Data from: Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous plant

Paniw M, Quintana-Ascencio P, Ojeda F, Salguero-Gomez R

Date Published: January 24, 2017

DOI: http://dx.doi.org/10.5061/dryad.40qt2

 

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Title Overview of the R code provided in the manuscript
Downloaded 7 times
Description Here, we provide an overview of the R scripts and data files to accompany the main text, "Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous subshrub" and found in this depository. The .R files should be opened with an R editor (e.g., R Studio). The R code is fully commented.
Download JPEpaniwSA2.docx (19.83 Kb)
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Title dataDroso
Downloaded 7 times
Description Demographic transitions of Drosophyllum lusitanicum populations recorded in five annual censuses (from 2011to 2015) in eight populations differing in time-since-fire (TSF) and livestock browsing (LS) in their habitats. These data are used to quantify vital rates of above-ground individuals.
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Title dataDrosoSB
Downloaded 3 times
Description Seed fates (in a binary format) inferred from two experiments. These data are used to quantify the transitions related to the seedbank.
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Title mcmcOUT
Downloaded 2 times
Description In case the reader wishes to forego the step of fitting the Bayesian models, which can be very time consuming (> 24 h on 3.40 GHz processor), we provided a mcmcOUT.csv file with 600 posterior parameter values for each of the parameters estimated with Bayesian models using uninformative priors.
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Title vitalRateModels
Downloaded 8 times
Description Executes and saves the results of a Bayesian model quantifying all vital rates using uniformed priors; illustrates basic diagnostics that can be run on the results of an MCMC run (i.e., the posterior parameter distribution) to check for model convergence and autocorrelation of the posterior samples.
Download vitalRateModels.R (44.46 Kb)
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Title makeIPM
Downloaded 4 times
Description Demonstrates how to construct IPMs including continuous (above-ground) and discrete (seedbank) transitions for parameter means of the Bayesian models; saves IPMs for each combination of TSF (n =5) × LS (n = 2) × site (n = 8) (Part A). The code also saves IPMs for each TSF × LS averaged over sites (Part B). Site-specific and average kernel transitions for the vital rate growth (γ in main text) are also saved. The IPMs in Part A are used to calculate the stochastic population growth rate log λs, and extinction probability, Pq(t) by t = 300 years. The IPMs in parts A and B are used to calculate elasticities of log λs to changes in mean transitions across environmental states (TSF & LS) and in the standard deviation of transitions.
Download makeIPM.R (20.68 Kb)
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Title sLambdafixedLS
Downloaded 7 times
Description Runs and plots results of simulations of log λs using IPMs constructed for mean parameter values. The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.
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Title sLambdaStochLS
Downloaded 5 times
Description Runs and plots results of simulations of log λs using IPMs constructed for mean parameter values. Here, the growth kernel transitions are also included alongside the full IPMs. The simulations consider both fire and livestock browsing as an integrated stochastic process in which transitions between combinations of TSF × LS states are based on fire return interval and browsing management efforts.
Download sLambdaStochLS.R (14.39 Kb)
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Title elastVR
Downloaded 5 times
Description Runs and plots results of simulations of log λs and elasticities using IPMs constructed for lower vital rate survival (σ). The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.
Download elastVR.R (24.16 Kb)
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When using this data, please cite the original publication:

Paniw M, Quintana-Ascencio PF, Ojeda F, Salguero-Gómez R (2017) Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous plant. Journal of Applied Ecology, online in advance of print. http://dx.doi.org/10.1111/1365-2664.12872

Additionally, please cite the Dryad data package:

Paniw M, Quintana-Ascencio P, Ojeda F, Salguero-Gomez R (2017) Data from: Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous plant. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.40qt2
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