# Executive Summary

# Maternal Preconception Study

## Pup Retrieval

# 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

- CRA dams were more likely to retrieve all their pups than Control dams.

Note: Pup numbers were not included in the analysis due to lack of variance in the data.

# 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

### Density Plot

Retrieved All Pups by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 0.2 | 0.4 | 0.0 | 1.0 | 83.3 | *
CR25 | 11.0 | 0.5 | 0.5 | 0.0 | 1.0 | 54.5 | *
CRA | 10.0 | 0.7 | 0.5 | 0.0 | 1.0 | 30.0 | !
CRV | 12.0 | 0.4 | 0.5 | 0.0 | 1.0 | 58.3 | *
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: bernoulli
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | −0.767 | 0.456 | −1.674 | 0.114 | Fixed Effects
DietCR25 | 0.416 | 0.628 | −0.822 | 1.650 | Fixed Effects
DietCRA | 1.139 | 0.637 | −0.098 | 2.404 | Fixed Effects
DietCRV | 0.305 | 0.615 | −0.892 | 1.495 | Fixed Effects

### Posterior Check

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### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | -0.41 | [-1.67, 0.78] | 75.25 | 18.45
Diet: Control vs CRA
Diet: Control vs CRA | -1.14 | [-2.36, 0.11] | 96.75 | 4.35
Diet: Control vs CRV
Diet: Control vs CRV | -0.30 | [-1.55, 0.89] | 68.90 | 19.35
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.73 | [-2.35, 0.66] | 83.90 | 13.70
Diet: CR25 vs CRV
Diet: CR25 vs CRV | 0.10 | [-1.29, 1.58] | 55.35 | 19.10
Diet: CRA vs CRV
Diet: CRA vs CRV | 0.85 | [-0.72, 2.39] | 86.65 | 10.45

No continuous ROPE effects available.

### Bar Plot

### Density Plot

All Pups Latency by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 19.2 | 45.0 | 0.0 | 125.2 | 83.3 | *
CR25 | 11.0 | 111.6 | 178.1 | 0.0 | 591.4 | 54.5 | *
CRA | 10.0 | 180.2 | 172.6 | 0.0 | 557.1 | 30.0 | !
CRV | 12.0 | 133.4 | 192.4 | 0.0 | 485.5 | 58.3 | *
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: bernoulli
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | −0.767 | 0.456 | −1.674 | 0.114 | Fixed Effects
DietCR25 | 0.416 | 0.628 | −0.822 | 1.650 | Fixed Effects
DietCRA | 1.139 | 0.637 | −0.098 | 2.404 | Fixed Effects
DietCRV | 0.305 | 0.615 | −0.892 | 1.495 | Fixed Effects

### Posterior Check

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### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | -0.42 | [-1.60, 0.86] | 74.60 | 18.65
Diet: Control vs CRA
Diet: Control vs CRA | -1.14 | [-2.36, 0.04] | 96.65 | 4.35
Diet: Control vs CRV
Diet: Control vs CRV | -0.30 | [-1.49, 1.00] | 67.95 | 20.80
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.74 | [-2.43, 0.68] | 83.60 | 12.15
Diet: CR25 vs CRV
Diet: CR25 vs CRV | 0.10 | [-1.31, 1.50] | 55.35 | 18.30
Diet: CRA vs CRV
Diet: CRA vs CRV | 0.83 | [-0.60, 2.40] | 87.45 | 10.75

No continuous ROPE effects available.

### Bar Plot

### Density Plot

Retrieved First Pup by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 0.6 | 0.5 | 0.0 | 1.0 | 41.7 | *
CR25 | 11.0 | 0.7 | 0.5 | 0.0 | 1.0 | 27.3 | !
CRA | 10.0 | 0.9 | 0.3 | 0.0 | 1.0 | 10.0 | !
CRV | 12.0 | 0.9 | 0.3 | 0.0 | 1.0 | 8.3 | !
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: bernoulli
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 0.953 | 0.478 | 0.049 | 1.921 | Fixed Effects
DietCR25 | 0.049 | 0.657 | −1.211 | 1.366 | Fixed Effects
DietCRA | 0.723 | 0.709 | −0.630 | 2.164 | Fixed Effects
DietCRV | 0.851 | 0.693 | −0.478 | 2.249 | 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] 1 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 1 3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 0 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] 0 6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 1 7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 1 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 1 9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 1 10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 1 # 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

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

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

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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>

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\(labels\)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 | -0.08 | [-1.37, 1.18] | 54.65 | 20.60
Diet: Control vs CRA
Diet: Control vs CRA | -0.72 | [-2.11, 0.74] | 85.20 | 12.10
Diet: Control vs CRV
Diet: Control vs CRV | -0.85 | [-2.07, 0.51] | 90.30 | 10.65
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.65 | [-2.35, 1.07] | 77.20 | 12.55
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.80 | [-2.44, 0.96] | 81.55 | 11.35
Diet: CRA vs CRV
Diet: CRA vs CRV | -0.14 | [-1.90, 1.58] | 55.90 | 15.10

No continuous ROPE effects available.

### Bar Plot

### Density Plot

First Pup Latency by Grouping Variables
Diet | n | Mean | SD | Min | Max | % of Zeros | Zero Flag
--- | --- | --- | --- | --- | --- | --- | ---
Control | 12.0 | 125.1 | 195.9 | 0.0 | 536.9 | 41.7 | *
CR25 | 11.0 | 72.6 | 104.5 | 0.0 | 275.8 | 27.3 | !
CRA | 10.0 | 41.3 | 46.9 | 0.0 | 122.5 | 10.0 | !
CRV | 12.0 | 73.2 | 84.5 | 0.0 | 281.7 | 8.3 | !
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: lognormal
Parameter | Estimate | Std. Error | 2.5% CI | 97.5% CI | Type
--- | --- | --- | --- | --- | ---
Fixed Effects
Intercept | 1.076 | 0.814 | −0.563 | 2.665 | Fixed Effects
DietCR25 | −0.162 | 0.862 | −1.864 | 1.510 | Fixed Effects
DietCRA | 0.321 | 0.881 | −1.416 | 2.038 | Fixed Effects
DietCRV | 0.556 | 0.848 | −1.111 | 2.224 | Fixed Effects

### Posterior Check

$data # A tibble: 385 × 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] 0.0598 2 1 1 2 italic(y)[rep] ( 2 ) FALSE italic(y)[rep] 11.6
3 1 1 3 italic(y)[rep] ( 3 ) FALSE italic(y)[rep] 3.53
4 1 1 4 italic(y)[rep] ( 4 ) FALSE italic(y)[rep] 0.112
5 1 1 5 italic(y)[rep] ( 5 ) FALSE italic(y)[rep] 891643.
6 1 1 6 italic(y)[rep] ( 6 ) FALSE italic(y)[rep] 9.25
7 1 1 7 italic(y)[rep] ( 7 ) FALSE italic(y)[rep] 0.00439 8 1 1 8 italic(y)[rep] ( 8 ) FALSE italic(y)[rep] 1620.
9 1 1 9 italic(y)[rep] ( 9 ) FALSE italic(y)[rep] 546.
10 1 1 10 italic(y)[rep] ( 10 ) FALSE italic(y)[rep] 180.
# ℹ 375 more rows

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$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: 0x0000020bdd958e70

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\(rect\)fill [1] “white”

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$title NULL

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\(labels\)y NULL

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attr(,“class”) [1] “gg” “ggplot”

### Convergence

Effect | Median | [95% HDI] | Direction Prob. | ROPE %
--- | --- | --- | --- | ---
Diet: Control vs CR25
Diet: Control vs CR25 | 0.16 | [-1.41, 2.00] | 57.55 | 13.15
Diet: Control vs CRA
Diet: Control vs CRA | -0.29 | [-2.00, 1.48] | 62.30 | 12.95
Diet: Control vs CRV
Diet: Control vs CRV | -0.54 | [-2.28, 1.04] | 74.35 | 12.05
Diet: CR25 vs CRA
Diet: CR25 vs CRA | -0.49 | [-2.80, 1.88] | 65.90 | 8.90
Diet: CR25 vs CRV
Diet: CR25 vs CRV | -0.71 | [-3.14, 1.47] | 73.70 | 8.70
Diet: CRA vs CRV
Diet: CRA vs CRV | -0.23 | [-2.47, 1.97] | 58.60 | 10.30

No continuous ROPE effects available.

# End of Document