Initial CRAN release v0.1.0

eebrown · Feb 12, 2021 · 4d92ce0 · 4d92ce0
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diff --git 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
@@ -18,7 +18,7 @@
 #'              (see reference).
 #'
 #' @return Proportion who would not be expected to show symptoms yet
-#' @references See McAloon et al. <https://bmjopen.bmj.com/content/10/8/e039652>
+#' @references See McAloon et al. <https://bmjopen.bmj.com/content/10/8/e039652/>
 #' @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. <https://bmjopen.bmj.com/content/10/8/e039652>
+#' @references See McAloon et al. <https://bmjopen.bmj.com/content/10/8/e039652/>
 #' @export
 #'
 adjust_pretest <- function(pre0, asympt, days = 14,

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # R package: covidprobability
 
 <!-- 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)
 <!-- badges: end -->
 
 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
@@ -6,7 +6,7 @@
 <!-- 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)
 <!-- badges: end -->
 
 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
diff --git a/man/prop_remaining.Rd b/man/prop_remaining.Rd
diff --git 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. <http://dx.doi.org/10.7326/M20-1495>
+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. <https://dx.doi.org/10.7326/M20-1495>
 
-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. <http://dx.doi.org/10.7326/M20-0504>
+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. <https://dx.doi.org/10.7326/M20-0504>
 
-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. <http://dx.doi.org/10.1136/bmjopen-2020-039652>
+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. <https://dx.doi.org/10.1136/bmjopen-2020-039652>
 
-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. <http://dx.doi.org/10.1371/journal.pone.0241536>
+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. <https://dx.doi.org/10.1371/journal.pone.0241536>