Add investigation of decreasing forecaster behavior (#195)

Co-authored-by: Dmitry Shemetov <[email protected]>

Author: dsweber2

.github/workflows/tests.yaml

@@ -38,7 +38,7 @@ jobs:
 
       - name: System dependencies
         run: |
-          sudo apt-get update && sudo apt-get -y install libglpk-dev
+          sudo apt-get update && sudo apt-get -y install libglpk-dev libcurl4-openssl-dev libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
 
       - uses: r-lib/actions/setup-renv@v2
 

.gitignore

@@ -22,3 +22,5 @@ data/
 .nhsn_covid_cache.parquet
 .nhsn_flu_cache.parquet
 meta/
+**/unnamed-chunk*
+decreasing_forecasters_cache/

R/forecasters/forecaster_scaled_pop_seasonal.R

@@ -52,6 +52,7 @@ scaled_pop_seasonal <- function(epi_data,
                                 quantile_levels = covidhub_probs(),
                                 filter_source = "",
                                 filter_agg_level = "",
+                                clip_lower = TRUE,
                                 ...) {
   scale_method <- arg_match(scale_method)
   center_method <- arg_match(center_method)
@@ -92,7 +93,7 @@ scaled_pop_seasonal <- function(epi_data,
   }
   args_input[["ahead"]] <- ahead
   args_input[["quantile_levels"]] <- quantile_levels
-  args_input[["nonneg"]] <- scale_method == "none"
+  args_input[["nonneg"]] <- if (!is.null(args_input[["nonneg"]])) args_input[["nonneg"]] else scale_method == "none"
   args_input[["seasonal_window"]] <- "window" %in% seasonal_method
   args_input[["seasonal_backward_window"]] <- seasonal_backward_window
   args_input[["seasonal_forward_window"]] <- seasonal_forward_window + ahead
@@ -228,8 +229,10 @@ scaled_pop_seasonal <- function(epi_data,
   pred_final <- pred %>%
     rename({{ outcome }} := value) %>%
     data_coloring(outcome, learned_params, join_cols = key_colnames(epi_data, exclude = "time_value"), nonlin_method = nonlin_method) %>%
-    rename(value = {{ outcome }}) %>%
-    mutate(value = pmax(0, value))
+    rename(value = {{ outcome }})
+  if (clip_lower) {
+    pred_final %<>% mutate(value = pmax(0, value))
+  }
   if (adding_source) {
     pred_final %<>% select(-source)
   }

renv.lock

@@ -7413,56 +7413,8 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Type": "Package",
-      "Title": "Project Environments",
-      "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"[email protected]\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )",
-      "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.",
-      "License": "MIT + file LICENSE",
-      "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv",
-      "BugReports": "https://github.com/rstudio/renv/issues",
-      "Imports": [
-        "utils"
-      ],
-      "Suggests": [
-        "BiocManager",
-        "cli",
-        "compiler",
-        "covr",
-        "cpp11",
-        "devtools",
-        "gitcreds",
-        "jsonlite",
-        "jsonvalidate",
-        "knitr",
-        "miniUI",
-        "modules",
-        "packrat",
-        "pak",
-        "R6",
-        "remotes",
-        "reticulate",
-        "rmarkdown",
-        "rstudioapi",
-        "shiny",
-        "testthat",
-        "uuid",
-        "waldo",
-        "yaml",
-        "webfakes"
-      ],
-      "Encoding": "UTF-8",
-      "RoxygenNote": "7.3.2",
-      "VignetteBuilder": "knitr",
-      "Config/Needs/website": "tidyverse/tidytemplate",
-      "Config/testthat/edition": "3",
-      "Config/testthat/parallel": "true",
-      "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes",
-      "NeedsCompilation": "no",
-      "Author": "Kevin Ushey [aut, cre] (<https://orcid.org/0000-0003-2880-7407>), Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>), Posit Software, PBC [cph, fnd]",
-      "Maintainer": "Kevin Ushey <[email protected]>",
-      "Repository": "RSPM"
+      "Version": "1.1.4",
+      "Source": "Repository"
     },
     "reprex": {
       "Package": "reprex",

renv/activate.R

@@ -2,7 +2,7 @@
 local({
 
   # the requested version of renv
-  version <- "1.1.3"
+  version <- "1.1.4"
   attr(version, "sha") <- NULL
 
   # the project directory