Merge pull request #37 from NOAA-FIMS/fix-rendering-issue

fix: resolve rendering issue for sardine qmd file
NOAA-FIMS · Jun 18, 2024 · a62ef24 · a62ef24
2 parents bdb6997 + 4c98d97
commit a62ef24
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/content/SWFSC-sardine.qmd b/content/SWFSC-sardine.qmd
@@ -324,7 +324,7 @@ recruitment$estimate_log_devs <- estimate_recdevs
 recruitment$log_devs <- rep(log(1), nyears) # set to no deviations (multiplier) to start
 
 # growth
-wtatage <- SS_readwtatage("data_files/sardine_wtatage.ss_new")
+wtatage <- r4ss::SS_readwtatage("data_files/sardine_wtatage.ss_new")
 
 ewaa_growth <- methods::new(EWAAgrowth)
 ewaa_growth$ages <- ages

diff --git a/content/pc.qmd b/content/pc.qmd
@@ -91,7 +91,7 @@ estimate_q3 <- TRUE
 estimate_q6 <- TRUE
 estimate_F <- TRUE
 estimate_recdevs <- TRUE
-source("pk_prepare_FIMS_inputs.R")
+source("R/pk_prepare_FIMS_inputs.R")
 ## make FIMS model
 success <- CreateTMBModel()
 parameters <- list(p = get_fixed())

diff --git a/content/setup.qmd b/content/setup.qmd
@@ -3,8 +3,7 @@
 #| label: package-installation
 
 # Names of required packages
-packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "remotes", "lubridate",
-              "r4ss")
+packages <- c("dplyr", "tidyr", "ggplot2", "TMB", "reshape2", "here", "remotes", "lubridate")
 
 # Install packages not yet installed
 installed_packages <- packages %in% rownames(installed.packages())