Updates for v0.2.0 release

.github/workflows/pkgdown.yaml

@@ -71,11 +71,6 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Check website links
-        uses: untitaker/[email protected]
-        with:
-          args: docs/
-
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
         uses: JamesIves/[email protected]

.lintr

@@ -2,7 +2,6 @@ linters: all_linters(
     packages = c("lintr", "etdev"),
     object_name_linter = NULL,
     implicit_integer_linter = NULL,
-    extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
     library_call_linter = NULL,
     undesirable_function_linter(
@@ -14,6 +13,7 @@ linters: all_linters(
     ),
     function_argument_linter = NULL,
     indentation_linter = NULL, # unstable as of lintr 3.1.0
+    one_call_pipe_linter = NULL,
     # Use minimum R declared in DESCRIPTION or fall back to current R version.
     # Install etdev package from https://github.com/epiverse-trace/etdev
     backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cfr
 Title: Estimate Disease Severity and Case Ascertainment
-Version: 0.1.3
+Version: 0.2.0
 Authors@R: c(
     person("Pratik R.", "Gupte", , "[email protected]", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0001-5294-7819")),
@@ -43,7 +43,7 @@ Suggests:
     ggplot2,
     incidence2,
     knitr,
-	magrittr,
+    magrittr,
     purrr,
     rmarkdown,
     scales,
@@ -58,4 +58,4 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2024-2025
+YEAR: 2022-2025
 COPYRIGHT HOLDER: cfr authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2024-2025 cfr authors
+Copyright (c) 2022-2025 cfr authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -1,8 +1,14 @@
-# cfr (development version)
+# cfr 0.2.0
 
-# cfr 0.1.3
+## New features
 
-Added vignette `estimate_from_individual_data.Rmd` describing relationship between individual-level data and aggregate estimation.
+* Added vignette `estimate_from_individual_data.Rmd` describing relationship between individual-level data and aggregate estimation (#170, @adamkucharski).
+
+## Minor improvements and fixes
+
+* Patch `unique(<difftime>)` for R-devel (v4.5.0) which now returns a `<difftime>` object instead of a `numeric`, so the `<difftime>` object is wrapped in `as.numeric()` as suggested by CRAN (#178, @adamkucharski).
+
+* Update `<epiparameter>` class name in documentation (#166, @joshwlambert).
 
 # cfr 0.1.2
 

R/estimate_ascertainment.R

@@ -86,7 +86,8 @@ estimate_ascertainment <- function(data,
   # throw a warning for ascertainment ration > 1.0
   if (any(df_ascertainment > 1.0)) {
     warning(
-      "Ascertainment ratios > 1.0 detected, setting these values to 1.0"
+      "Ascertainment ratios > 1.0 detected, setting these values to 1.0",
+      call. = FALSE
     )
   }
   df_ascertainment[df_ascertainment > 1.0] <- 1.0

R/prepare_data.R

@@ -138,10 +138,8 @@ prepare_data.incidence2 <- function(data, cases_variable = "cases",
   stopifnot(
     "`cases_variable` and `deaths_variable` should be in
     `count_variable` column of <incidence2> object `data`" =
-      all(
-        c(cases_variable, deaths_variable) %in%
-          unique(data[[count_var_col]])
-      )
+      c(cases_variable, deaths_variable) %in%
+      unique(data[[count_var_col]])
   )
 
   # complete dates for all groups in the data and fill any NAs per user input
@@ -161,10 +159,10 @@ prepare_data.incidence2 <- function(data, cases_variable = "cases",
   index <- index == cases_variable | index == deaths_variable
   data <- data[index, ]
 
-  formula <- stats::reformulate(count_var_col, "...")
+  count_formula <- stats::reformulate(count_var_col, "...")
   # cast wide and fill any NAs per user input
   data <- data.table::dcast(
-    data, formula,
+    data, count_formula,
     value.var = count_col
   )
 

inst/WORDLIST

@@ -7,73 +7,73 @@ Allarangar
 Anoko
 Aruna
 Breman
+Camacho
 CFRs
 CMD
-COVID
-Camacho
-Codecov
-Covid
-DPG
-EVD
-EpiNow
-Epiverse
-GHA
-HFR
-Heesterbeek
-IFR
-Jonnie
-Klinkenberg
-Lifecycle
-Mundeke
-Nishiura
-ORCID
-PLOS
-PMF
-Piot
-Poisson
-Pratik
-RepoStatus
-SaMD
-Sherratt
-Tidyverse
-Yahaya
-Yokouide
 coarseDataTools
 codecov
+Codecov
 com
+Covid
+COVID
 covidregionaldata
 dbinom
 dfrac
 distcrete
 doi
+DPG
 ebola
 epiday
+EpiNow
 epiparameter
+Epiverse
 epiweek
 etc
+EVD
 frac
 geq
 ggplot
 gh
+GHA
 github
+Heesterbeek
+HFR
+IFR
 infty
 io
+Jonnie
+Klinkenberg
 leq
 lifecycle
+Lifecycle
 linelist
 lockdowns
 md
+Mundeke
+Nishiura
 np
+ORCID
 org
 packagename
 parameterise
 parameterised
+Piot
 pkg
+PLOS
+PMF
+Poisson
+Pratik
+RepoStatus
 rightarrow
+SaMD
+Sherratt
 sim
 st
 svg
 th
+Tidyverse
 u
 www
+Yahaya
 yaml
+Yokouide

pkgdown/favicon/site.webmanifest

@@ -0,0 +1,21 @@
+{
+  "name": "",
+  "short_name": "",
+  "icons": [
+    {
+      "src": "/web-app-manifest-192x192.png",
+      "sizes": "192x192",
+      "type": "image/png",
+      "purpose": "maskable"
+    },
+    {
+      "src": "/web-app-manifest-512x512.png",
+      "sizes": "512x512",
+      "type": "image/png",
+      "purpose": "maskable"
+    }
+  ],
+  "theme_color": "#ffffff",
+  "background_color": "#ffffff",
+  "display": "standalone"
+}

revdep/README.md

@@ -1,25 +1,26 @@
 # Platform
 
-|field    |value                                                                                      |
-|:--------|:------------------------------------------------------------------------------------------|
-|version  |R version 4.3.2 (2023-10-31)                                                               |
-|os       |macOS Monterey 12.6.3                                                                      |
-|system   |x86_64, darwin20                                                                           |
-|ui       |RStudio                                                                                    |
-|language |(EN)                                                                                       |
-|collate  |en_US.UTF-8                                                                                |
-|ctype    |en_US.UTF-8                                                                                |
-|tz       |Europe/London                                                                              |
-|date     |2024-09-11                                                                                 |
-|rstudio  |2023.12.1+402 Ocean Storm (desktop)                                                        |
-|pandoc   |3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) |
+|field    |value                                      |
+|:--------|:------------------------------------------|
+|version  |R version 4.4.2 (2024-10-31)               |
+|os       |macOS Sequoia 15.0                         |
+|system   |aarch64, darwin20                          |
+|ui       |RStudio                                    |
+|language |(EN)                                       |
+|collate  |en_US.UTF-8                                |
+|ctype    |en_US.UTF-8                                |
+|tz       |Europe/London                              |
+|date     |2025-02-20                                 |
+|rstudio  |2024.04.1+748 Chocolate Cosmos (desktop)   |
+|pandoc   |3.6.2 @ /opt/homebrew/bin/ (via rmarkdown) |
 
 # Dependencies
 
 |package   |old   |new   |Δ  |
 |:---------|:-----|:-----|:--|
-|cfr       |0.1.1 |0.1.2 |*  |
-|checkmate |NA    |2.3.2 |*  |
+|cfr       |0.1.2 |0.1.3 |*  |
+|backports |1.5.0 |1.5.0 |   |
+|checkmate |2.3.2 |2.3.2 |   |
 
 # Revdeps
 

vignettes/estimate_from_individual_data.Rmd

@@ -125,7 +125,7 @@ pp <- 0.1 # Assumed CFR
 set.seed(10) # Set seed for reproducibility
 
 # Generate random case onset timings in Jan & Feb 2024
-case_onsets <- as.Date("2024-01-01") + sample(1:60, nn, replace = TRUE)
+case_onsets <- as.Date("2024-01-01") + sample.int(60, nn, replace = TRUE)
 
 # Define current date of data availability (i.e. max follow up)
 max_obs <- as.Date("2024-01-20")
@@ -175,7 +175,7 @@ data <- data.frame(
 )
 
 # Filter out unknown outcomes (after the max_obs date)
-data <- data %>% filter(known_outcome != "")
+data <- data %>% filter(nzchar(known_outcome))
 
 # Arrange data by onset date
 data <- data %>%