Prepare covariate data for abundance pipeline

Usage

ppl_create_data_ssm(
  sp_code,
  year,
  catchment,
  config,
  force_gee = TRUE,
  force_gee_upload = TRUE,
  steps = c("subset", "missing", "gee", "model"),
  ...
)

Arguments

sp_code: SAFRING reference number of the species we want to analyse.
year: Year for which the SSM data should be prepared.
catchment: A sf object with polygons corresponding to the catchment, or reference area considered for the covariates associated with CWAC sites.
config: A list with pipeline configuration parameters. See configPipeline
force_gee: Logical. If TRUE (default), then count data will be annotated with environmental information from GEE. If FALSE, then we assume data have already been annotated and only some manipulation to join catchment environmental data with count data is required.
force_gee_upload: Logical. If TRUE (default), then the catchment polygons will be uploaded to GEE under the name 'quin_catchm'. If FALSE, then we assume these polygons are already #' present in GEE server and we don't need to upload them again.
steps: A character vector expressing the processing steps for the CWAC data. It can be one or more of: "missing" - add missing counts as missing data, "gee" - annotate data with covariates from Google Earth Engine, "subset" - subset data to those sites with presence of the species and a coverage of at least 10 years from 1993 to 2021, and "model" prepare data for model fitting by adding some aux variables and ordering the data. It defaults to all steps.
...: Other arguments passed on to prepGEECatchmData