From 59240162cd1243d6863b865a9ba1a8b8220d74df Mon Sep 17 00:00:00 2001 From: Kathryn Doering Date: Thu, 27 Jul 2023 09:07:11 -0400 Subject: [PATCH] add note about sourcing fxns --- inst/bookdown/02-ex-simple.Rmd | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/inst/bookdown/02-ex-simple.Rmd b/inst/bookdown/02-ex-simple.Rmd index 1321189b..d60c13d0 100644 --- a/inst/bookdown/02-ex-simple.Rmd +++ b/inst/bookdown/02-ex-simple.Rmd @@ -392,9 +392,6 @@ This code was used to examine how different natural mortality scenarios performe library(SSMSE) library(r4ss) -# functions for convergence and performance metrics, get from other gh repo -source("https://raw.githubusercontent.com/k-doering-NOAA/ssmse-afs/master/code/get_metrics.R") - # specify locations, create folders ---- cod_mod_path <- system.file("extdata", "models", "cod", package = "SSMSE") datfile_path <- file.path(cod_mod_path, "ss3.dat") @@ -563,10 +560,15 @@ To examine simulations for non-convergance, calculate, and plot performance metr library(SSMSE) library(r4ss) library(dplyr) +library(tidyr) library(ggplot2) library(patchwork) + # functions for convergence and performance metrics, get from other gh repo -source("https://raw.githubusercontent.com/k-doering-NOAA/ssmse-afs/master/code/get_metrics.R") +# uncomment if using SSMSE v0.2.5 and lower +# note: no need to source functions if using SSMSE >0.2.5, as these functions were moved into SSMSE +# source("https://raw.githubusercontent.com/k-doering-NOAA/ssmse-afs/master/code/get_metrics.R") + # path names ---- mods_path <- "input_models"