Prepare Rodents Data for Forecasting

prepare_dataset is the workhorse function for creating portalcasting rodent datasets using existing functions.
Wraps around portalr::summarize_rodent_data to produce a data.frame associated with a set of data specifications. Inputs are ready for implementation via prepare_rodents.
prepare_rodents creates specified datasets using their associated function (typically prepare_dataset) and arguments, according to the directory_settings.
prepare_abundance creates a model-ready vector of abundances for fitting and casting, according to the model's requirements and time settings.

Usage

prepare_abundance(main = ".", dataset = NULL, species = NULL, model = NULL)

prepare_rodents(
  main = ".",
  datasets = prefab_datasets(),
  new_datasets_controls = NULL
)

prepare_dataset(
  name = "all",
  main = ".",
  filename = "rodents_all.csv",
  clean = FALSE,
  level = "Site",
  type = "Rodents",
  plots = "all",
  unknowns = FALSE,
  shape = "crosstab",
  time = "newmoon",
  output = "abundance",
  fillweight = FALSE,
  treatment = NULL,
  na_drop = FALSE,
  zero_drop = FALSE,
  min_traps = 1,
  min_plots = 24,
  effort = TRUE,
  species = prefab_species(main = main),
  total = TRUE,
  save = TRUE
)

read_datasets_controls(main = ".")

datasets_controls(main = ".", datasets = NULL)

write_datasets_controls(
  main = ".",
  new_datasets_controls = NULL,
  datasets = prefab_datasets()
)

Arguments

main: character value of the name of the main component of the directory tree.
dataset, datasets: character value(s) of name(s) of rodent dataset(s) to include.
species: character-valued vector of species names to include.
model: character value of the model name.
new_datasets_controls: Optional list of controls for new datasets. See datasets_controls.
name: character name to be given to the dataset.
filename: character value of the file for saving the output.
clean: logical indicator of if only the rodent data that passed QA/QC (clean = TRUE) or if all data (clean = FALSE) should be loaded.
level: character indicating the type of summary: "Plot", "Treatment", or "Site". Pipes directly to portalr::summarize_rodent_data.
type: character value of the rodent data set type, according to pre-existing definitions. An alternative toggle to species.

Either all species (type = "Rodents") or only granivoes (type = "Granivores").
plots: Specification of subset of plots. Can be a vector of numeric plots indicators or specific sets indicated by character values: "all" plots or "Longterm" plots (plots that have had the same treatment for the entire time series).
unknowns: logical indicator to either remove all individuals not identified to species (unknowns = FALSE) or sum them in an additional column (unknowns = TRUE.
shape: character value indicating a "crosstab" or "flat" output.
time: character value specifying the format of the time index in the output. Options are "period" (sequential Portal surveys), "newmoon" (lunar cycle numbering), and "date" (calendar date).
The default time = "newmoon" produces an equispaced observation timestep, a common format format for discrete-time modeling.
output: character indicating the type of data: "abundance", "biomass", or "energy".
fillweight: logical specifier of whether to fill in unknown weights with other records from that individual or species, where possible.
treatment: character indicating the specific treatment(s) to trim to if level = "Treatment": "control", "exclosure", "removal", or "spectabs"
na_drop: logical indicator of if NA values (representing insufficient sampling) should be dropped.
zero_drop: logical indicator of if 0 values (representing sufficient sampling but no detection) should be dropped.
min_traps: integer (or integer numeric) of the minimum number of traps collected for a plot to be used.
min_plots: integer (or integer numeric) of the minimum number of plots surveyed for a survey to be used.
effort: logical indicator of if the effort columns should be included in the output.
total: logical value indicating if a total (sum across species should be added or not. Only available if more than one species is included.
save: logical indicator controlling if the output should be saved out.

Value

prepare_dataset: data.frame for the specified dataset.
prepare_rodents: list of data.frames for the specified datasets.
prepare_abundance: numeric vector of abundance data corresponding to the time articulated in the metadata file. Missing values are interpolated if requested via the model controls.
read_datasets_controls, write_datasets_controls, datasets_controls: list of datasets' control lists, invisible-ly for write_datasets_controls.

Examples

if (FALSE) { # \dontrun{
   main1 <- file.path(tempdir(), "rodents")

   create_dir(main = main1)
   fill_resources(main = main1)
   fill_forecasts(main = main1)
   fill_fits(main = main1)
   fill_models(main = main1)

   prepare_newmoons(main   = main1)
   prepare_rodents(main    = main1) 

   write_datasets_controls(main = main1)
   read_datasets_controls(main = main1)
   datasets_controls(main = main1)

   unlink(main1, recursive = TRUE)
} # }

Usage

Arguments

Value

See also

Examples