R package with advanced diagnostics to evaluate a Stock Synthesis model. Diagnostics include residual analyses, hindcasting and cross-validation techniques, and retrospective analyses.
indexfleets in SSplotModelComp and SSplotHCxval default to 1 and defined as:
#' @param indexfleets CHECK IF NEEDED or how to adjust indexfleets
Indexfleets in r4ss documentation (SSplotComparisions) include a more detailed version, but also states that the value is used in different states:
#' @param indexfleets Fleet numbers for each model to compare
#' indices of abundance. Can take different forms:
#' \itemize{
#' \item NULL: (default) create a separate plot for each index as long as the fleet
#' numbering is the same across all models.
#' \item integer: create a single comparison plot for the chosen index
#' \item vector of length equal to number of models: a single fleet number
#' for each model to be compared in a single plot
#' \item list: list of fleet numbers associated with indices within each
#' model to be compared, where the list elements are each a vector of the
#' same length but the names of the list elements don't matter and can be
#' absent.
#' }
Potentially, this would cause errors passing the wrong type of indexfleets. However, checking r4ss's SSplotComparisions.r code, the script has these type checks in place. SSplotModelComp and SSplotHCxval are similar in this way.
indexfleetsin SSplotModelComp and SSplotHCxval default to1and defined as:Indexfleets in r4ss documentation (SSplotComparisions) include a more detailed version, but also states that the value is used in different states:
Potentially, this would cause errors passing the wrong type of
indexfleets. However, checking r4ss'sSSplotComparisions.rcode, the script has these type checks in place. SSplotModelComp and SSplotHCxval are similar in this way.