Fix URLs

problems detected by urlchecker pkg

R/bias.R

@@ -51,7 +51,7 @@
 #' Kucharski AJ, Lowe R, Eggo RM, et al. (2019) Assessing the performance of
 #' real-time epidemic forecasts: A case study of Ebola in the Western Area
 #' region of Sierra Leone, 2014-15. PLOS Computational Biology 15(2): e1006785.
-#' <doi:10.1371/journal.pcbi.1006785>
+#' \doi{10.1371/journal.pcbi.1006785}
 #' @keywords metric
 
 bias_sample <- function(true_values, predictions) {

R/pit.R

@@ -78,7 +78,7 @@
 #' Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe,
 #' Rosalind M. Eggo, W. John Edmunds (2019) Assessing the performance of
 #' real-time epidemic forecasts: A case study of Ebola in the Western Area
-#' region of Sierra Leone, 2014-15, <doi:10.1371/journal.pcbi.1006785>
+#' region of Sierra Leone, 2014-15, \doi{10.1371/journal.pcbi.1006785}
 #' @keywords metric
 
 pit_sample <- function(true_values,
@@ -176,7 +176,7 @@ pit_sample <- function(true_values,
 #' Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe,
 #' Rosalind M. Eggo, W. John Edmunds (2019) Assessing the performance of
 #' real-time epidemic forecasts: A case study of Ebola in the Western Area
-#' region of Sierra Leone, 2014-15, <doi:10.1371/journal.pcbi.1006785>
+#' region of Sierra Leone, 2014-15, \doi{10.1371/journal.pcbi.1006785}
 #' @keywords scoring
 
 pit <- function(data,

R/score.R

@@ -66,7 +66,7 @@
 #' @references Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ
 #' (2019) Assessing the performance of real-time epidemic forecasts: A
 #' case study of Ebola in the Western Area region of Sierra Leone, 2014-15.
-#' PLoS Comput Biol 15(2): e1006785. <doi:10.1371/journal.pcbi.1006785>
+#' PLoS Comput Biol 15(2): e1006785. \doi{10.1371/journal.pcbi.1006785}
 #' @export
 
 score <- function(data,

R/sharpness.R

@@ -18,7 +18,7 @@
 #' Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ (2019)
 #' Assessing the performance of real-time epidemic forecasts: A case study of
 #' Ebola in the Western Area region of Sierra Leone, 2014-15.
-#' PLoS Comput Biol 15(2): e1006785. <doi:10.1371/journal.pcbi.1006785>
+#' PLoS Comput Biol 15(2): e1006785. \doi{10.1371/journal.pcbi.1006785}
 #'
 #' @export
 #' @examples

README.Rmd

@@ -7,7 +7,7 @@ output:
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/epiforecasts/scoringutils/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiforecasts/scoringutils/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/epiforecasts/scoringutils/branch/master/graphs/badge.svg)](https://codecov.io/gh/epiforecasts/scoringutils/) 
+[![codecov](https://app.codecov.io/gh/epiforecasts/scoringutilsbranch/master/graphs/badge.svg)](https://app.codecov.io/gh/epiforecasts/scoringutils) 
 [![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version-ago/scoringutils)](https://CRAN.R-project.org/package=scoringutils)
 [![develVersion](https://img.shields.io/badge/devel%20version-1.0.0-green.svg?style=flat)](https://github.com/epiforecasts/scoringutils)
 [![metacran

README.md

@@ -4,7 +4,7 @@ scoringutils: Utilities for Scoring and Assessing Predictions
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/epiforecasts/scoringutils/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiforecasts/scoringutils/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/epiforecasts/scoringutils/branch/master/graphs/badge.svg)](https://codecov.io/gh/epiforecasts/scoringutils/)
+[![codecov](https://app.codecov.io/gh/epiforecasts/scoringutilsbranch/master/graphs/badge.svg)](https://app.codecov.io/gh/epiforecasts/scoringutils)
 [![CRAN_Release_Badge](https://www.r-pkg.org/badges/version-ago/scoringutils)](https://CRAN.R-project.org/package=scoringutils)
 [![develVersion](https://img.shields.io/badge/devel%20version-1.0.0-green.svg?style=flat)](https://github.com/epiforecasts/scoringutils)
 [![metacran