SampPost: SampPost - Sample posterior function
In GPowney/TrendSummaries: TrendSummaries - summarising occupancy model outputs

Description Usage Arguments Value

View source: R/SampPost.R

This function is used to extract a number of annual occupancy estimates from any given posterior produced using the occDetFunc() in the package sparta. The function loops through BUGS output files within a given location.

SampPost(
  indata = "../data/model_runs/",
  output_path = "../data/sampled_posterior_1000/",
  REGION_IN_Q = "psi.fs",
  sample_n = 1000,
  group_name = "",
  combined_output = TRUE,
  max_year_model = NULL,
  min_year_model = NULL,
  write = FALSE
)

`indata`	The file path to a location containing .rdata files of the bugs outputs, one for each species
`output_path`	The location where the output will be saved.
`REGION_IN_Q`	The region for which occupancy estimates will be extracted. UK based occupancy model examples include, 'psi.fs', 'psi.fs.r_GB', 'psi.fs.r_ENGLAND'.
`sample_n`	The number of values extracted from the posterior.
`group_name`	The name of the species group we are running, used for naming output files.
`combined_output`	This specifies whether the output should be a single .csv, containing all species (TRUE) or a single .csv file per species (FALSE). Default is TRUE. If TRUE all outputs must have the same start and end year. To combine outputs run over different year ranges please use `SampBind()`.
`max_year_model`	The last year for which estimates are available in the posterior. If this is available in the metadata (models run using sparta >= 0.2.06) then it will be added automatically. If this is not available then any input value for this argument will be used or this will default to NULL.
`min_year_model`	The first year for which estimates are available in the posterior. If this is available in the metadata (models run using sparta >= 0.2.06) then it will be added automatically. If this is not available then any input value for this argument will be used or this will default to NULL.
`write`	Boolean. If write = TRUE and combine_outputs = TRUE then then the .rdata files are written to output_path.

A .csv file for each species containing annual occupancy estimates for each year as columns, and an iteration and species name column. If combined_output = TRUE the results are saved as an rdata file instead.

GPowney/TrendSummaries documentation built on Nov. 15, 2021, 6:14 p.m.