diff --git a/.Rbuildignore b/.Rbuildignore index 0a2fccb3..ff287c21 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^examples ^codecov\.yml$ ^\.github$ +^docs diff --git a/NAMESPACE b/NAMESPACE index b7ae6fbd..af52844e 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/helpers.R b/R/helpers.R index 5d1db186..4f91eabf 100644 --- a/R/helpers.R +++ b/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 diff --git a/R/inline_fun.R b/R/inline_fun.R index 82d23ac2..bd9f1218 100644 --- a/R/inline_fun.R +++ b/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. diff --git a/R/nutrition.R b/R/nutrition.R index 6df3409f..e9c50017 100644 --- a/R/nutrition.R +++ b/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(), diff --git a/R/sample-size.R b/R/sample-size.R index 2b8a2698..7fe2360f 100644 --- a/R/sample-size.R +++ b/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 #' #' -#' @export +#' @keywords internal +#' @noRd sample_size_households <- function(sample_size, avg_hh, prop_under_5, frac_6_59, non_response_rate = 0) { diff --git a/README.Rmd b/README.Rmd index 071fd91a..b97b3dab 100644 --- a/README.Rmd +++ b/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 .** +**Detailed information about the project and the templates can be found at .** An online manual for the functions in {sitrep} can be found at . ## 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. + + diff --git a/README.md b/README.md index 70db729e..d0258608 100644 --- a/README.md +++ b/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 .** +at .** An online manual for the functions in +{sitrep} can be found at . ## 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. diff --git a/docs/404.html b/docs/404.html index 1005ca9a..eb697937 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,6 +81,9 @@
  • Reference +
    • +
  • + Changelog
      • diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html new file mode 100644 index 00000000..7c592b13 --- /dev/null +++ b/docs/CODE_OF_CONDUCT.html @@ -0,0 +1,141 @@ + + + + + + + + +Contributor Code of Conduct • sitrep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + + + + +
      + +
      +
      +
      +

      Contributor Code of Conduct

      +
      + +
      + +

      As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.

      +

      We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

      +

      Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.

      +

      Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.

      +

      Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.

      +

      This Code of Conduct is adapted from the Contributor Covenant (https://www.contributor-covenant.org), version 1.0.0, available at https://contributor-covenant.org/version/1/0/0/.

      +
      + +
      + +
      + + + +
      +
      +

      Developed by Dirk Schumacher, Zhian N. Kamvar, Alex Spina, Kate Doyle, Chris Jarvis, Lukas Richter.

      +
      + +
      +

      Site built with pkgdown 1.4.1.

      +
      + +
      +
      + + + + + + + + diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html new file mode 100644 index 00000000..68934cd8 --- /dev/null +++ b/docs/CONTRIBUTING.html @@ -0,0 +1,178 @@ + + + + + + + + +Contributing to sitrep • sitrep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + + + + +
      + +
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      +

      Contributing to sitrep

      +
      + +
      + +

      This outlines how to propose a change to sitrep. For more detailed info about contributing to this, and other tidyverse packages, please see the development contributing guide.

      +
      +

      +Fixing typos

      +

      Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the source file.

      +
        +
      • YES: you edit a roxygen comment in a .R file below R/.
        • +
      • NO: you edit an .Rd file below man/.
        • +
      +
      +
      +

      +Prerequisites

      +

      Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. If you’ve found a bug, create an associated issue and illustrate the bug with a minimal reprex.

      +
      +
      +

      +Pull request process

      +
        +
      • We recommend that you create a Git branch for each pull request (PR).
        +
        • +
      • Look at the Travis and AppVeyor build status before and after making changes. The README should contain badges for any continuous integration services used by the package.
        +
        • +
      • New code should follow the tidyverse style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.
        +
        • +
      • We use roxygen2, with Markdown syntax, for documentation.
        +
        • +
      • We use testthat. Contributions with test cases included are easier to accept.
        +
        • +
      • For user-facing changes, add a bullet to the top of NEWS.md below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
        • +
      +
      +
      +

      +Code of Conduct

      +

      Please note that the sitrep project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.

      +
      +
      +

      +See tidyverse development contributing guide +

      +

      for further details.

      +
      +
      + +
      + +
      + + + +
      +
      +

      Developed by Dirk Schumacher, Zhian N. Kamvar, Alex Spina, Kate Doyle, Chris Jarvis, Lukas Richter.

      +
      + +
      +

      Site built with pkgdown 1.4.1.

      +
      + +
      +
      + + + + + + + + diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html new file mode 100644 index 00000000..70cf0d91 --- /dev/null +++ b/docs/ISSUE_TEMPLATE.html @@ -0,0 +1,139 @@ + + + + + + + + +NA • sitrep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + + + + +
      + +
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      NA

      +
      + + +

      Please briefly describe your problem and what output you expect. If you have a question, please don’t use this form. Instead, ask on https://stackoverflow.com/ or https://community.rstudio.com/.

      +

      Please include a minimal reproducible example (AKA a reprex). If you’ve never heard of a reprex before, start by reading https://www.tidyverse.org/help/#reprex.

      +
      +

      Brief description of the problem

      + + + +
      + +
      + + + +
      +
      +

      Developed by Dirk Schumacher, Zhian N. Kamvar, Alex Spina, Kate Doyle, Chris Jarvis, Lukas Richter.

      +
      + +
      +

      Site built with pkgdown 1.4.1.

      +
      + +
      +
      + + + + + + + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index a1fd52a6..ef12df4b 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -81,6 +81,9 @@
    • Reference +
      • +
    • + Changelog
      diff --git a/docs/SUPPORT.html b/docs/SUPPORT.html new file mode 100644 index 00000000..ccc85e85 --- /dev/null +++ b/docs/SUPPORT.html @@ -0,0 +1,148 @@ + + + + + + + + +Getting help with sitrep • sitrep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      +
      + + + + +
      + +
      +
      +
      +

      Getting help with sitrep

      +
      + +
      + +

      Thanks for using sitrep. Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.

      +

      Start by making a minimal reproducible example using the reprex package. If you haven’t heard of or used reprex before, you’re in for a treat! Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it’ll take you to learn what it’s all about). For additional reprex pointers, check out the Get help! section of the tidyverse site.

      +

      Armed with your reprex, the next step is to figure out where to ask.

      +
        +
      • If it’s a question: start with community.rstudio.com, and/or StackOverflow. There are more people there to answer questions.
        +
        • +
      • If it’s a bug: you’re in the right place, file an issue.
        +
        • +
      • If you’re not sure: let the community help you figure it out! If your problem is a bug or a feature request, you can easily return here and report it.
        • +
      +

      Before opening a new issue, be sure to search issues and pull requests to make sure the bug hasn’t been reported and/or already fixed in the development version. By default, the search will be pre-populated with is:issue is:open. You can edit the qualifiers (e.g. is:pr, is:closed) as needed. For example, you’d simply remove is:open to search all issues in the repo, open or closed.

      +

      If you are in the right place, and need to file an issue, please review the “File issues” paragraph from the tidyverse contributing guidelines.

      +

      Thanks for your help!

      +
      + +
      + +
      + + + +
      +
      +

      Developed by Dirk Schumacher, Zhian N. Kamvar, Alex Spina, Kate Doyle, Chris Jarvis, Lukas Richter.

      +
      + +
      +

      Site built with pkgdown 1.4.1.

      +
      + +
      +
      + + + + + + + + diff --git a/docs/authors.html b/docs/authors.html index 360e1b46..cbc5faa5 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,6 +81,9 @@
    • Reference +
      • +
    • + Changelog
      diff --git a/docs/index.html b/docs/index.html index df9426f0..b45f04d7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,6 +45,9 @@
    • Reference +
      • +
    • + Changelog
      @@ -65,7 +68,7 @@

      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

      @@ -75,6 +78,69 @@

      +
      +

      +Available templates

      +

      Sitrep has four outbreak templates and three survey templates available. These templates will generate the following:

      +
        +
      1. A word document with the situation report
        2. +
      2. A plain text markdown document (for conversion to other formats such as HTML or PDF)
        3. +
      3. A directory with all of the figures produced
        4. +
      +

      You can generate an example template by using the check_sitrep_templates() function:

      +
      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. By contributing to this project, you agree to abide by its terms.

      +
      @@ -86,6 +152,13 @@

      License

    • GPL-3
      • +
      +

      Community

      + +

      Developers

        diff --git a/docs/news/index.html b/docs/news/index.html new file mode 100644 index 00000000..e129ef89 --- /dev/null +++ b/docs/news/index.html @@ -0,0 +1,148 @@ + + + + + + + + +Changelog • sitrep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        +
        + + + + +
        + +
        +
        +
        +

        Changelog

        + +
        + +
        +

        +sitrep 0.1.0

        +
          +
        • Added a NEWS.md file to track changes to the package.
          • +
        • First official release of the {sitrep} package.
          • +
        +
        +
        + + + +
        + + +
        +
        +

        Developed by Dirk Schumacher, Zhian N. Kamvar, Alex Spina, Kate Doyle, Chris Jarvis, Lukas Richter.

        +
        + +
        +

        Site built with pkgdown 1.4.1.

        +
        + +
        +
        + + + + + + + + diff --git a/docs/reference/add_weights_cluster.html b/docs/reference/add_weights_cluster.html index 2ebc7e79..3496c47d 100644 --- a/docs/reference/add_weights_cluster.html +++ b/docs/reference/add_weights_cluster.html @@ -84,6 +84,9 @@
      • Reference +
        • +
      • + Changelog
        diff --git a/docs/reference/add_weights_strata.html b/docs/reference/add_weights_strata.html index c9498eac..4b1b4e13 100644 --- a/docs/reference/add_weights_strata.html +++ b/docs/reference/add_weights_strata.html @@ -88,6 +88,9 @@
      • Reference +
        • +
      • + Changelog
        diff --git a/docs/reference/age_categories.html b/docs/reference/age_categories.html index f0d0c5be..95728c08 100644 --- a/docs/reference/age_categories.html +++ b/docs/reference/age_categories.html @@ -83,6 +83,9 @@
      • Reference +
        • +
      • + Changelog
        diff --git a/docs/reference/attack_rate.html b/docs/reference/attack_rate.html index 5b2a1515..37155e42 100644 --- a/docs/reference/attack_rate.html +++ b/docs/reference/attack_rate.html @@ -83,6 +83,9 @@
      • Reference +
        • +
      • + Changelog
        diff --git a/docs/reference/available_sitrep_templates.html b/docs/reference/available_sitrep_templates.html index ddb15aed..dbae22d0 100644 --- a/docs/reference/available_sitrep_templates.html +++ b/docs/reference/available_sitrep_templates.html @@ -83,6 +83,9 @@
      • Reference +
        • +
      • + Changelog
        @@ -137,15 +140,15 @@

        Examp #> $survey #> [1] "mortality" "nutrition" "vaccination" #>

      available_sitrep_templates(categorise = TRUE, full.names = TRUE)
      #> $outbreak -#> [1] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/ajs_outbreak" -#> [2] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/cholera_outbreak" -#> [3] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/measles_outbreak" -#> [4] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/meningitis_outbreak" +#> [1] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/ajs_outbreak" +#> [2] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/cholera_outbreak" +#> [3] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/measles_outbreak" +#> [4] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/meningitis_outbreak" #> #> $survey -#> [1] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/mortality" -#> [2] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/nutrition" -#> [3] "/tmp/RtmpwyNsp9/temp_libpath603f413d161e/sitrep/rmarkdown/templates/vaccination" +#> [1] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/mortality" +#> [2] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/nutrition" +#> [3] "/tmp/RtmpVoMCI9/temp_libpath488280d8fe9/sitrep/rmarkdown/templates/vaccination" #>