CheckInput: CheckInput function

In femoerman/PBPGM: Parallellised Bayesian Population Growth Models

Description

Checks the user input variables, and creates an error if it encounters a problem for fitting the models

Usage

CheckInput(
  dd,
  K.prior,
  Ksd.prior,
  r0.prior,
  r0sd.prior,
  d.prior,
  dsd.prior,
  N0.prior,
  N0sd.prior,
  sdev.prior,
  cores,
  iter,
  warmup,
  chains,
  graphname,
  outputtype,
  modelname
)

Arguments

dd	Dataframe with columns for population size data (colname=popsize), time data (colname=time) and unique identifiers for each population (colname=ident)
K.prior	Prior value for the mean carrying capacity (K). Must be on log scale and numeric
Ksd.prior	Prior value for the standard deviation on carrying capacity (K). Must be on log scale and numeric
r0.prior	Prior value for the mean intrinsic rate of growth (r0). Must be on log scale and numeric
r0sd.prior	Prior value for the standard deviation on intrinsic rate of growth (r0). Must be on log scale and numeric
d.prior	Prior value for the mean death rate (d). Must be on log scale and numeric
dsd.prior	Prior value for the standard deviation on death rate (d). Must be on log scale and numeric
N0.prior	Prior value for the mean starting population size (N0). Must be on log scale and numeric
N0sd.prior	Prior value for the standard deviation on starting population size (N0). Must be on log scale and numeric
sdev.prior	Prior value for the standard deviation for the model fitting. Must be numeric. Defaults to 1.
cores	Optional argument detailing the number of cores to use. Must be integer. Defaults to NA, in which case all available cores - 1 will be used
iter	Number of iterations to run for the model, defaults to 1e4. Must be integer
warmup	Number of iterations to run warmup. Defaults to 1e3. Must be integer and smaller than warmup
chains	Number of chains to run for each fit. Must be integer. Defaults to 1
graphname	Path with filename to save the figure showing the fits of the data with the posterior predictions. Defaults to NA, in which the plot will not be saved
outputtype	Type of output that will be returned. Must be "summary", "full" or "both". summary return the summarised posteriors (mean and sd on log scale), full returns dataframe containing lists of all the posterior samples, both returns a list with both the summary and full output. Defaults to summary

Examples

CheckInput()

femoerman/PBPGM documentation built on Aug. 22, 2021, 11:46 p.m.