Merge pull request #214 from R4EPI/znk-hide-unused-functions

ZNK final cleanup

.Rbuildignore

@@ -7,3 +7,4 @@
 ^examples
 ^codecov\.yml$
 ^\.github$
+^docs

NAMESPACE

@@ -18,11 +18,9 @@ export(find_end_date)
 export(find_start_date)
 export(fmt_ci)
 export(fmt_ci_df)
-export(fmt_ci_df_sep)
 export(fmt_count)
 export(fmt_pci)
 export(fmt_pci_df)
-export(fmt_pci_df_sep)
 export(gen_data)
 export(gen_polygon)
 export(gen_population)
@@ -35,9 +33,6 @@ export(msf_dict_rename_helper)
 export(msf_dict_survey)
 export(plot_age_pyramid)
 export(rename_redundant)
-export(sample_size)
-export(sample_size_households)
-export(stratify_zscores)
 export(tab_linelist)
 export(tab_survey)
 export(tab_univariate)

R/helpers.R

@@ -1,20 +1,3 @@
-# Helper function to splice a data.frame with multiple columns
-# into a dplyr function
-# example
-# dplyr::summarise(mtcars,
-# n = n(),
-# x = sum(hp > 100),
-# !!!splice_df(binom::binom.wilson(x, n), mean, lower, upper)
-# )
-splice_df <- function(x, ...) {
-  expr <- rlang::enquo(x)
-  cols <- lapply(rlang::ensyms(..., .named = TRUE), as.character)
-  lapply(cols, function(col_name) {
-    rlang::quo(`[[`(!!expr, !!col_name))
-  })
-}
-
-
 # This will convert numbers to factors.
 #
 # If the number of unique numbers is five or fewer, then they will simply

R/inline_fun.R

@@ -71,26 +71,6 @@ merge_pci_df <- function(x, e = 3, l = e + 1, u = e + 2, digits = 2) {
   x
 }
 
-#' @export
-#' @rdname fmt_ci
-fmt_ci_df_sep <- function(x, e = 3, l = e + 1, u = e + 2, digits = 2, percent = TRUE) {
-  x   <- merge_ci_df(x, e, l, u, digits)
-  fun <- if (percent) match.fun(scales::percent) else match.fun(scales::number)
-  ee  <- fun(x[[e]], scale = 1, accuracy = 1/(10^digits), big.mark = ",")
-  x[e] <- ee
-  x
-}
-
-#' @export
-#' @rdname fmt_ci
-fmt_pci_df_sep <- function(x, e = 3, l = e + 1, u = e + 2, digits = 2, percent = TRUE) {
-  x <- merge_pci_df(x, e, l, u, digits)
-  fun <- if (percent) match.fun(scales::percent) else match.fun(scales::number)
-  ee  <- fun(x[[e]] * 100, scale = 1, accuracy = 1/(10^digits), big.mark = ",")
-  x[e] <- ee
-  x
-}
-
 #' Counts and proportions inline
 #'
 #' These functions will give proportions for different variables inline.

R/nutrition.R

@@ -5,7 +5,8 @@
 #' @param ... columns having zscore indicators
 #'
 #' @include helpers.R
-#' @export
+#' @keywords internal
+#' @noRd
 #' @examples
 #' # A crude example, but it works
 #' stratify_zscores(mtcars, by = "gear", am, vs)
@@ -19,7 +20,7 @@ stratify_zscores <- function(survey_data, by, ...) {
               flagged = sum(.data$flagged, na.rm = TRUE),
               rel = .data$flagged / .data$n,
               ci = list(binom::binom.wilson(.data$flagged, .data$n)[, c("lower", "upper")]))
-    tidyr::unnest(res)
+    tidyr::unnest(res, cols = c("ci"))
   }
   dplyr::bind_rows(
     comput_result(),

R/sample-size.R

@@ -11,7 +11,8 @@
 #' This method is based on the work of Kevin M. Sullivan and Andrew G. Dean
 #' of OpenEpi.
 #'
-#' @export
+#' @keywords internal
+#' @noRd
 sample_size <- function(population_size, expected_prevalence,
                         precision, design_effect, alpha = 0.05) {
   num <- (design_effect * population_size * expected_prevalence *
@@ -33,7 +34,8 @@ sample_size <- function(population_size, expected_prevalence,
 #' Sampling Methods and Sample Size Calculation for the SMART Methodology
 #' <https://www.humanitarianresponse.info/sites/www.humanitarianresponse.info/files/documents/files/Sampling_Paper_June_2012.pdf>
 #'
-#' @export
+#' @keywords internal
+#' @noRd
 sample_size_households <- function(sample_size, avg_hh,
                                    prop_under_5,
                                    frac_6_59, non_response_rate = 0) {

README.Rmd

@@ -27,7 +27,7 @@ The goal of {sitrep} is provide report templates for common epidemiological
 surveys and outbreak reports. The package further contains helper function that
 standardize certain analyses. 
 
-**Detailed information about the project and the templates can be found at <https://r4epis.netlify.com>.**
+**Detailed information about the project and the templates can be found at <https://r4epis.netlify.com>.** An online manual for the functions in {sitrep} can be found at <https://r4epi.github.io/sitrep>. 
 
 
 ## Installation
@@ -45,8 +45,38 @@ And the development version from [GitHub](https://github.com/) with:
 remotes::install_github("R4EPI/sitrep")
 ```
 
+## Available templates
+
+Sitrep has [four outbreak templates](https://r4epis.netlify.com/outbreaks/) and
+[three survey templates](https://r4epis.netlify.com/surveys/) available. These
+templates will generate the following:
+
+1. A word document with the situation report
+2. A plain text markdown document (for conversion to other formats such as HTML or PDF)
+3. A directory with all of the figures produced
+
+You can generate an example template by using the `check_sitrep_templates()`
+function:
+
+```{r check_templates, warning = FALSE, message = FALSE}
+library("sitrep")
+output_dir <- file.path(tempdir(), "sitrep_example")
+dir.create(output_dir)
+
+# view the available templates, categorized by type
+available_sitrep_templates(categorise = TRUE)
+
+# generate the measles outbreak template in the output directory
+check_sitrep_templates("measles_outbreak", path = output_dir)
+
+# view the contents
+list.files(output_dir, recursive = TRUE)
+```
+
 
 Please note that the 'sitrep' project is released with a
 [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md).
 By contributing to this project, you agree to abide by its terms.
 
+
+

README.md

@@ -22,7 +22,8 @@ epidemiological surveys and outbreak reports. The package further
 contains helper function that standardize certain analyses.
 
 **Detailed information about the project and the templates can be found
-at <https://r4epis.netlify.com>.**
+at <https://r4epis.netlify.com>.** An online manual for the functions in
+{sitrep} can be found at <https://r4epi.github.io/sitrep>.
 
 ## Installation
 
@@ -39,3 +40,76 @@ And the development version from [GitHub](https://github.com/) with:
 # install.packages("remotes")
 remotes::install_github("R4EPI/sitrep")
 ```
+
+## Available templates
+
+Sitrep has [four outbreak
+templates](https://r4epis.netlify.com/outbreaks/) and [three survey
+templates](https://r4epis.netlify.com/surveys/) available. These
+templates will generate the following:
+
+1.  A word document with the situation report
+2.  A plain text markdown document (for conversion to other formats such
+    as HTML or PDF)
+3.  A directory with all of the figures produced
+
+You can generate an example template by using the
+`check_sitrep_templates()` function:
+
+``` r
+library("sitrep")
+output_dir <- file.path(tempdir(), "sitrep_example")
+dir.create(output_dir)
+
+# view the available templates, categorized by type
+available_sitrep_templates(categorise = TRUE)
+#> $outbreak
+#> [1] "ajs_outbreak"        "cholera_outbreak"    "measles_outbreak"   
+#> [4] "meningitis_outbreak"
+#> 
+#> $survey
+#> [1] "mortality"   "nutrition"   "vaccination"
+
+# generate the measles outbreak template in the output directory
+check_sitrep_templates("measles_outbreak", path = output_dir)
+#> [1] "/tmp/RtmpkK0upp/sitrep_example"
+
+# view the contents
+list.files(output_dir, recursive = TRUE)
+#>  [1] "measles_outbreak_files/figure-docx/age_pyramid-1.png"              
+#>  [2] "measles_outbreak_files/figure-docx/bar_attack_rate_by_region-1.png"
+#>  [3] "measles_outbreak_files/figure-docx/biweekly_epicurve-1.png"        
+#>  [4] "measles_outbreak_files/figure-docx/choropleth_maps-1.png"          
+#>  [5] "measles_outbreak_files/figure-docx/epicurve_ar_cfr-1.png"          
+#>  [6] "measles_outbreak_files/figure-docx/epicurve-1.png"                 
+#>  [7] "measles_outbreak_files/figure-docx/incidence_by_case_def-1.png"    
+#>  [8] "measles_outbreak_files/figure-docx/incidence_by_gender-1.png"      
+#>  [9] "measles_outbreak_files/figure-docx/incidence_by_sex_facility-1.png"
+#> [10] "measles_outbreak_files/figure-docx/incidence_by_vax_status-1.png"  
+#> [11] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-1.png"     
+#> [12] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-10.png"    
+#> [13] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-11.png"    
+#> [14] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-12.png"    
+#> [15] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-13.png"    
+#> [16] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-14.png"    
+#> [17] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-15.png"    
+#> [18] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-16.png"    
+#> [19] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-17.png"    
+#> [20] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-18.png"    
+#> [21] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-19.png"    
+#> [22] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-2.png"     
+#> [23] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-20.png"    
+#> [24] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-3.png"     
+#> [25] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-4.png"     
+#> [26] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-5.png"     
+#> [27] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-6.png"     
+#> [28] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-7.png"     
+#> [29] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-8.png"     
+#> [30] "measles_outbreak_files/figure-docx/map_for_loop_epiweek-9.png"     
+#> [31] "measles_outbreak.md"                                               
+#> [32] "measles_outbreak.Rmd"
+```
+
+Please note that the ‘sitrep’ project is released with a [Contributor
+Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this
+project, you agree to abide by its terms.