DOI: 10.5061/dryad.59zw3r291
title: Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

description: Integral projection models (IPMs) can estimate the population dynamics of
 species for which both discrete life stages and continuous variables
 influence demographic rates. Stochastic IPMs for imperiled species, in
 turn, can facilitate population viability analyses (PVAs) to guide
 conservation decision-making. Biphasic amphibians are globally
 distributed, often highly imperiled, and ecologically well-suited to the
 IPM approach. Herein, we present the first stochastic size- and
 stage-structured IPM for a biphasic amphibian, the U.S. federally
 threatened California tiger salamander (Ambystoma californiense; CTS).
 This Bayesian model reveals that CTS population dynamics show the greatest
 elasticity to changes in juvenile and metamorph growth and that
 populations are likely to experience rapid growth at low density. We
 integrated this IPM with climatic drivers of CTS demography to develop a
 PVA and examined CTS extinction risk under the primary threats of habitat
 loss and climate change. The PVA indicates that long-term viability is
 possible with surprisingly high (20–50%) terrestrial mortality, but
 simultaneously identified likely minimum terrestrial buffer requirements
 of 600–1000 m while accounting for numerous parameter uncertainties
 through the Bayesian framework. These analyses underscore the value of
 stochastic and Bayesian IPMs for understanding both climate-dependent taxa
 and those with cryptic life histories (e.g., biphasic amphibians) in
 service of ecological discovery and biodiversity conservation. In addition
 to providing guidance for CTS recovery, the contributed IPM and PVA supply
 a framework for applying these tools to investigations of
 ecologically-similar species.
description: Please see the associated manuscript for full methodological
 details.
description: 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:<br>    "CTS-Frequentist-IPM.R" -- Frequentist code to
 build the IPM and run the PVA. -The primary scripts to
 run the IPM and PVA are:<br>    "CTS_SOURCE.R" -- Source
 code for the vital rate functions.<br>    "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:<br>  
  "CTS_Best_Survival.R" -- The best Cormack-Jolly-Seber model of
 metamorph and juvenile/adult CTS survival and recapture
 probabilities.<br>    "CTS_Growth.R" -- CTS metamorph and
 juvenile/adult growth functions.<br>    "CTS_Fertility.R"
 -- CTS fertility function.<br>    "CTS_Maturity.R" -- CTS
 maturity function.<br>    "CTS_Larval_Survival.R" -- CTS
 larval survival given egg density function.<br>  
  "CTS_Females_Precip.R" -- The proportion of CTS females
 breeding given annual December-January precipitation function.<br>  
  "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.