filing plot output in one directory

Author: kathsherratt

R/plot-model-flow.R

@@ -87,6 +87,6 @@ create_model_flow <- function() {
   flow_chart <- flow |>
     fc_merge() |>
     fc_draw() |>
-    fc_export(filename = "flowchart.png", path = here("plots"),
+    fc_export(filename = "flowchart.png", path = here("output", "plots"),
               width = 3000, height = 3000, res = 500)
 }

plots/check_Cases.pdf output/plots/check_Cases.pdfplots/check_Cases.pdf renamed to output/plots/check_Cases.pdf

@@ -57,7 +57,7 @@ Data for this work were downloaded on 30th May 2023. These data are available in
 ```{r model-flow, fig.cap="Eligibility criteria for models contributing case (left) and death (right) forecasts to the European COVID-19 Forecast Hub, March 2021 - March 2023"}
 # source(here("R", "plot-model-flow.R"))
 # flow_chart <- create_model_flow()
-knitr::include_graphics(here("plots", "flowchart.png"))
+knitr::include_graphics(here("output", "plots", "flowchart.png"))
 ```
 
 ## Model characteristics
@@ -133,14 +133,14 @@ results <- readRDS(here("output", "results.rds"))
 
 ```{r gamm-diagnostics-cases}
 # QQ plot, residuals
-knitr::include_graphics(here("plots", "check_Cases.pdf"))
+knitr::include_graphics(here("output", "plots", "check_Cases.pdf"))
 ```
 
 #### Deaths
 
 ```{r gamm-diagnostics-deaths}
 # QQ plot, residuals
-knitr::include_graphics(here("plots", "check_Deaths.pdf"))
+knitr::include_graphics(here("output", "plots", "check_Deaths.pdf"))
 ```
 
 ## Model results