regime 2 wip

.Rprofile

@@ -169,6 +169,4 @@ if (Sys.getenv("CI") == "") {
   )
 }
 
-
-
 # nolint end

.github/R-version

@@ -1 +1 @@
-R-4.1
+R-4.3

.github/linters/.lintr

@@ -0,0 +1,43 @@
+linters: linters_with_defaults(
+  absolute_path_linter(lax = TRUE),
+  any_duplicated_linter(),
+  any_is_na_linter(),
+  backport_linter(),
+  class_equals_linter(),
+  commented_code_linter = NULL,
+  condition_message_linter(),
+  consecutive_assertion_linter(),
+  cyclocomp_linter(50),
+  duplicate_argument_linter(),
+  fixed_regex_linter(),
+  ifelse_censor_linter(),
+  inner_combine_linter(),
+  line_length_linter(150),
+  literal_coercion_linter(),
+  missing_argument_linter(),
+  missing_package_linter(),
+  namespace_linter(),
+  nested_ifelse_linter(),
+  nonportable_path_linter(lax = TRUE),
+  numeric_leading_zero_linter(),
+  object_length_linter(30),
+  object_usage_linter = NULL,
+  outer_negation_linter(),
+  package_hooks_linter(),
+  paste_linter(),
+  pipe_call_linter(),
+  redundant_ifelse_linter(),
+  regex_subset_linter(),
+  semicolon_linter(allow_compound = TRUE),
+  sprintf_linter(),
+  string_boundary_linter(),
+  strings_as_factors_linter(),
+  system_file_linter(),
+  undesirable_operator_linter(all_undesirable_operators),
+  unnecessary_concatenation_linter(),
+  unreachable_code_linter(),
+  unused_import_linter(),
+  yoda_test_linter()
+  )
+exclusions: list("dev", "renv", "R/RcppExports.R", "README.Rmd")
+

.gitignore

@@ -1,75 +1,43 @@
+# Directories
 library/
 local/
 cellar/
 lock/
 python/
 staging/
+
+# Files
 .Rhistory*
 .Renviron
 .Rapp.history
 Pprof.out
-Rprof.out
-
-# Session Data files
 .RData
 .RDataTmp
-
-# User-specific files
 .Ruserdata
-
-# Example code in package build process
 *-Ex.R
-
-# Output files from R CMD build
 /*.tar.gz
-
-# Output files from R CMD check
 /*.Rcheck/
-
-# RStudio files
 .Rproj.user/
-
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+*.html
+*.pdf
 .httr-oauth
 .gitconfig
-
-# knitr and R markdown default cache directories
 *_cache/
 /cache/
-
-# Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-
-# VSCode
-#.vscode/
 .vscode/*.log
 .devcontainer/exts
 .devcontainer/gpg-agent.conf
 .devcontainer/gpg.conf
-
-### R.Bookdown Stack ###
-# R package: bookdown caching files
 /*_files/
-
-# End of https://www.gitignore.io/api/r
-
-# Personalized
 tmp
 /tmp/
 /tmp_*/
 .future
 debugme.log
-
-#Local history plugin
 .history
 .radian_history
-
-# use github-actions to build the webpage
 /.travis.yml
 /R/RcppExports.R
 /code/
@@ -90,15 +58,11 @@ debugme.log
 LOCAL_APPDATA_FONTCONFIG_CACHE/
 README.html
 Rplots.pdf
-dev
 dev/
-dev
 packrat/lib*/
 packrat/src/
 src-*/
 workspace.RData
-
-# Workflowr
 .DS_Store
 analysis/figure
 analysis/*png
@@ -109,7 +73,6 @@ analysis/site_libs
 output/*.svg
 output/*.rds
 protocol/**/*.html
-# docs/**/*.svg
 protocol/**/*.svg
 protocol/**/*.rmarkdown
 mpxtest.RData
@@ -118,8 +81,6 @@ mpxtest.RData
 docs/thesis/*.log
 docs/thesis/__*.tex
 **/rsconnect/**
-
-# Temp
-# docs
-
 /.luarc.json
+.Rhistory
+

.lintr

@@ -6,7 +6,7 @@ linters: linters_with_defaults(
   class_equals_linter(),
   commented_code_linter = NULL,
   condition_message_linter(),
-  consecutive_stopifnot_linter(),
+  consecutive_assertion_linter(),
   cyclocomp_linter(50),
   duplicate_argument_linter(),
   fixed_regex_linter(),
@@ -34,7 +34,7 @@ linters: linters_with_defaults(
   strings_as_factors_linter(),
   system_file_linter(),
   undesirable_operator_linter(all_undesirable_operators),
-  unneeded_concatenation_linter(),
+  unnecessary_concatenation_linter(),
   unreachable_code_linter(),
   unused_import_linter(),
   yoda_test_linter()

.renvignore

@@ -1,12 +1,20 @@
+/analysis/*/*
+!/analysis/*/*.R
 /inst/
 /dev/
 /_*/
 /docs/
 /tmp/
 /output/
+/presentations/*/*
+!/presentations/*/*.Rmd
+!/presentations/*/*.qmd
+/thesis/*/*
+!/thesis/*/*.Rmd
 /.trunk/
 /.devcontainer/
 /.github/
+/renv/
 figures
 logos
 *_files

.vscode/settings.json

@@ -5,6 +5,8 @@
   "C_Cpp.default.defines": [
     "RC_INVOKED"
   ],
+  "markdown.validate.enabled": true,
+  "isGitignoreExtActive": true,
   "C_Cpp.intelliSenseEngineFallback": "Enabled",
   "editor.formatOnSave": true,
   "editor.tabCompletion": "on",

analysis/blog-202204.Rmd

@@ -186,7 +186,8 @@ if (file.exists(here::here("dev/backtofilters.rds"))) {
 } else {
   filenames <- find_all_files(classes = "asystole", limit_per_class = max(neg, pos))
 
-  # filenames <- find_all_files(here("inst/extdata/afib_regimes"), data_type = "regimes", classes = "paroxysmal_afib", limit_per_class = max(neg, pos))
+  # filenames <- find_all_files(here("inst", "extdata", "afib_regimes"), data_type = "regimes",
+  # classes = "paroxysmal_afib", limit_per_class = max(neg, pos))
 
   pos_files <- list()
   i <- 1
@@ -1283,7 +1284,6 @@ invisible(gc())
 
 
 ```{r posfiles2, warning=FALSE}
-
 values_pos_raw <- values_pos_raw_gain <- values_pos_norm_gain <- values_pos_norm <- list()
 
 for (a in algorithms) {