diff --git a/vignettes/ex4_model_validation.Rmd b/vignettes/ex4_model_validation.Rmd index a43f6c7..e520ce0 100644 --- a/vignettes/ex4_model_validation.Rmd +++ b/vignettes/ex4_model_validation.Rmd @@ -25,6 +25,7 @@ knitr::opts_chunk$set(warning = FALSE, message = FALSE) ``` ```{r setup, warning = FALSE, message = FALSE, echo=FALSE,results='hide',fig.keep='all'} +knitr::opts_chunk$set(echo = TRUE) library(ggplot2) library(readr) @@ -88,7 +89,7 @@ First, we run the model for each stock. The AI Pcod model (pcod_mod) uses a sing set.seed(415) # for reproducibility, use a seed # first, get the p-cod data set up -pcod_bio_dat <- read_csv("ai_pcod_2022_biomass_dat.csv") +pcod_bio_dat <- readr::read_csv("ai_pcod_2022_biomass_dat.csv") pcod_input <- prepare_rema_input(model_name = "p_cod", biomass_dat = pcod_bio_dat, # one strata @@ -98,8 +99,8 @@ pcod_input <- prepare_rema_input(model_name = "p_cod", pcod_mod <- fit_rema(pcod_input) # next, get the thornyhead data set up -thrn_bio_dat <- read_csv("goa_thornyhead_2022_biomass_dat.csv") -thrn_cpue_dat <- read_csv("goa_thornyhead_2022_cpue_dat.csv") +thrn_bio_dat <- readr::read_csv("goa_thornyhead_2022_biomass_dat.csv") +thrn_cpue_dat <- readr::read_csv("goa_thornyhead_2022_cpue_dat.csv") thrn_input <- prepare_rema_input(model_name = 'thrnhead_rockfish', multi_survey = TRUE, biomass_dat = thrn_bio_dat,