Rename package to {cfr}

.github/CONTRIBUTING.md

@@ -1,18 +1,18 @@
-# Contributing to _datadelay_
+# Contributing to _cfr_
 
-This outlines how to propose a change to _datadelay_.
+This outlines how to propose a change to _cfr_.
 
 ## Making changes
 
 If you want to make a change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
 If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
-[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). See [bug report template](https://github.com/epiverse-trace/datadelay/issues/new?assignees=&labels=&template=bug_report.md&title=). If you have a feature request see [feature request](https://github.com/epiverse-trace/datadelay/issues/new?assignees=&labels=&template=feature_request.md&title=).
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). See [bug report template](https://github.com/epiverse-trace/cfr/issues/new?assignees=&labels=&template=bug_report.md&title=). If you have a feature request see [feature request](https://github.com/epiverse-trace/cfr/issues/new?assignees=&labels=&template=feature_request.md&title=).
 
 ### Pull request process
 
-See [pull request template](https://github.com/epiverse-trace/datadelay/blob/main/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
+See [pull request template](https://github.com/epiverse-trace/cfr/blob/main/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md)
 
-*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("epiverse-trace/datadelay", fork = TRUE)`.
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("epiverse-trace/cfr", fork = TRUE)`.
 
 *   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
     If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
@@ -36,6 +36,6 @@ See [pull request template](https://github.com/epiverse-trace/datadelay/blob/mai
 
 ## Code of Conduct
 
-Please note that the _datadelay_ project is released with a
+Please note that the _cfr_ project is released with a
 [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this
 project you agree to abide by its terms.

.gitignore

@@ -8,3 +8,4 @@ inst/doc
 /doc/
 /Meta/
 scratch.R
+pkgdown/

DESCRIPTION

@@ -1,34 +1,54 @@
-Package: datadelay
+Package: cfr
 Title: Estimate Disease Severity and Under-reporting
 Version: 0.1
 Authors@R: c(
+    person(
+        given = "Pratik",
+        family = "Gupte",
+        role = c("aut", "cre", "cph"),
+        email = "[email protected]",
+        comment = c(ORCID = "0000-0001-5294-7819")
+        ),
     person(
         given = "Adam",
         family = "Kucharski",
         email = "[email protected]", 
-        role = c("aut", "cre"),
+        role = c("aut", "cph"),
         comment = c(ORCID = "0000-0001-8814-9421")
         ),
     person(
-          given = "Tim",
-          family = "Russell",
-          email = "[email protected]", 
-          role = c("aut"),
-          comment = c(ORCID = "0000-0001-5610-6080")
+        given = "Tim",
+        family = "Russell",
+        email = "[email protected]", 
+        role = c("aut", "cph"),
+        comment = c(ORCID = "0000-0001-5610-6080")
+        ),
+    person(
+        given = "Joshua W.",
+        family = "Lambert",
+        role = c("rev"),
+        email = "[email protected]",
+        comment = c(ORCID = "https://orcid.org/0000-0001-5218-3046")
+        ),
+    person(
+        given = "Hugo",
+        family = "Gruson",
+        role = c("rev"),
+        email = "[email protected]",
+        comment = c(ORCID = "https://orcid.org/0000-0002-4094-1476")
         ),
     person(
-          given = "Pratik",
-          family = "Gupte",
-          role = c("aut"),
-          email = "[email protected].uk",
-          comment = c(ORCID = "0000-0001-5294-7819")
+        given = "Tim",
+        family = "Taylor",
+        role = c("rev"),
+        email = "[email protected].uk",
+        comment = c(ORCID = "https://orcid.org/0000-0002-8587-7113")
         )
     )
 Description: Estimate the severity of a disease and under-reporting of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.
 License: MIT + file LICENSE
-URL: https://github.com/epiverse-trace/datadelay,
-    https://epiverse-trace.github.io/datadelay/
-BugReports: https://github.com/epiverse-trace/datadelay/issues
+URL: https://github.com/epiverse-trace/cfr, https://epiverse-trace.github.io/cfr/
+BugReports: https://github.com/epiverse-trace/cfr/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3

R/ebola1976.R

@@ -1,6 +1,6 @@
 #' Ebola 1976 outbreak case data
 #'
-#' An example epidemic outbreak dataset for use with the `datadelay` package.
+#' An example epidemic outbreak dataset for use with the `cfr` package.
 #' This dataset comes from the first Ebola outbreak in Zaire in 1976 as analysed
 #' in Camacho et al. (2014).
 #'

R/estimate_reporting.R

@@ -25,7 +25,7 @@
 #' @export
 #'
 #' @examples
-#' library(datadelay)
+#' library(cfr)
 #' library(epiparameter)
 #' library(covidregionaldata)
 #'

R/prepare_data.R

@@ -48,7 +48,7 @@ prepare_data <- function(data, ...) {
 #'
 #' @export
 #' @return A data.frame suitable for disease severity estimation functions
-#' provided in `{datadelay}`, with the columns "date", "cases", and "deaths".
+#' provided in `{cfr}`, with the columns "date", "cases", and "deaths".
 #' Note that groups in `<incidence2>` are not retained, and cases and deaths
 #' are summed by date.
 #' The result has a continuous sequence of dates between the start and end date

README.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# _{{ packagename }}_: Estimating disease severity and under-reporting
+# _{{ packagename }}_: Estimate disease severity and under-reporting <img src="man/figures/logo.svg" align="right" width="130"/>
 
 <!-- badges: start -->
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
@@ -53,11 +53,11 @@ pak::pak("epiverse-trace/epiparameter")
 
 ### Overall severity of the 1976 Ebola outbreak
 
-This example of basic usage shows how to use _{{ packagename }}_ to estimate the overall case fatality ratios from the 1976 Ebola outbreak.
+This example of basic usage shows how to use _{{ packagename }}_ to estimate the overall case fatality ratios from the 1976 Ebola outbreak [@camacho2014].
 
 ```{r example-ebola-calc}
 # Load package
-library(datadelay)
+library(cfr)
 
 # Load the Ebola 1976 data provided with the package
 data("ebola1976")

README.md

@@ -1,39 +1,38 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# *datadelay*: Estimating disease severity and under-reporting
+# *cfr*: Estimate disease severity and under-reporting <img src="man/figures/logo.svg" align="right" width="130"/>
 
 <!-- badges: start -->
 
 [![License:
 MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
-[![R-CMD-check](https://github.com/epiverse-trace/datadelay/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/datadelay/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/epiverse-trace/cfr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/cfr/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/epiverse-trace/datadelay/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/datadelay?branch=main)
+coverage](https://codecov.io/gh/epiverse-trace/cfr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/cfr?branch=main)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Project Status: WIP – Initial development is in progress, but there
 has not yet been a stable, usable release suitable for the
 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![CRAN
-status](https://www.r-pkg.org/badges/version/datadelay)](https://CRAN.R-project.org/package=datadelay)
+status](https://www.r-pkg.org/badges/version/cfr)](https://CRAN.R-project.org/package=cfr)
 <!-- badges: end -->
 
-*datadelay* is an R package to estimate disease severity and
-under-reporting in real-time, accounting for delays in epidemic
-time-series.
+*cfr* is an R package to estimate disease severity and under-reporting
+in real-time, accounting for delays in epidemic time-series.
 
-*datadelay* provides simple, fast methods to calculate the overall or
-static case fatality ratio (CFR) of an outbreak up to a given time
-point, as well as how the CFR changes over the course of the outbreak.
-*datadelay* can help estimate disease under-reporting in real-time,
-accounting for delays reporting the outcomes of cases.
+*cfr* provides simple, fast methods to calculate the overall or static
+case fatality ratio (CFR) of an outbreak up to a given time point, as
+well as how the CFR changes over the course of the outbreak. *cfr* can
+help estimate disease under-reporting in real-time, accounting for
+delays reporting the outcomes of cases.
 
-*datadelay* implements methods outlined in Nishiura et al.
+*cfr* implements methods outlined in Nishiura et al.
 ([2009](#ref-nishiura2009)), and CFR estimates based on more methods are
 likely to be added.
 
-*datadelay* uses the [*epiparameter*
+*cfr* uses the [*epiparameter*
 package](https://epiverse-trace.github.io/epiparameter/) for
 delay-corrected CFR estimates, and both packages are developed at the
 [Centre for the Mathematical Modelling of Infectious
@@ -43,12 +42,12 @@ at the London School of Hygiene and Tropical Medicine as part of the
 
 ## Installation
 
-The current development version of *datadelay* can be installed from
+The current development version of *cfr* can be installed from
 [GitHub](https://github.com/) using the `pak` package.
 
 ``` r
 if(!require("pak")) install.packages("pak")
-pak::pak("epiverse-trace/datadelay")
+pak::pak("epiverse-trace/cfr")
 
 # Also install R package {epiparameter} for epidemiological parameter values
 pak::pak("epiverse-trace/epiparameter")
@@ -58,12 +57,13 @@ pak::pak("epiverse-trace/epiparameter")
 
 ### Overall severity of the 1976 Ebola outbreak
 
-This example of basic usage shows how to use *datadelay* to estimate the
-overall case fatality ratios from the 1976 Ebola outbreak.
+This example of basic usage shows how to use *cfr* to estimate the
+overall case fatality ratios from the 1976 Ebola outbreak ([Camacho et
+al. 2014](#ref-camacho2014)).
 
 ``` r
 # Load package
-library(datadelay)
+library(cfr)
 
 # Load the Ebola 1976 data provided with the package
 data("ebola1976")
@@ -162,33 +162,41 @@ estimates are shown.
 
 ## Package vignettes
 
-More details on how to use *datadelay* can be found in the [online
+More details on how to use *cfr* can be found in the [online
 documentation as package
-vignettes](https://epiverse-trace.github.io/datadelay/), under
-“Articles”.
+vignettes](https://epiverse-trace.github.io/cfr/), under “Articles”.
 
 ## Help
 
 To report a bug please open an
-[issue](https://github.com/epiverse-trace/datadelay/issues/new/choose).
+[issue](https://github.com/epiverse-trace/cfr/issues/new/choose).
 
 ## Contribute
 
-Contributions to *datadelay* are welcomed. Please follow the [package
+Contributions to *cfr* are welcomed. Please follow the [package
 contributing
-guide](https://github.com/epiverse-trace/datadelay/blob/main/.github/CONTRIBUTING.md).
+guide](https://github.com/epiverse-trace/cfr/blob/main/.github/CONTRIBUTING.md).
 
 ## Code of conduct
 
-Please note that the *datadelay* project is released with a [Contributor
-Code of
+Please note that the *cfr* project is released with a [Contributor Code
+of
 Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).
 By contributing to this project, you agree to abide by its terms.
 
 ## References
 
 <div id="refs" class="references csl-bib-body hanging-indent">
 
+<div id="ref-camacho2014" class="csl-entry">
+
+Camacho, A., A. J. Kucharski, S. Funk, J. Breman, P. Piot, and W. J.
+Edmunds. 2014. “Potential for Large Outbreaks of Ebola Virus Disease.”
+*Epidemics* 9 (December): 70–78.
+<https://doi.org/10.1016/j.epidem.2014.09.003>.
+
+</div>
+
 <div id="ref-nishiura2009" class="csl-entry">
 
 Nishiura, Hiroshi, Don Klinkenberg, Mick Roberts, and Johan A. P.

_pkgdown.yml

@@ -1,3 +1,3 @@
-url: https://epiverse-trace.github.io/datadelay/
+url: https://epiverse-trace.github.io/cfr/
 template:
   package: epiversetheme

data-raw/ebola1976.R

@@ -3,7 +3,7 @@
 ebola1976 <- read.csv(
   system.file(
     "extdata", "ebola_1976.csv",
-    package = "datadelay",
+    package = "cfr",
     mustWork = TRUE
   )
 )