Merge pull request #36 from R4EPI/cran-release-02-2023

cran release 02 2023

.Rbuildignore

@@ -12,3 +12,4 @@
 ^docs$
 ^pkgdown$
 ^CRAN-RELEASE$
+^CRAN-SUBMISSION$

.github/workflows/R-CMD-check.yaml

@@ -41,7 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: local::., any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.1.6
+Date: 2024-01-22 23:59:23 UTC
+SHA: 07478e47d4472f6943691aaa254a28c1365b6e4a

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: epikit
-Title: Miscellaneous helper tools for epidemiologists
-Version: 0.1.4
+Title: Miscellaneous Helper Tools for Epidemiologists
+Version: 0.1.6
 Authors@R: 
     c(person(given = "Alexander",
              family = "Spina",
              email = "[email protected]", 
              comment = c(ORCID = "0000-0001-8425-1867"),
-             role = c("aut", "cre")),
+             role = c("aut")),
       person(given = "Zhian N.",
              family = "Kamvar",
-             role = "aut",
+             role = c("aut", "cre"),
              email = "[email protected]",
              comment = c(ORCID = "0000-0003-1458-7108")),
       person(given = "Dirk",
@@ -23,7 +23,7 @@ Description: Contains tools for formatting inline code, renaming redundant
   columns, aggregating age categories, adding survey weights, finding the earliest
   date of an event, plotting z-curves, generating population counts and 
   calculating proportions with confidence intervals. This is part of the 
-  'R4Epis' project <https://r4epis.netlify.com>.
+  'R4Epis' project <https://r4epis.netlify.app/>.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -52,7 +52,7 @@ Suggests:
     rmarkdown
 Additional_repositories: https://r4epi.github.io/drat
 URL: https://github.com/R4EPI/epikit,
-    https://r4epis.netlify.com,
+    https://r4epis.netlify.app,
     https://r4epi.github.io/epikit/
 BugReports: https://github.com/R4EPI/epikit/issues
 VignetteBuilder: knitr

NAMESPACE

@@ -42,5 +42,6 @@ importFrom(sf,st_make_grid)
 importFrom(sf,st_polygon)
 importFrom(sf,st_set_crs)
 importFrom(sf,st_sf)
+importFrom(stats,setNames)
 importFrom(tibble,as_tibble)
 importFrom(utils,read.csv)

NEWS.md

@@ -1,7 +1,21 @@
+# epikit 0.1.6 
+
+* internal documentation fix. No user-visible changes.
+
+# epikit 0.1.5 
+
+* removed tidyr::unite() in favour of paste-ing two columns together
+* added `separator` argument to `_ci()` functions which now defaults to `-`
+  (@aspina7, #31)
+
 # epikit 0.1.4 
+
 * unecessary bump because {pkgdown}
 
 # epikit 0.1.3
+
+(non-cran release)
+
 * migrated functions and tests from {sitrep} including: `add_weights_cluster()`, 
   `add_weights_strata()`, `find_date_cause()`, `find_end_date()`, 
   `find_start_date()`, `gen_polygon()`, `gen_population()` and `zcurve()` (@aspina7, #22)

R/epikit-package.R

@@ -5,6 +5,7 @@
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start
 #' @importFrom rlang .data :=
+#' @importFrom stats setNames
 #' @importFrom ggplot2 ggplot
 #' @importFrom ggplot2 aes 
 #' @importFrom ggplot2 stat_density

R/relabel_proportions.R

@@ -58,9 +58,8 @@ augment_redundant <- function(x, ...) {
 #' calls for the express purpose of renaming functions. This function is
 #' intended for internal use to be passed to other MSF packages.
 #'
-#' @param call a language object reflecting the current call.
-#' @param ... passed from the calling function
-#'
+#' @param parent the level of the parent function. Defaults to 1, which
+#'   selects the dots from the immediate parent.
 #'
 #' @return a list of character vectors
 #' @export

README.Rmd

@@ -16,9 +16,9 @@ knitr::opts_chunk$set(
 
 
 <!-- badges: start -->
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN status](https://www.r-pkg.org/badges/version/epikit)](https://CRAN.R-project.org/package=epikit)
-[![Codecov test coverage](https://codecov.io/gh/R4EPI/epikit/branch/master/graph/badge.svg)](https://codecov.io/gh/R4EPI/epikit?branch=master)
+[![Codecov test coverage](https://app.codecov.io/gh/R4EPI/epikit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/R4EPI/epikit?branch=master)
 [![R-CMD-check](https://github.com/R4EPI/epikit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/R4EPI/epikit/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 

README.md

@@ -5,17 +5,17 @@ epikit
 <!-- badges: start -->
 
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/epikit)](https://CRAN.R-project.org/package=epikit)
 [![Codecov test
-coverage](https://codecov.io/gh/R4EPI/epikit/branch/master/graph/badge.svg)](https://codecov.io/gh/R4EPI/epikit?branch=master)
+coverage](https://app.codecov.io/gh/R4EPI/epikit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/R4EPI/epikit?branch=master)
 [![R-CMD-check](https://github.com/R4EPI/epikit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/R4EPI/epikit/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of {epikit} is to provide miscellaneous functions for applied
 epidemiologists. This is a product of the R4EPIs project; learn more at
-<https://r4epis.netlify.com>.
+<https://r4epis.netlify.app/>.
 
 ## Installation
 
@@ -105,28 +105,78 @@ df %>%
 #> 20     30-39       <NA>  30-39 years
 ```
 
+## Quick proportions with conficence intervals
+
+There are three functions that will provide quick statistics for
+different rates based on binomial estimates of proportions from
+`binom::binom.wilson()`
+
+-   `attack_rate()`
+-   `case_fatality_rate()`
+-   `mortality_rate()`
+
+``` r
+attack_rate(10, 50)
+#>   cases population ar    lower    upper
+#> 1    10         50 20 11.24375 33.03711
+case_fatality_rate(2, 50)
+#>   deaths population cfr    lower    upper
+#> 1      2         50   4 1.103888 13.46009
+mortality_rate(40, 50000)
+#>   deaths population mortality per 10 000   lower    upper
+#> 1     40      50000                    8 5.87591 10.89109
+```
+
+In addition, it’s possible to rapidly calculate Case fatality rate from
+a linelist, stratified by different groups (e.g. gender):
+
+``` r
+library("outbreaks")
+case_fatality_rate_df(ebola_sim_clean$linelist, 
+  outcome == "Death", 
+  group = gender,
+  add_total = TRUE,
+  mergeCI = TRUE
+)
+#> Warning: There was 1 warning in `dplyr::mutate()`.
+#> ℹ In argument: `gender = forcats::fct_explicit_na(gender, "(Missing)")`.
+#> Caused by warning:
+#> ! `fct_explicit_na()` was deprecated in forcats 1.0.0.
+#> ℹ Please use `fct_na_value_to_level()` instead.
+#> ℹ The deprecated feature was likely used in the epikit package.
+#>   Please report the issue at <https://github.com/R4EPI/epikit/issues>.
+#> # A tibble: 3 × 5
+#>   gender deaths population   cfr ci           
+#>   <fct>   <int>      <int> <dbl> <chr>        
+#> 1 f        1291       2280  56.6 (54.58-58.64)
+#> 2 m        1273       2247  56.7 (54.59-58.69)
+#> 3 Total    2564       4527  56.6 (55.19-58.08)
+```
+
 ## Inline functions
 
 The inline functions make it easier to print estimates with confidence
 intervals in reports with the correct number of digits.
 
-- `fmt_ci()` formats confidence intervals from three numbers.
-  (e.g. `fmt_ci(50, 10, 80)` produces 50.00% (CI 10.00-80.00)
-- `fmt_pci()` formats confidence intervals from three fractions,
-  multiplying by 100 beforehand.
-
-<!-- 
-The `_df` suffixes (`fmt_ci_df()`, `fmt_pci_df()`) will print the confidence 
-intervals for data stored in data frames. These are designed to work with the
-outputs of the rates functions. For example, `fmt_ci_df(attack_rate(10, 50))`
-will produce . All of these suffixes will have
-three options `e`, `l`, and `u`. These refer to `estimate`, `lower`, and `upper`
-column positions or names.
-
- - `fmt_count()` will count a condition in a data frame and present the number
-   and percent of `TRUE` values. For example, if you wanted to count the number
-    of women patients from Rokupa hospital, you would write: `fmt_count(ebola_sim_clean$linelist, gender == "f", hospital == "Rokupa Hospital")` and it would produce:  
- -->
+
+-   `fmt_ci()` formats confidence intervals from three numbers.
+    (e.g. `fmt_ci(50, 10, 80)` produces 50.00% (CI 10.00-80.00)
+-   `fmt_pci()` formats confidence intervals from three fractions,
+    multiplying by 100 beforehand.
+
+The `_df` suffixes (`fmt_ci_df()`, `fmt_pci_df()`) will print the
+confidence intervals for data stored in data frames. These are designed
+to work with the outputs of the rates functions. For example,
+`fmt_ci_df(attack_rate(10, 50))` will produce 20.00% (CI 11.24-33.04).
+All of these suffixes will have three options `e`, `l`, and `u`. These
+refer to `estimate`, `lower`, and `upper` column positions or names.
+
+-   `fmt_count()` will count a condition in a data frame and present the
+    number and percent of `TRUE` values. For example, if you wanted to
+    count the number of women patients from Rokupa hospital, you would
+    write:
+    `fmt_count(ebola_sim_clean$linelist, gender == "f", hospital == "Rokupa Hospital")`
+    and it would produce: 210 (3.6%)
 
 ## Confidence interval manipulation
 

man/rmdhunks/introduction.Rmd

@@ -1,5 +1,5 @@
 The goal of {epikit} is to provide miscellaneous functions for applied epidemiologists. 
-This is a product of the R4EPIs project; learn more at <https://r4epis.netlify.com>.
+This is a product of the R4EPIs project; learn more at <https://r4epis.netlify.app/>.
 
 ## Installation