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Annuals

Analyses of bet-hedging in desert annuals.

Workflow:

  1. speciescorrect + plot_sizes + national_climate_process
  2. dataprocess
  3. reprod + GO_descriptive
  4. bootstrap + seedpredict
  5. poplevel + prcp_projections
  6. popsims
  7. traitmeasures

Data

Master copies of data files used in the analysis.

Models

Parameters stored from Stan model runs.

Output

Data produced by R scripts (csv, rds, etc.).

  • aggregate_rainfall: Daily total precipitation 1946-2014 (10ths of a mm?).
  • cd: Raw plant reproduction census data.
  • cdpos: cd for plants that produced at least one seed.
  • census_data_date_errors: Date errors identified by Ursula (?).
  • csy: cd aggregated over individuals within plots, then aggregated over plots within years.
  • csyp: cd aggregated over individuals within plots.
  • csyp_seedests: csyp with reproduction estimates added for all plots (based on reproduction model predictions).
  • DI_survival: Table of density-independent seed survival rates as calculated from model.
  • gnzhh_onhh_pars_medians: Variance components (plot,year,species) for germination and old seed counts (?), based on descriptive Stan model.
  • medtraits: Species-averaged vital rates, for use in explaining population simulation results.
  • msy: Combined census and seed bank aggregated data, with single count values for each species-year combination.
  • msy: msy with estimated new seed densities added (based on reproduction model predictions).
  • ncy: Total precipitation over germination and growing season periods 1946-2014 (10ths of a mm?).
  • observation_error_byspecies: observation errors for germinant, old seed, and new seed densities, based on non parametric bootstrap (?).
  • pr_pars: Parameters from probability of reproduction model.
  • rs_pars: Parameters from model of expected number of seeds, given that the plant reproduced.
  • sb: Raw seed bank data.
  • Seed_Bank_sharedspecies: UNCERTAIN.
  • species_list: List of species abbreviations and full scientific names.
  • ssy: sb, aggregated across replicates within plots, then plots within years.
  • ssyp: sb, aggregated across replicates within plots.
  • Tvalues: Duration of each part of season, estimated from germination and death dates.
  • venablePlots_processed: Areas for each plant census plot (how have these been processed?).

Plots

Graphical plots of results.

Sims

Stored runs of population simulations.

Source

R code.

  • annual_climate_exploration: Expolore distribution and time series of rainfall data.
  • dataprocess: Set up seedling and seed databases.
  • speciescorrect: Correct names of species in Census and Seed data and remove low-abundance species.
  • plot_sizes: Check and edit Venable plot area data.
  • national_climate_process: Process rainfall data from US to produce single daily rainfall time series
  • prcp_projections: Running mean of prcp values.
  • outputgraphs_GO: Create model fit plots for germination and seed survival models.
  • outputgraphs_PrRs: Create model fit plots for reproduction models.
  • prediction_functions: Functions for predicting reproduction, germination, and seed survival.
  • bootstrap_nonparametric: Non-parametric bootstrap of total counts.
  • seedpredict: Predictions of new seed density for all plots.
  • popsims_stochastic: Simulations of population dynamics for finite area.
  • popsims_stochastic_medpars: Simulations of population dynamics for finite area, using species-level median values for all parameters except germination ones.
  • popsims_analytical: Simulations of population dynamics for infinite area.
  • poplevel_binomialG: Germination and seed survival models in Stan, with binomial germination calculation.
  • poplevel_lnpoisdist: Germination and seed survival models in Stan, with poisson seed counts.
  • talk_plots: Population size and germination graphs for presentations.
  • traitmeasures: Calculate species-level predictive traits (partially obsolete).
  • trait_functions: Functions for calculating derived trait values from popualtion parameters.
  • simulation_functions_stochastic: Functions for simulations of population dynamics for finite area.
  • simulation_functions_analytical: Functions for simulations of population dynamics for infinite area.
  • figure_functions: Functions to plot figures from Stan model output.
  • reprod: Estimate per-capita reproduction parameters in Stan.
  • GO_descriptive: Model to describe G and O values as function of species, year, and site, comparing negative binomial and lognormal-Poisson models (currently saving two versions, not sure which is right)
  • popsims_analytical_old: Simulations of population dynamics for infinite area, density-independent growth (depricated).
  • mortality_priors: Simulate gamma distributions to develop reasonable priors for density-independent seed mortality.
  • seasonwindow: Find best times for open and close of growing season.
  • correlations: Look at among-species correlations across years and plots.
  • popsize_timeseries: Plot population sizes of seedlings and seeds through time. Only two versions, debatable whether to keep / update.
  • queries_reproduction: Subset and save census data to provide examples of potential problems for Venable to investigate
  • site_germinant_distributions: How does distributing germinants among discrete sites affect the among-site variance in the number of germinants?
  • invasion_sims: Iterated simulations of resident population dynamics and invasions by new strategies.
  • invasion_functions: Calculate ES alpha_G and beta_G by iteratively perturbing parameters and attempting re-invasion.
  • ESS_explore: Develop explanations for patterns in ESS germination results.