Silver spoons, reproduction, and growth catch-up in eastern grey kangaroos - code and data

This database and code necessary for conducting the analyses from the article titled "".Kelly Forrester (corresponding author), Andrew Macdonald, Marco Festa-BianchetAll questions should be directed towards the corresponding author.<br><br>The data were analyzed using R (version 4.2.3) via RStudio (version 2023.12.1-402) (R Core Team 2023; Posit Team 2024).Required software and packages:<b>Data manipulation:</b> dplyr, tidyr, stringr, forcats<b>Bayesian modeling and diagnostics:</b> brms, tidybayes, bayesplot, bayestestR<b>Statistical summaries:</b> broom<b>Visualization:</b> ggplot2, gridExtra, patchwork, cowplot, ggh4xFile: Early_reproduction.csv<b>Variables:</b><b>ID:</b> Unique identifier for each individual kangaroo.<b>Year:</b> Year of the capture/measurement.<b>Age:</b> Age of the individual in years at the time of capture.<b>Age_certainty:</b> Certainty of the age estimate (e.g., known vs. estimated).<b>Cohort:</b> Birth year or age class of the individual.<b>PY_survival:</b> Survival status of the pouch young (see data description for codes).<b>Month:</b> Month of capture/measurement.<b>Survival:</b> Annual survival status of the individual (e.g., 1 = survived, 0 = did not survive).<b>Age_months:</b> Age of the individual in months at the time of capture.<b>Measurer:</b> ID or initials of the person who took the measurements.<b>Mass:</b> Body mass of the individual (kg).<b>Leg:</b> Hind leg length of the individual (mm).<b>PY_survival_at_least_LPY_2023:</b> Indicator of whether the pouch young survived to at least the LPY stage in all years including 2023. At the time of publication, survival to weaning was unknown in 2023, but this does not impact results, as RS was measured based on survival to the LPY stage at a minimum.<b>Yearly_veg_sum:</b> Total available forage in the study area for a given year (kg/ha).<b>Density:</b> Estimated population density (kangaroos/ha) for a given year.<b>Veg_per_roo:</b> Available vegetation per kangaroo (kg/kangaroo), calculated as yearly available forage divided by population density.Data files and script's code and vector definitions:<b>Age certainty</b>: how we aged the female kangarooAge_certainty = 0 - Unknown ageAge_certainty = 1 - Aged in pouchAge_certainty = 2 - First caught as subadult or &lt; 20 kgAge_certainty = 3 - First caught when over 20 kgAge_certainty = 4 - Aged from molar progression<b>Pouch young survival</b>: specific to the female's reproductive successPY_survival = 0 - Female had no pouch youngPY_survival = 1 - Females' pouch young died before large pouch young stage (LPY)PY_survival = 2 - Females' pouch young died as large pouch young (LPY)PY_survival = 3 - Females' pouch young died as young at foot (YAF)PY_survival = 4 - Females weaned a young<b>Early reproduction total</b>: number of LPY a female had per year between ages 3-5 at age 5Earlyreproduction_total = 0 - No LPY between ages 3-5Earlyreproduction_total = 1 - One LPY between ages 3-5Earlyreproduction_total = 2 - Two LPY between ages 3-5Earlyreproduction_total = 3 - Three LPY between ages 3-5<b>Vector definitions</b>: (ellipses indicate a variable placeholder as a prefix or suffix (e.g., 'scaled_...' could represent 'scaled_mass')):<i>Prim_age</i>: Age of primiparity<i>Following_RS</i>: Reproductive success to LPY stage in the following year<i>Current_RS</i>: Reproductive success to LPY stage in the current year<i>Veg_per_roo</i>: available vegetation per kangaroo (kg/kangaroo)<i>cum_vegperroo</i>: cumulative vegetation per kangaroo, from age 1 to current age<i>Kn</i>: Relative condition index (Kn)<i>Juvenile_survival</i>: Annual proportion of offspring that survived to weaning from the LPY stage (kangaroos weaned / LPY).<i>scaled_</i>...: variable was scaled or standardized (variable - mean of variable / standard deviation of variable)<i>..._age2</i>: variable measured at age 2<i>..._age5</i>: variable measured at age 5<b>von Bertalanffy growth equation parameters</b> (Vincenzi et al. 2016):<i>loginitialsize:</i> logarithm of the initial size of kangaroos at LPY stage for von Bertalanffy growth function (~250mm) parameterized through priors<i>logMSP</i>: logarithm of the metabolic scaling parameter<i>logEP</i>: logarithm of the environmental parameter<i>psi</i>: logarithm of the environmental-behavioral interaction parameterVincenzi S, Crivelli AJ, Munch S, Skaug HJ, Mangel M. 2016. Trade-offs between accuracy and interpretability in von Bertalanffy random-effects models of growth. Ecol Appl. [accessed 2024 Dec 10];26(5):1535–1552. https://doi.org/10.1890/15-1177