diff --git a/NEWS.md b/NEWS.md index f08af1e..f5ecfb0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,3 @@ # covidprobability 0.1.0 -Initial beta release. +Initial beta release. Inital CRAN release. diff --git a/R/functions.R b/R/functions.R index 247a5d5..18862c7 100644 --- a/R/functions.R +++ b/R/functions.R @@ -18,7 +18,7 @@ #' (see reference). #' #' @return Proportion who would not be expected to show symptoms yet -#' @references See McAloon et al. +#' @references See McAloon et al. #' @export #' prop_remaining <- function(t, asympt, mu = 1.63, sigma = 0.5) { @@ -46,7 +46,7 @@ prop_remaining <- function(t, asympt, mu = 1.63, sigma = 0.5) { #' (see reference). #' #' @return pretest probability by day (time series) -#' @references See McAloon et al. +#' @references See McAloon et al. #' @export #' adjust_pretest <- function(pre0, asympt, days = 14, diff --git a/README.Rmd b/README.Rmd index 64e834a..02d2975 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( # R package: covidprobability -[![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) This package provides the functions, data and documentation that support a @@ -31,6 +31,12 @@ An [interactive web app](http://covid.eebc.ca) of this calculator is available. ## Installation +You can install the latest CRAN version of covidprobability from with: + +``` r +install.packages("covidprobability") +``` + You can install the latest version of covidprobability from [Github](https://github.com/eebrown/covidprobability) with: ``` r diff --git a/README.md b/README.md index c60f1bc..1dc304a 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![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) This package provides the functions, data and documentation that support @@ -23,6 +23,12 @@ available. ## Installation +You can install the latest CRAN version of covidprobability from with: + +``` r +install.packages("covidprobability") +``` + You can install the latest version of covidprobability from [Github](https://github.com/eebrown/covidprobability) with: diff --git a/man/adjust_pretest.Rd b/man/adjust_pretest.Rd index 2abb587..0f9e3d0 100644 --- a/man/adjust_pretest.Rd +++ b/man/adjust_pretest.Rd @@ -30,5 +30,5 @@ not develop symptoms, by taking into account the distribution of incubation periods (defined as the time from exposure to symptom onset). } \references{ -See McAloon et al. \url{https://bmjopen.bmj.com/content/10/8/e039652} +See McAloon et al. \url{https://bmjopen.bmj.com/content/10/8/e039652/} } diff --git a/man/prop_remaining.Rd b/man/prop_remaining.Rd index 8a6516e..888bdd9 100644 --- a/man/prop_remaining.Rd +++ b/man/prop_remaining.Rd @@ -31,5 +31,5 @@ symptoms yet. So if no one has developed symptoms, this proportion of people could still have undetected COVID-19. } \references{ -See McAloon et al. \url{https://bmjopen.bmj.com/content/10/8/e039652} +See McAloon et al. \url{https://bmjopen.bmj.com/content/10/8/e039652/} } diff --git a/vignettes/unit-example.Rmd b/vignettes/unit-example.Rmd index 4d0d7f2..5bcdd69 100644 --- a/vignettes/unit-example.Rmd +++ b/vignettes/unit-example.Rmd @@ -236,11 +236,11 @@ This R package and accompanying Shiny app are available to the public for review ## References -Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure. Annals of Internal Medicine. 2020;173(4):262-267. +Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure. Annals of Internal Medicine. 2020;173(4):262-267. -A. Lauer S, H. Grantz K, Bi Q, et al. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Annals of Internal Medicine. Published online March 10, 2020. +A. Lauer S, H. Grantz K, Bi Q, et al. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Annals of Internal Medicine. Published online March 10, 2020. -McAloon C, Collins Á, Hunt K, et al. Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research. BMJ Open. 2020;10(8):e039652. +McAloon C, Collins Á, Hunt K, et al. Incubation period of COVID-19: a rapid systematic review and meta-analysis of observational research. BMJ Open. 2020;10(8):e039652. -Yanes-Lane M, Winters N, Fregonese F, et al. Proportion of asymptomatic infection among COVID-19 positive persons and their transmission potential: A systematic review and meta-analysis. PLOS ONE. 2020;15(11):e0241536. +Yanes-Lane M, Winters N, Fregonese F, et al. Proportion of asymptomatic infection among COVID-19 positive persons and their transmission potential: A systematic review and meta-analysis. PLOS ONE. 2020;15(11):e0241536.