Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

Available files to conduct a Bayesian integral projection model (IPM) and population viability analysis (PVA) for the California tiger salamander (CTS) include: -The preliminary frequentist CTS IPM and PVA script created by Christopher A. Searcy is: "CTS-Frequentist-IPM.R" -- Frequentist code to build the IPM and run the PVA. -The primary scripts to run the IPM and PVA are: "CTS_SOURCE.R" -- Source code for the vital rate functions. "CTS_IPM_PVA.R' -- Code to build the IPM, conduct sensitivity and elasticity analyses, and run the PVA. -The scripts used to build the vital rate functions that inform the IPM are: "CTS_Best_Survival.R" -- The best Cormack-Jolly-Seber model of metamorph and juvenile/adult CTS survival and recapture probabilities. "CTS_Growth.R" -- CTS metamorph and juvenile/adult growth functions. "CTS_Fertility.R" -- CTS fertility function. "CTS_Maturity.R" -- CTS maturity function. "CTS_Larval_Survival.R" -- CTS larval survival given egg density function. "CTS_Females_Precip.R" -- The proportion of CTS females breeding given annual December-January precipitation function. "CTS_Replacement.R" -- Adult-only replacement and reproductive success functions to construct piecewise environmental-dependency function. -All necessary data files to run the CTS_IPM_PVA.R script and support the findings of our study are: "adults-v2.txt" -- The adult CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA. "covariates-v2.txt" -- The CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA specifying individual body masses (ln-transformed; g). "metamorphs-v2.txt" -- The metamorph CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA. "precip.csv" -- Study rain year-specific November-February and October-June precipitation values (mm). "density-distance.csv" -- Proportion of the post-metamorphic life stage individuals (from 0 to 1) found within 100-m distance radius increments from the pond shoreline. "Larval-Survival-Density.csv" -- Ln-transformed larval survival and Ln-transformed egg density (eggs/m^3) data. "meta-size-by-egg-density.csv" -- Study year-specific metamorph size and egg density (eggs/m^3) data. "Olcott20**.txt" -- Body size distributions of each cohort of CTS from the mark-recapture study across the 122 body size bins, where "**" indicates study year in the file name. "Stochastic_Climate_Pool.txt" -- Historic precipitation record from 1893-2012 (Vacaville and Nut Tree Airport station records). "Stochastic_Climate_Pool_Rev.txt" -- Historic precipitation record from 1893-2008 (Nut Tree Airport-only station records). "females-precip-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of female CTS breeding given December-January precipitation (mm). "fertility-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of clutch size (# eggs) given female CTS body mass (g). "growth-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distributions of the life stage-specific growth functions. "larval-survival-posterior-samples.csv" -- The 500 random samples from the posterior distribution of the function of larval survival probability given egg density (eggs/m^3). "maturity-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of maturity probabilitygiven CTS body mass (g). "replace-success-infection-samples-CENTERED.csv" -- The 500 random samples of the inflection point from the posterior distribution of the function of probability of metamorph recruitment being above the replacement rate given October-June precipitation (mm). "repro-success-infection-samples-CENTERED.csv" -- The 500 random samples of the inflection point from the posterior distribution of the function of probability of reproductive success given October-June precipitation (mm). "survival-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the Cormack-Jolly-Seber model of life stage-specific survival probabilities given body mass (g). Scripts were developed and run using R version 4.0.0.