From 8c30d2ce6e541b8a17401beeafce8325ceb55e82 Mon Sep 17 00:00:00 2001 From: Jim Thorson <50178738+James-Thorson-NOAA@users.noreply.github.com> Date: Sun, 9 Aug 2020 15:13:03 -0700 Subject: [PATCH] fix make_settings... ... to track change from Index_cyl to Index_ctl --- R/make_settings.R | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/R/make_settings.R b/R/make_settings.R index c3c6a2e..81851cf 100644 --- a/R/make_settings.R +++ b/R/make_settings.R @@ -19,7 +19,7 @@ #' @return Tagged list containing default settings for a given purpose, use \code{names} on output to see list of settings. #' #' @family wrapper functions -#' @seealso \code{?VAST} for general documentation, \code{?make_settings} for generic settings, \code{?fit_model} for model fitting, and \code{?plot_results} for generic plots +#' @seealso \code{\link[VAST]{VAST}} for general documentation, \code{\link[FishStatsUtils]{make_settings}} for generic settings, \code{\link[FishStatsUtils]{fit_model}} for model fitting, and \code{\link[FishStatsUtils]{plot_results}} for generic plots #' #' @export make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, @@ -52,7 +52,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(bias.correct)) bias.correct = TRUE if(missing(treat_nonencounter_as_zero)) treat_nonencounter_as_zero = TRUE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=TRUE, "Calculate_effective_area"=TRUE, "treat_nonencounter_as_zero"=treat_nonencounter_as_zero ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "samples" if(missing(max_cells)) max_cells = Inf } @@ -72,7 +72,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(bias.correct)) bias.correct = TRUE if(missing(treat_nonencounter_as_zero)) treat_nonencounter_as_zero = TRUE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=TRUE, "Calculate_effective_area"=TRUE, "treat_nonencounter_as_zero"=treat_nonencounter_as_zero ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "grid" if(missing(max_cells)) max_cells = max( 2000, n_x*10 ) } @@ -95,7 +95,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(treat_nonencounter_as_zero)) treat_nonencounter_as_zero = FALSE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=FALSE, "Calculate_effective_area"=FALSE, "Calculate_Cov_SE"=TRUE, "treat_nonencounter_as_zero"=treat_nonencounter_as_zero, "Project_factors"=TRUE ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "samples" if(missing(max_cells)) max_cells = Inf } @@ -118,7 +118,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(bias.correct)) bias.correct = TRUE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=FALSE, "Calculate_effective_area"=FALSE, "Calculate_Cov_SE"=FALSE, "Calculate_Fratio"=TRUE, "Estimate_B0"=TRUE ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Bratio_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Bratio_cyl", "Index_ctl", "Bratio_ctl" ) if(missing(knot_method)) knot_method = "samples" if(missing(max_cells)) max_cells = Inf } @@ -140,7 +140,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(ObsModel)) ObsModel = c(1,1) if(missing(bias.correct)) bias.correct = FALSE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=FALSE, "Calculate_effective_area"=FALSE, "Calculate_Cov_SE"=TRUE, "Project_factors"=TRUE ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "samples" if(missing(max_cells)) max_cells = Inf } @@ -166,7 +166,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(ObsModel)) ObsModel = c(1,1) if(missing(bias.correct)) bias.correct = FALSE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=FALSE, "Calculate_effective_area"=FALSE, "Calculate_Cov_SE"=TRUE, "Project_factors"=TRUE ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "samples" if(missing(max_cells)) max_cells = Inf } @@ -183,7 +183,7 @@ make_settings = function( n_x, Region, purpose="index", fine_scale=TRUE, if(missing(ObsModel)) ObsModel = c(2,1) if(missing(bias.correct)) bias.correct = FALSE if(missing(Options)) Options = c("SD_site_logdensity"=FALSE, "Calculate_Range"=FALSE, "Calculate_effective_area"=FALSE, "Calculate_Cov_SE"=TRUE, "Project_factors"=TRUE ) - if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl" ) + if(missing(vars_to_correct)) vars_to_correct = c( "Index_cyl", "Index_ctl" ) if(missing(knot_method)) knot_method = "grid" if(missing(max_cells)) max_cells = max( 2000, n_x*10 ) }