From 3da8fbf80cd1c02bc457b361e364b2d20b39a7d7 Mon Sep 17 00:00:00 2001 From: Chantel Wetzel Date: Tue, 1 Oct 2024 07:27:14 -0700 Subject: [PATCH] document --- man/get_param_values.Rd | 4 +++- man/get_summary.Rd | 7 +++---- man/plot_profile.Rd | 7 ++++--- man/profile_wrapper.Rd | 32 +------------------------------- 4 files changed, 11 insertions(+), 39 deletions(-) diff --git a/man/get_param_values.Rd b/man/get_param_values.Rd index 749767d..6f034af 100644 --- a/man/get_param_values.Rd +++ b/man/get_param_values.Rd @@ -14,7 +14,9 @@ There is no default entry for \code{mydir}. An example of user input could be \code{mydir = file.path("C:/my_models", "base_model")}.} -\item{para}{SS3 parameter name (string) that the profile was run across.} +\item{para}{A character string specifying the SS3 parameter name that the +profile pertains to. The parameter name should match the name in the +control.ss_new file from SS3.} \item{vec}{Vector of parameter values or retrospective runs the summary object contains} diff --git a/man/get_summary.Rd b/man/get_summary.Rd index be25257..aceb315 100644 --- a/man/get_summary.Rd +++ b/man/get_summary.Rd @@ -4,7 +4,7 @@ \alias{get_summary} \title{Generate results from likelihood profiles} \usage{ -get_summary(mydir, para, vec, name, profilemodels, profilesummary) +get_summary(mydir, para, vec, profilemodels, profilesummary) } \arguments{ \item{mydir}{Directory where model files are located. @@ -13,13 +13,12 @@ An example of user input could be \code{mydir = file.path("C:/my_models", "base_model")}.} \item{para}{A character string specifying the SS3 parameter name that the -profile pertains to.} +profile pertains to. The parameter name should match the name in the +control.ss_new file from SS3.} \item{vec}{A numeric vector specifying the parameter values that the profile covers.} -\item{name}{Identify if the csv file show jitter, retro, or profile results.} - \item{profilemodels}{An object returned from \code{\link[r4ss:SSgetoutput]{r4ss::SSgetoutput()}}.} \item{profilesummary}{An object returned from \code{\link[r4ss:SSsummarize]{r4ss::SSsummarize()}}.} diff --git a/man/plot_profile.Rd b/man/plot_profile.Rd index fc4e9ea..59c1883 100644 --- a/man/plot_profile.Rd +++ b/man/plot_profile.Rd @@ -14,8 +14,9 @@ An example of user input could be \item{rep}{A list of model output as returned by \code{\link[r4ss:SS_output]{r4ss::SS_output()}}.} -\item{para}{A character value that matches a parameter name as used in the -SS control.ss_new parameter names. +\item{para}{A character string specifying the SS3 parameter name that the +profile pertains to. The parameter name should match the name in the +control.ss_new file from SS3. The name will be cleaned up for plotting purposes internally within the function. For example, \code{SR_BH_steep} becomes "Steepness (\emph{h})".} @@ -28,7 +29,7 @@ Create plots to be included in presentations and documents that summarize a likelihood profile. } \seealso{ -\link{profile_wrapper} and \link{rerun_profile_vals} call \code{profile_plot}. +\link{profile_wrapper} and \link{rerun_profile_vals} call \code{plot_profile}. } \author{ Chantel Wetzel. diff --git a/man/profile_wrapper.Rd b/man/profile_wrapper.Rd index 6aa6b15..37ff168 100644 --- a/man/profile_wrapper.Rd +++ b/man/profile_wrapper.Rd @@ -1,11 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/profile_wrapper.R, R/profile_wrapper_backup.R +% Please edit documentation in R/profile_wrapper.R \name{profile_wrapper} \alias{profile_wrapper} \title{Run \code{\link[r4ss:profile]{r4ss::profile()}} based on \code{model_settings}} \usage{ -profile_wrapper(mydir, model_settings) - profile_wrapper(mydir, model_settings) } \arguments{ @@ -19,19 +17,6 @@ Typically, created using \link{get_settings} but users can create their own list as long as it has all of the necessary components for the function at hand.} } \value{ -Nothing is explicitly returned from \code{profile_wrapper()}. -The following objects are saved to the disk: -\itemize{ -\item \verb{*_profile_output.Rdata} -\item \verb{*_trajectories_*} from \code{\link[r4ss:SSplotComparisons]{r4ss::SSplotComparisons()}} -\item \code{piner_panel_*.png} -\item \code{parameter_panel_*.png} -\item \code{run_diag_warning.txt} -\item a copy of the control file saved to \code{model_settings$newctlfile} -\item \code{backup_oldctlfile.ss} -\item \code{backup_ss.par} -} - Nothing is explicitly returned from \code{profile_wrapper()}. The following objects are saved to the disk: \itemize{ @@ -46,13 +31,6 @@ The following objects are saved to the disk: } } \description{ -Setting up the specifications, running the profile using \code{\link[r4ss:profile]{r4ss::profile()}}, -and generating figures and tables can be tedious, error prone, and time -consuming. Thus, \code{profile_wrapper()} aims to further decrease the work -needed to generate a profile that is easily included in a assessment report -for the Pacific Fisheries Management Council. See the See Also section for -information on a workflow to use this function. - Setting up the specifications, running the profile using \code{\link[r4ss:profile]{r4ss::profile()}}, and generating figures and tables can be tedious, error prone, and time consuming. Thus, \code{profile_wrapper()} aims to further decrease the work @@ -61,14 +39,6 @@ for the Pacific Fisheries Management Council. See the See Also section for information on a workflow to use this function. } \seealso{ -The following functions interact with \code{profile_wrapper()}: -\itemize{ -\item \code{\link[=get_settings]{get_settings()}}: populates a list of settings for \code{model_settings} -\item \code{\link[=run_diagnostics]{run_diagnostics()}}: calls \code{profile_wrapper()} -\item \code{\link[r4ss:profile]{r4ss::profile()}}: the workhorse of \code{profile_wrapper()} that does the -parameter profiles -} - The following functions interact with \code{profile_wrapper()}: \itemize{ \item \code{\link[=get_settings]{get_settings()}}: populates a list of settings for \code{model_settings}