Estimating the Spatial Dynamics of Plant Recruitment using Approximate Bayesian Computation

Supporting Data for MSc Thesis

Author: Jennifer Freeman
Supervisor: Ben Bolker
Institution: McMaster University, Hamilton, ON, Canada
Date: June 3, 2023

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Directory structure and description of files:

ABC_Slash_Pine

• ┣ data
  • ┣ LingsUTM-3.txt seedling data from original source
  • ┣ pine2.RData seed and seedling data used in all analysis (transformed coordinates)
  • ┗ SeedsUTM-2.txt seed data from original source
• ┣ estimates
  • ┣ abc.R ABC estimates
  • ┗ mle.R MLE seed estimates
• ┣ general
  • ┣ abc_local.R local ABC function modified from abc::abc() to remove MAD scaling
  • ┣ functions.R general functions for priors, data simulations and data prep
  • ┗ R_sessionInfo.txt output from R sessionInfo() (all required packages with version numbers)
• ┣ priors
  • ┣ priors.html output from priors.Rmd
  • ┗ priors.Rmd prior visualization, PPD for mean seed count and mean establishment probability, exploring reparameterized Matérn scale
• ┣ simulations
  • ┣ farm META-Farm shell scripts and case file for simulations, run in SIMPLE mode. No modifications were made to single_case.sh.
    • ┣ final.sh
    • ┣ job_script.sh
    • ┣ resubmit_script.sh
    • ┗ table.dat
  • ┣ output
    • ┣ params_meta_splinecorr.RDS 1e6 prior parameter draws from META-Farm run using files in farm, output from simulate.R and combine.R
    • ┗ summary_statistics_meta_splinecorr.RDS 1e6 summary statistics from META-Farm run, output from simulate.R and combine.R.
  • ┣ combine.R post-processing script using META-Farm package to aggregate results
  • ┣ r_parallel.R exploratory script to investigate R parallel packages to generate simulations
  • ┗ simulate.R script to generate simulations using META-Farm package
• ┣ summary_statistics
  • ┣ output
    • ┗ observed_stats.RDS output from observed_sumstats.R
  • ┣ observed_sumstats.R script to compute summary statistics of observed data
  • ┗ spline_correlogram.R exploratory analysis of spline correlograms, setting degrees of freedom and testing distance breaks
• ┣ thesis_plots
  • ┣ output TikZ thesis plot images, output from thesis_plots.R
    • ┣ abc_parameters.tex
    • ┣ coverage.tex
    • ┣ cv_quant.tex
    • ┣ dataset.tex
    • ┣ grf_shape.tex
    • ┣ grf_shape_ras1.png
    • ┣ grf_shape_ras2.png
    • ┣ grf_shape_ras3.png
    • ┣ grf_shape_ras4.png
    • ┣ interpoint_distances.tex
    • ┣ matern_reparam.tex
    • ┣ profile_likelihood.tex
    • ┣ profile_likelihood_nugget.tex
    • ┣ rmsre.tex
    • ┣ sbc.tex
    • ┗ splinecorr.tex
  • ┗ thesis_plots.R - generates all plots in thesis
• ┣ validation
  • ┣ farm META-Farm shell scripts and case file for SBC validation, run in SIMPLE mode. No modifications were made to single_case.sh.
    • ┣ job_script.sh
    • ┣ resubmit_script.sh
    • ┗ table.dat
  • ┣ output
    • ┣ sbc output from sbc.R and sbc_plot.R with MAD scaling
    • ┣ sbc_ac output from sbc.R and sbc_plot.R with 0.5% acceptance rate
    • ┣ sbc_noscale output from sbc.R and sbc_plot.R with no scaling
    • ┣ sbc_scale.default output from sbc.R and sbc_plot.R with scale.default() (subtract mean, divide by standard deviation)
    • ┣ sbc_scaleonly output from sbc.R and sbc_plot.R with scaling by standard deviation
    • ┣ cat_plot.RDS output from coverage.R
    • ┣ check_coverage.RDS output from coverage.R
    • ┣ knownparam_stats_splinecorr.RDS output from known_parameter.R
    • ┗ rmsre_results.RDS output from rmsre.R
  • ┣ coverage.R percent coverage
  • ┣ known_parameter.R ABC run using known parameter set
  • ┣ rmsre.R validating acceptance rate using RMSRE
  • ┣ sbc.R script to generate SBC results using META-Farm package
  • ┗ sbc_plot.R plots of all SBC results