0

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$lineheight NULL

$margin [1] 0points 0points 2.8points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

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$size NULL

$hjust [1] 1

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.8points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

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$hjust [1] 0

$vjust NULL

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$margin [1] 0points 0points 0points 2.8points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

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$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.8points 0points 2.8points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x.top NULL

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$axis.ticks.y NULL

$axis.ticks.y.left NULL

$axis.ticks.y.right NULL

$axis.ticks.theta NULL

$axis.ticks.r NULL

$axis.minor.ticks.x.top NULL

$axis.minor.ticks.x.bottom NULL

$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 3.5points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

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$axis.line.y NULL

$axis.line.y.left NULL

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$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 7points 7points 7points 7points

$legend.spacing [1] 14points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

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$legend.key.spacing.x NULL

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\(legend.text\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust NULL

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$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 14points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 7points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

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attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

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$angle NULL

$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 7points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 7points 7points 7points 7points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 5.6points 5.6points 5.6points 5.6points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 3.5points

$strip.switch.pad.wrap [1] 3.5points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b9005b6e78>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Eye Opening (PND)”

\(labels\)y [1] “”

\(labels\)colour [1] “group_interaction”

\(labels\)fill [1] “group_interaction”

\(labels\)group [1] “y_group”

\(labels\)label [1] “label_text”

attr(,“class”) [1] “gg” “ggplot”

### Density Plot

$data # A tibble: 46 × 5 ID Diet value group_interaction color
1 356 Control 15 Control #2E2E2E 2 344 CR25 15 CR25 #E69F00 3 350 CR25 15 CR25 #E69F00 4 349 CRV 15 CRV #009E73 5 357 Control 16 Control #2E2E2E 6 360 Control 14 Control #2E2E2E 7 334 CRA 14 CRA #56B4E9 8 331 CRV 14 CRV #009E73 9 345 CR25 15 CR25 #E69F00 10 365 CR25 15 CR25 #E69F00 # ℹ 36 more rows

\(layers\)layers[[1]] mapping: colour = ~group_interaction, fill = ~group_interaction geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE stat_density_ridges: na.rm = FALSE, jittered_points = TRUE, quantile_lines = TRUE, quantiles = 2 position_points_sina

$layers[[2]] mapping: x = ~label_x_position, y = ~group_interaction, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^value env: 0x000002b902860070

$y expr: ^group_interaction env: 0x000002b902860070

$fill expr: ^group_interaction env: 0x000002b902860070

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

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$hjust NULL

$vjust [1] 1

$angle [1] -90

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$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 1

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$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

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$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

$colour NULL

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$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.y.left NULL

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$axis.ticks.theta NULL

$axis.ticks.r NULL

$axis.minor.ticks.x.top NULL

$axis.minor.ticks.x.bottom NULL

$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

$axis.line.x.bottom NULL

$axis.line.y NULL

$axis.line.y.left NULL

$axis.line.y.right NULL

$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

$legend.key.width NULL

$legend.key.spacing [1] 5.5points

$legend.key.spacing.x NULL

$legend.key.spacing.y NULL

$legend.frame NULL

$legend.ticks NULL

$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.minor.x NULL

$panel.grid.minor.y list() attr(,“class”) [1] “element_blank” “element”

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: TRUE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b902860070>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Eye Opening (PND)”

\(labels\)y [1] “”

\(labels\)fill [1] “group_interaction”

\(labels\)colour [1] “group_interaction”

\(labels\)label [1] “label_text”

\(labels\)height [1] “density” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

Eye Opening by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 15.2 | 0.8 | 14.0 | 16.0 | 0.0 |
CR25 | 12.0 | 15.1 | 0.3 | 15.0 | 16.0 | 0.0 |
CRA | 10.0 | 14.8 | 0.4 | 14.0 | 15.0 | 0.0 |
CRV | 12.0 | 15.2 | 0.6 | 14.0 | 16.0 | 0.0 |
Warning symbols: * = >40% zeros in this group, ! = >20% zeros in entire sample Either flag triggers the use of a binary choice model.

### Summary Table

Model Summary
Family: poisson
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 2.721 | 0.073 | 2.573 | 2.858 | Fixed Effects
DietCR25 | −0.011 | 0.104 | −0.216 | 0.196 | Fixed Effects
DietCRA | −0.029 | 0.110 | −0.244 | 0.185 | Fixed Effects
DietCRV | −0.005 | 0.103 | −0.205 | 0.196 | Fixed Effects

### Posterior Check

$data # A tibble: 506 × 7 y_id y_name rep_id rep_label is_y is_y_label value 1 1 1 1 italic(y)[rep] ( 1 ) FALSE italic(y)[rep] 15 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 8 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 15 4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 14 5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 13 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 13 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 15 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 26 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 14 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 16 # ℹ 496 more rows

\(layers\)layers[[1]] mapping: group = ~.data$rep_id, colour = yrep geom_line: na.rm = FALSE, orientation = NA stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$layers[[2]] mapping: colour = y geom_line: na.rm = FALSE, orientation = NA, lineend = round stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^.data$value env: 0x000002b95708ef90

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

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$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

$colour NULL

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$hjust [1] 1

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

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$hjust [1] 0

$vjust NULL

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$lineheight NULL

$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

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$axis.ticks.y NULL

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$axis.ticks.y.right NULL

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$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

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$axis.ticks.length.y NULL

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$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

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$axis.line.theta NULL

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$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

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$legend.axis.line NULL

\(legend.text\)family NULL

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$hjust NULL

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$angle NULL

$lineheight NULL

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$debug NULL

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attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “right”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

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$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

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\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

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$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

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$panel.grid.major.x NULL

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$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

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\(plot.title\)family NULL

$face NULL

$colour NULL

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$angle NULL

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$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

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$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

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$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

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\(plot.caption\)family NULL

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$colour NULL

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$debug NULL

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\(plot.tag\)family NULL

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$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: FALSE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b95708ef90>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$title [1] “Posterior Predictive Check”

\(labels\)x NULL

\(labels\)y NULL

\(labels\)group [1] “rep_id”

\(labels\)colour [1] “colour”

\(labels\)fill [1] “fill” attr(,“fallback”) [1] TRUE

\(labels\)weight [1] “weight” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.02 | [-0.18, 0.23] | 56.50 | 2.90
Diet: Control vs CRA
Diet: Control vs CRA | 0.03 | [-0.16, 0.27] | 59.55 | 2.85
Diet: Control vs CRV
Diet: Control vs CRV | 0.01 | [-0.19, 0.20] | 52.25 | 3.05
Diet: CR25 vs CRA
Diet: CR25 vs CRA | 0.01 | [-0.20, 0.23] | 53.85 | 2.20
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.01 | [-0.23, 0.19] | 53.20 | 2.10
Diet: CRA vs CRV
Diet: CRA vs CRV | -0.02 | [-0.23, 0.19] | 58.90 | 2.20

No continuous ROPE effects available.

### Bar Plot

$data list() attr(,“class”) [1] “waiver”

\(layers\)layers[[1]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, fill = ~group_interaction, group = ~y_group geom_boxplot: outliers = TRUE, outlier.colour = NULL, outlier.fill = NULL, outlier.shape = NA, outlier.size = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, na.rm = FALSE, orientation = y, width = 0.5, fatten = 8.2 stat_boxplot: na.rm = FALSE, orientation = y, width = 0.5 position_dodge2

$layers[[2]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, group = ~y_group geom_point: na.rm = FALSE stat_identity: na.rm = FALSE position_beeswarm

$layers[[3]] mapping: x = ~label_x, y = ~y_group, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

$mapping named list() attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 14

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

$axis.title.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 3.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 3.5points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 3.5points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

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$margin [1] 0points 0points 2.8points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

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$hjust [1] 1

$vjust NULL

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$margin [1] 0points 2.8points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

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$hjust [1] 0

$vjust NULL

$angle NULL

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$margin [1] 0points 0points 0points 2.8points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

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$hjust [1] 0.5

$vjust NULL

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$lineheight NULL

$margin [1] 0points 2.8points 0points 2.8points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y NULL

$axis.ticks.y.left NULL

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$axis.ticks.theta NULL

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$axis.minor.ticks.x.top NULL

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$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 3.5points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

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$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

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$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

$axis.line.x.bottom NULL

$axis.line.y NULL

$axis.line.y.left NULL

$axis.line.y.right NULL

$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 7points 7points 7points 7points

$legend.spacing [1] 14points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

$legend.key.width NULL

$legend.key.spacing [1] 7points

$legend.key.spacing.x NULL

$legend.key.spacing.y NULL

$legend.frame NULL

$legend.ticks NULL

$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 14points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 7points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

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attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

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attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 7points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 7points 7points 7points 7points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 5.6points 5.6points 5.6points 5.6points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 3.5points

$strip.switch.pad.wrap [1] 3.5points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b900975698>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Vaginal Opening (PND)”

\(labels\)y [1] “”

\(labels\)colour [1] “group_interaction”

\(labels\)fill [1] “group_interaction”

\(labels\)group [1] “y_group”

\(labels\)label [1] “label_text”

attr(,“class”) [1] “gg” “ggplot”

### Density Plot

$data # A tibble: 46 × 5 ID Diet value group_interaction color
1 356 Control 34 Control #2E2E2E 2 344 CR25 34 CR25 #E69F00 3 350 CR25 34 CR25 #E69F00 4 349 CRV 33 CRV #009E73 5 357 Control 29 Control #2E2E2E 6 360 Control 34 Control #2E2E2E 7 334 CRA 33 CRA #56B4E9 8 331 CRV 30 CRV #009E73 9 345 CR25 32 CR25 #E69F00 10 365 CR25 33 CR25 #E69F00 # ℹ 36 more rows

\(layers\)layers[[1]] mapping: colour = ~group_interaction, fill = ~group_interaction geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE stat_density_ridges: na.rm = FALSE, jittered_points = TRUE, quantile_lines = TRUE, quantiles = 2 position_points_sina

$layers[[2]] mapping: x = ~label_x_position, y = ~group_interaction, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^value env: 0x000002b902f2a580

$y expr: ^group_interaction env: 0x000002b902f2a580

$fill expr: ^group_interaction env: 0x000002b902f2a580

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 0

$angle NULL

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$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

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$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

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$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

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$margin [1] 2.2points 0points 0points 0points

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attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

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$vjust [1] 0

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$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

$axis.text.y list() attr(,“class”) [1] “element_blank” “element”

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\(axis.text.y.right\)family NULL

$face NULL

$colour NULL

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$hjust [1] 0

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$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

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$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

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$axis.ticks.y.left NULL

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$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

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$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

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$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

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$legend.key.spacing.x NULL

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$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

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$hjust NULL

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$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

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$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.minor.x NULL

$panel.grid.minor.y list() attr(,“class”) [1] “element_blank” “element”

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: TRUE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b902f2a580>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Vaginal Opening (PND)”

\(labels\)y [1] “”

\(labels\)fill [1] “group_interaction”

\(labels\)colour [1] “group_interaction”

\(labels\)label [1] “label_text”

\(labels\)height [1] “density” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

Vaginal Opening by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 32.0 | 2.1 | 29.0 | 35.0 | 0.0 |
CR25 | 12.0 | 31.9 | 1.5 | 30.0 | 34.0 | 0.0 |
CRA | 10.0 | 32.4 | 2.0 | 30.0 | 36.0 | 0.0 |
CRV | 12.0 | 33.3 | 2.4 | 30.0 | 38.0 | 0.0 |
Warning symbols: * = >40% zeros in this group, ! = >20% zeros in entire sample Either flag triggers the use of a binary choice model.

### Summary Table

Model Summary
Family: gaussian
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 32.250 | 0.477 | 31.317 | 33.201 | Fixed Effects
DietCR25 | −0.263 | 0.621 | −1.500 | 0.957 | Fixed Effects
DietCRA | 0.097 | 0.629 | −1.138 | 1.313 | Fixed Effects
DietCRV | 0.735 | 0.641 | −0.528 | 1.993 | Fixed Effects

### Posterior Check

$data # A tibble: 440 × 7 y_id y_name rep_id rep_label is_y is_y_label value 1 1 1 1 italic(y)[rep] ( 1 ) FALSE italic(y)[rep] 34.4 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 28.1 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 32.1 4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 29.0 5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 31.3 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 32.9 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 29.9 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 33.2 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 32.6 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 33.6 # ℹ 430 more rows

\(layers\)layers[[1]] mapping: group = ~.data$rep_id, colour = yrep geom_line: na.rm = FALSE, orientation = NA stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$layers[[2]] mapping: colour = y geom_line: na.rm = FALSE, orientation = NA, lineend = round stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^.data$value env: 0x000002b958bc2f20

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

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attr(,“class”) [1] “element_text” “element”

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\(axis.text\)family NULL

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\(plot.caption\)family NULL

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attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

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$margin [1] 4.4points 4.4points 4.4points 4.4points

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\(strip.text.y\)family NULL

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\(strip.text.y.left\)family NULL

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$margin NULL

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attr(,“class”) [1] “element_text” “element”

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$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: FALSE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b958bc2f20>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$title [1] “Posterior Predictive Check”

\(labels\)x NULL

\(labels\)y NULL

\(labels\)group [1] “rep_id”

\(labels\)colour [1] “colour”

\(labels\)fill [1] “fill” attr(,“fallback”) [1] TRUE

\(labels\)weight [1] “weight” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.23 | [-1.05, 1.48] | 63.20 | 23.55
Diet: Control vs CRA
Diet: Control vs CRA | -0.08 | [-1.31, 1.18] | 55.05 | 24.70
Diet: Control vs CRV
Diet: Control vs CRV | -0.74 | [-2.01, 0.49] | 87.65 | 12.65
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.31 | [-1.69, 1.14] | 65.80 | 18.60
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.97 | [-2.35, 0.70] | 89.95 | 9.25
Diet: CRA vs CRV
Diet: CRA vs CRV | -0.66 | [-2.14, 0.77] | 81.60 | 14.70

No continuous ROPE effects available.

### Bar Plot

$data list() attr(,“class”) [1] “waiver”

\(layers\)layers[[1]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, fill = ~group_interaction, group = ~y_group geom_boxplot: outliers = TRUE, outlier.colour = NULL, outlier.fill = NULL, outlier.shape = NA, outlier.size = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL, notch = FALSE, notchwidth = 0.5, staplewidth = 0, varwidth = FALSE, na.rm = FALSE, orientation = y, width = 0.5, fatten = 8.2 stat_boxplot: na.rm = FALSE, orientation = y, width = 0.5 position_dodge2

$layers[[2]] mapping: x = ~value, y = ~y_group, colour = ~group_interaction, group = ~y_group geom_point: na.rm = FALSE stat_identity: na.rm = FALSE position_beeswarm

$layers[[3]] mapping: x = ~label_x, y = ~y_group, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

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\(theme\)line $colour [1] “black”

$linewidth [1] 0.6363636

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

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attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

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$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 14

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

$axis.title.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.title.x.top\)family NULL

$face NULL

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$vjust [1] 0

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$margin [1] 0points 0points 3.5points 0points

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attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

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$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 3.5points 0points 0points

$debug NULL

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attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

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$angle [1] -90

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$margin [1] 0points 0points 0points 3.5points

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$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

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$colour [1] “grey30”

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$hjust NULL

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$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x list() attr(,“class”) [1] “element_blank” “element”

\(axis.text.x.top\)family NULL

$face NULL

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$hjust NULL

$vjust [1] 0

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$margin [1] 0points 0points 2.8points 0points

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$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

\(axis.text.y\)family NULL

$face NULL

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$hjust [1] 1

$vjust NULL

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$margin [1] 0points 2.8points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

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$hjust [1] 0

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$margin [1] 0points 0points 0points 2.8points

$debug NULL

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attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

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$hjust [1] 0.5

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$margin [1] 0points 2.8points 0points 2.8points

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attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

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$axis.minor.ticks.length [1] 0.75 *

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$axis.line list() attr(,“class”) [1] “element_blank” “element”

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$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 7points 7points 7points 7points

$legend.spacing [1] 14points

$legend.spacing.x NULL

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$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

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$legend.key.spacing [1] 7points

$legend.key.spacing.x NULL

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$legend.frame NULL

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$legend.ticks.length [1] 0.2 *

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\(legend.text\)family NULL

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attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

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$hjust [1] 0

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$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

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$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 14points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 7points

$panel.spacing.x NULL

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\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

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$size [1] 1.2 *

$hjust [1] 0

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$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

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$hjust [1] 0

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$lineheight NULL

$margin [1] 0points 0points 7points 0points

$debug NULL

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attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

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$margin [1] 7points 0points 0points 0points

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attr(,“class”) [1] “element_text” “element”

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\(plot.tag\)family NULL

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$hjust [1] 0.5

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$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 7points 7points 7points 7points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 5.6points 5.6points 5.6points 5.6points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 3.5points

$strip.switch.pad.wrap [1] 3.5points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordFlip, CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b900d0cba0>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Testes Descent (PND)”

\(labels\)y [1] “”

\(labels\)colour [1] “group_interaction”

\(labels\)fill [1] “group_interaction”

\(labels\)group [1] “y_group”

\(labels\)label [1] “label_text”

attr(,“class”) [1] “gg” “ggplot”

### Density Plot

$data # A tibble: 46 × 5 ID Diet value group_interaction color
1 356 Control 20 Control #2E2E2E 2 344 CR25 23 CR25 #E69F00 3 350 CR25 20 CR25 #E69F00 4 349 CRV 22 CRV #009E73 5 357 Control 23 Control #2E2E2E 6 360 Control 21 Control #2E2E2E 7 334 CRA 20 CRA #56B4E9 8 331 CRV 23 CRV #009E73 9 345 CR25 20 CR25 #E69F00 10 365 CR25 20 CR25 #E69F00 # ℹ 36 more rows

\(layers\)layers[[1]] mapping: colour = ~group_interaction, fill = ~group_interaction geom_density_ridges: na.rm = FALSE, panel_scaling = TRUE stat_density_ridges: na.rm = FALSE, jittered_points = TRUE, quantile_lines = TRUE, quantiles = 2 position_points_sina

$layers[[2]] mapping: x = ~label_x_position, y = ~group_interaction, label = ~label_text, fill = ~group_interaction, colour = ~group_interaction geom_label: parse = FALSE, label.padding = 0.25, label.r = 0.15, label.size = 0, size.unit = mm, na.rm = FALSE stat_identity: na.rm = FALSE position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^value env: 0x000002b903dae270

$y expr: ^group_interaction env: 0x000002b903dae270

$fill expr: ^group_interaction env: 0x000002b903dae270

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

$colour NULL

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$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.2points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.x.bottom NULL

$axis.text.y list() attr(,“class”) [1] “element_blank” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.y.left NULL

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$axis.ticks.theta NULL

$axis.ticks.r NULL

$axis.minor.ticks.x.top NULL

$axis.minor.ticks.x.bottom NULL

$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

$axis.line.x.bottom NULL

$axis.line.y NULL

$axis.line.y.left NULL

$axis.line.y.right NULL

$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

$legend.key.width NULL

$legend.key.spacing [1] 5.5points

$legend.key.spacing.x NULL

$legend.key.spacing.y NULL

$legend.frame NULL

$legend.ticks NULL

$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “none”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y list() attr(,“class”) [1] “element_blank” “element”

$panel.grid.minor.x NULL

$panel.grid.minor.y list() attr(,“class”) [1] “element_blank” “element”

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: TRUE distance: function draw_panel: function expand: TRUE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b903dae270>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$x [1] “Testes Descent (PND)”

\(labels\)y [1] “”

\(labels\)fill [1] “group_interaction”

\(labels\)colour [1] “group_interaction”

\(labels\)label [1] “label_text”

\(labels\)height [1] “density” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

Testes Descent by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 20.8 | 1.2 | 19.0 | 23.0 | 0.0 |
CR25 | 12.0 | 20.8 | 1.3 | 19.0 | 23.0 | 0.0 |
CRA | 10.0 | 21.1 | 1.4 | 20.0 | 24.0 | 0.0 |
CRV | 12.0 | 21.2 | 1.4 | 19.0 | 24.0 | 0.0 |
Warning symbols: * = >40% zeros in this group, ! = >20% zeros in entire sample Either flag triggers the use of a binary choice model.

### Summary Table

Model Summary
Family: poisson
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 3.029 | 0.063 | 2.905 | 3.150 | Fixed Effects
DietCR25 | 0.004 | 0.090 | −0.172 | 0.178 | Fixed Effects
DietCRA | 0.018 | 0.093 | −0.166 | 0.202 | Fixed Effects
DietCRV | 0.021 | 0.089 | −0.151 | 0.196 | Fixed Effects

### Posterior Check

$data # A tibble: 495 × 7 y_id y_name rep_id rep_label is_y is_y_label value 1 1 1 1 italic(y)[rep] ( 1 ) FALSE italic(y)[rep] 35 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 19 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 20 4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 16 5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 24 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 20 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 19 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 26 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 21 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 15 # ℹ 485 more rows

\(layers\)layers[[1]] mapping: group = ~.data$rep_id, colour = yrep geom_line: na.rm = FALSE, orientation = NA stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$layers[[2]] mapping: colour = y geom_line: na.rm = FALSE, orientation = NA, lineend = round stat_density: bw = nrd0, adjust = 1, kernel = gaussian, n = 1024, trim = FALSE, na.rm = FALSE, bounds = c(-Inf, Inf), orientation = NA position_identity

$scales <ggproto object: Class ScalesList, gg> add: function add_defaults: function add_missing: function backtransform_df: function clone: function find: function get_scales: function has_scale: function input: function map_df: function n: function non_position_scales: function scales: list set_palettes: function train_df: function transform_df: function super: <ggproto object: Class ScalesList, gg>

$guides <Guides[0] ggproto object>

\(mapping\)x expr: ^.data$value env: 0x000002b95a673f20

attr(,“class”) [1] “uneval”

\(theme\)line $colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$lineend [1] “butt”

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

\(rect\)fill [1] “white”

$colour [1] “black”

$linewidth [1] 0.5

$linetype [1] 1

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_rect” “element”

\(text\)family [1] “”

$face [1] “plain”

$colour [1] “black”

$size [1] 11

$hjust [1] 0.5

$vjust [1] 0.5

$angle [1] 0

$lineheight [1] 0.9

$margin [1] 0points 0points 0points 0points

$debug [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$title NULL

$aspect.ratio NULL

$axis.title NULL

\(axis.title.x\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.75points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.title.x.top\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 0

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 2.75points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.x.bottom NULL

\(axis.title.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] 90

$lineheight NULL

$margin [1] 0points 2.75points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.title.y.left NULL

\(axis.title.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust [1] 1

$angle [1] -90

$lineheight NULL

$margin [1] 0points 0points 0points 2.75points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text\)family NULL

$face NULL

$colour [1] “grey30”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x\)family NULL

$face NULL

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$hjust NULL

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 2.2points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(axis.text.x.top\)family NULL

$face NULL

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$hjust NULL

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$margin [1] 0points 0points 2.2points 0points

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$inherit.blank [1] TRUE

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$axis.text.x.bottom NULL

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$hjust [1] 1

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$margin [1] 0points 2.2points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.y.left NULL

\(axis.text.y.right\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.text.theta NULL

\(axis.text.r\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0.5

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 0points 2.2points 0points 2.2points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$axis.ticks list() attr(,“class”) [1] “element_blank” “element”

$axis.ticks.x NULL

$axis.ticks.x.top NULL

$axis.ticks.x.bottom NULL

$axis.ticks.y NULL

$axis.ticks.y.left NULL

$axis.ticks.y.right NULL

$axis.ticks.theta NULL

$axis.ticks.r NULL

$axis.minor.ticks.x.top NULL

$axis.minor.ticks.x.bottom NULL

$axis.minor.ticks.y.left NULL

$axis.minor.ticks.y.right NULL

$axis.minor.ticks.theta NULL

$axis.minor.ticks.r NULL

$axis.ticks.length [1] 2.75points

$axis.ticks.length.x NULL

$axis.ticks.length.x.top NULL

$axis.ticks.length.x.bottom NULL

$axis.ticks.length.y NULL

$axis.ticks.length.y.left NULL

$axis.ticks.length.y.right NULL

$axis.ticks.length.theta NULL

$axis.ticks.length.r NULL

$axis.minor.ticks.length [1] 0.75 *

$axis.minor.ticks.length.x NULL

$axis.minor.ticks.length.x.top NULL

$axis.minor.ticks.length.x.bottom NULL

$axis.minor.ticks.length.y NULL

$axis.minor.ticks.length.y.left NULL

$axis.minor.ticks.length.y.right NULL

$axis.minor.ticks.length.theta NULL

$axis.minor.ticks.length.r NULL

$axis.line list() attr(,“class”) [1] “element_blank” “element”

$axis.line.x NULL

$axis.line.x.top NULL

$axis.line.x.bottom NULL

$axis.line.y NULL

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$axis.line.y.right NULL

$axis.line.theta NULL

$axis.line.r NULL

$legend.background list() attr(,“class”) [1] “element_blank” “element”

$legend.margin [1] 5.5points 5.5points 5.5points 5.5points

$legend.spacing [1] 11points

$legend.spacing.x NULL

$legend.spacing.y NULL

$legend.key list() attr(,“class”) [1] “element_blank” “element”

$legend.key.size [1] 1.2lines

$legend.key.height NULL

$legend.key.width NULL

$legend.key.spacing [1] 5.5points

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$legend.key.spacing.y NULL

$legend.frame NULL

$legend.ticks NULL

$legend.ticks.length [1] 0.2 *

$legend.axis.line NULL

\(legend.text\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.text.position NULL

\(legend.title\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust NULL

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$legend.title.position NULL

$legend.position [1] “right”

$legend.position.inside NULL

$legend.direction NULL

$legend.byrow NULL

$legend.justification [1] “center”

$legend.justification.top NULL

$legend.justification.bottom NULL

$legend.justification.left NULL

$legend.justification.right NULL

$legend.justification.inside NULL

$legend.location NULL

$legend.box NULL

$legend.box.just NULL

$legend.box.margin [1] 0cm 0cm 0cm 0cm

$legend.box.background list() attr(,“class”) [1] “element_blank” “element”

$legend.box.spacing [1] 11points

$panel.background list() attr(,“class”) [1] “element_blank” “element”

$panel.border list() attr(,“class”) [1] “element_blank” “element”

$panel.spacing [1] 5.5points

$panel.spacing.x NULL

$panel.spacing.y NULL

\(panel.grid\)colour [1] “grey92”

$linewidth NULL

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major NULL

\(panel.grid.minor\)colour NULL

$linewidth [1] 0.5 *

$linetype NULL

$lineend NULL

$arrow [1] FALSE

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_line” “element”

$panel.grid.major.x NULL

$panel.grid.major.y NULL

$panel.grid.minor.x NULL

$panel.grid.minor.y NULL

$panel.ontop [1] FALSE

$plot.background list() attr(,“class”) [1] “element_blank” “element”

\(plot.title\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] FALSE

attr(,“class”) [1] “element_text” “element”

$plot.title.position [1] “panel”

\(plot.subtitle\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust [1] 0

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 0points 0points 5.5points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(plot.caption\)family NULL

$face NULL

$colour NULL

$size [1] 0.8 *

$hjust [1] 1

$vjust [1] 1

$angle NULL

$lineheight NULL

$margin [1] 5.5points 0points 0points 0points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.caption.position [1] “panel”

\(plot.tag\)family NULL

$face NULL

$colour NULL

$size [1] 1.2 *

$hjust [1] 0.5

$vjust [1] 0.5

$angle NULL

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$plot.tag.position [1] “topleft”

$plot.tag.location NULL

$plot.margin [1] 5.5points 5.5points 5.5points 5.5points

$strip.background list() attr(,“class”) [1] “element_blank” “element”

$strip.background.x NULL

$strip.background.y NULL

$strip.clip [1] “inherit”

$strip.placement [1] “inside”

\(strip.text\)family NULL

$face NULL

$colour [1] “grey10”

$size [1] 0.8 *

$hjust NULL

$vjust NULL

$angle NULL

$lineheight NULL

$margin [1] 4.4points 4.4points 4.4points 4.4points

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.x NULL

$strip.text.x.bottom NULL

$strip.text.x.top NULL

\(strip.text.y\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] -90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

\(strip.text.y.left\)family NULL

$face NULL

$colour NULL

$size NULL

$hjust NULL

$vjust NULL

$angle [1] 90

$lineheight NULL

$margin NULL

$debug NULL

$inherit.blank [1] TRUE

attr(,“class”) [1] “element_text” “element”

$strip.text.y.right NULL

$strip.switch.pad.grid [1] 2.75points

$strip.switch.pad.wrap [1] 2.75points

attr(,“class”) [1] “theme” “gg”
attr(,“complete”) [1] TRUE attr(,“validate”) [1] TRUE

$coordinates <ggproto object: Class CoordCartesian, Coord, gg> aspect: function backtransform_range: function clip: on default: FALSE distance: function draw_panel: function expand: FALSE is_free: function is_linear: function labels: function limits: list modify_scales: function range: function render_axis_h: function render_axis_v: function render_bg: function render_fg: function reverse: none setup_data: function setup_layout: function setup_panel_guides: function setup_panel_params: function setup_params: function train_panel_guides: function transform: function super: <ggproto object: Class CoordCartesian, Coord, gg>

$facet <ggproto object: Class FacetNull, Facet, gg> attach_axes: function attach_strips: function compute_layout: function draw_back: function draw_front: function draw_labels: function draw_panel_content: function draw_panels: function finish_data: function format_strip_labels: function init_gtable: function init_scales: function map_data: function params: list set_panel_size: function setup_data: function setup_panel_params: function setup_params: function shrink: TRUE train_scales: function vars: function super: <ggproto object: Class FacetNull, Facet, gg>

$plot_env <environment: 0x000002b95a673f20>

$layout <ggproto object: Class Layout, gg> coord: NULL coord_params: list facet: NULL facet_params: list finish_data: function get_scales: function layout: NULL map_position: function panel_params: NULL panel_scales_x: NULL panel_scales_y: NULL render: function render_labels: function reset_scales: function resolve_label: function setup: function setup_panel_guides: function setup_panel_params: function train_position: function super: <ggproto object: Class Layout, gg>

\(labels\)labels$title [1] “Posterior Predictive Check”

\(labels\)x NULL

\(labels\)y NULL

\(labels\)group [1] “rep_id”

\(labels\)colour [1] “colour”

\(labels\)fill [1] “fill” attr(,“fallback”) [1] TRUE

\(labels\)weight [1] “weight” attr(,“fallback”) [1] TRUE

attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.00 | [-0.19, 0.17] | 50.05 | 4.70
Diet: Control vs CRA
Diet: Control vs CRA | -0.02 | [-0.21, 0.15] | 56.90 | 4.50
Diet: Control vs CRV
Diet: Control vs CRV | -0.01 | [-0.20, 0.15] | 56.60 | 4.85
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.02 | [-0.20, 0.16] | 57.70 | 5.25
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.02 | [-0.20, 0.15] | 57.25 | 5.25
Diet: CRA vs CRV
Diet: CRA vs CRV | 0.00 | [-0.18, 0.16] | 50.10 | 4.70

No continuous ROPE effects available.

# End of Document