Run abundance pipeline ABU1

Usage

ppl_run_pipe_abu1(
  sp_code,
  config,
  steps = c("data", "fit", "diagnose", "summary"),
  prep_data_steps,
  summary_scale = c("linear", "model"),
  ...
)

Arguments

sp_code: SAFRING reference number of the species we want to analyse.
config: A list with pipeline configuration parameters. See configPipeline
steps: Pipeline steps to run. It can be one or more of: c("data", "fit", "diagnose", "summary").
prep_data_steps: Data preparation steps to pass on to ppl_create_data_ssm
summary_scale: Either "linear", summaries are given the linear scale or "model", summaries are given in the modelling scale (typically log scale)
...: Other parameters to pass on to prepGEECatchmData

Value

This function will run the whole abundance module of the BIRDIE pipeline