From 3d068436635ece878178ca0915916d3a602cbb42 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 10 Nov 2023 11:48:12 +0000 Subject: [PATCH] Automatic readme update --- README.md | 28 +++++++++++------------ man/figures/README-unnamed-chunk-2-1.png | Bin 29944 -> 29962 bytes 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index e7e93229..2cc5d07d 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![License: -MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit) +MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit/) [![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/cfr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/cfr?branch=main) @@ -40,6 +40,12 @@ at the London School of Hygiene and Tropical Medicine as part of the ## Installation +*cfr* can be installed from CRAN using + +``` r +install.packages("cfr") +``` + The current development version of *cfr* can be installed from [GitHub](https://github.com/) using the `pak` package. @@ -87,10 +93,11 @@ as more data on cases and deaths over time becomes available, using the function `cfr_rolling()`. Because there is a delay from onset-to-death, a simple “naive” calculation that just divides deaths-to-date by cases-to-date will underestimate severity. The `cfr_rolling()` function -uses the `cfr_severity()` adjustment to account for delays, and instead -compares deaths-to-date with cases-with-known-outcome-to-date. The -adjusted estimate converges to the naive estimate as the outbreak -declines and a larger proportion of cases have known outcomes. +uses the `estimate_severity()` adjustment internally to account for +delays, and instead compares deaths-to-date with +cases-with-known-outcome-to-date. The adjusted estimate converges to the +naive estimate as the outbreak declines and a larger proportion of cases +have known outcomes. ``` r # Calculate the CFR without correcting for delays on each day of the outbreak @@ -98,9 +105,6 @@ rolling_cfr_naive <- cfr_rolling( data = ebola1976 ) -# add the date from the outbreak -rolling_cfr_naive <- cbind(date = ebola1976[, "date"], rolling_cfr_naive) - # see the first few rows head(rolling_cfr_naive) #> date severity_mean severity_low severity_high @@ -117,15 +121,9 @@ rolling_cfr_corrected <- cfr_rolling( delay_density = function(x) dgamma(x, shape = 2.40, scale = 3.33) ) -# add the date from the outbreak -rolling_cfr_corrected <- cbind( - date = ebola1976[, "date"], - rolling_cfr_corrected -) - head(rolling_cfr_corrected) #> date severity_mean severity_low severity_high -#> 1 1976-08-25 0.001 NA NA +#> 1 1976-08-25 NA NA NA #> 2 1976-08-26 0.001 0.001 0.999 #> 3 1976-08-27 0.001 0.001 0.999 #> 4 1976-08-28 0.001 0.001 0.999 diff --git 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