fix merge conflicts

.github/workflows/codemeta.yaml

@@ -38,7 +38,7 @@ jobs:
           body: "This is an automated pull request to update the codemeta.json file."
           branch: "update-codemeta-${{ github.run_number }}"
           labels: "metadata"
-          reviewers: seabbs
+          reviewers: kaitejohnson
           add-paths: |
             codemeta.json
           token: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -26,10 +26,10 @@ Description: Provides functions for nowcasting right-truncated epidemiological
   data, based heavily on the method implemented in
   https://github.com/KITmetricslab/RESPINOW-Hub/tree/main/code/baseline
 License: MIT + file LICENSE
-URL: https://github.com/epinowcast/baselinenowcast/
+URL: https://baselinenowcast.epinowcast.org, https://github.com/epinowcast/baselinenowcast/
 BugReports: https://github.com/epinowcast/baselinenowcast/issues
 Depends:
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports:
   cli,
   checkmate,
@@ -46,6 +46,8 @@ Suggests:
     withr,
     knitr
 Encoding: UTF-8
+Language: en-GB
+LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr

R/apply_delay.R

@@ -1,11 +1,10 @@
 #' Apply the delay to generate a point nowcast
-#' @description
 #' Generate a point estimate of a completed reporting square (or rectangle)
-#'  from a reporting triangle that we want to complete with a nowcast and a
-#'  delay pmf. This code was adapted from code written (under an MIT license)
-#'  by the Karlsruhe Institute of Technology RESPINOW
-#'  German Hospitalization Nowcasting Hub.
-#'  Modified from: https://github.com/KITmetricslab/RESPINOW-Hub/blob/7cce3ae2728116e8c8cc0e4ab29074462c24650e/code/baseline/functions.R#L55 #nolint
+#'   from a reporting triangle that we want to complete with a nowcast and a
+#'   delay pmf. This code was adapted from code written (under an MIT license)
+#'   by the Karlsruhe Institute of Technology RESPINOW
+#'   German Hospitalization Nowcasting Hub.
+#'   Modified from: https://github.com/KITmetricslab/RESPINOW-Hub/blob/7cce3ae2728116e8c8cc0e4ab29074462c24650e/code/baseline/functions.R#L55 #nolint
 #' @param triangle_to_nowcast Matrix of the incomplete reporting triangle to be
 #'   nowcasted, with rows representing the time points of reference and columns
 #'   representing the delays

R/get_delay_estimate.R

@@ -1,19 +1,18 @@
 #' Estimate a delay distribution from a reporting triangle
-#' @description
 #' Provides an estimate of the reporting delay as a function
-#'  of the delay, based on the reporting triangle and the specified maximum
-#'  delay and number of reference date observations to be used in the
-#'  estimation. This point estimate of the delay is computed empirically,
-#'  using an iterative algorithm starting from the most recent observations.
-#'  This code was adapted from code written (under an MIT license)
-#'  by the Karlsruhe Institute of Technology RESPINOW
-#'  German Hospitalization Nowcasting Hub.
-#'  Modified from: https://github.com/KITmetricslab/RESPINOW-Hub/blob/7cce3ae2728116e8c8cc0e4ab29074462c24650e/code/baseline/functions.R#L55 #nolint
+#'   of the delay, based on the reporting triangle and the specified maximum
+#'   delay and number of reference date observations to be used in the
+#'   estimation. This point estimate of the delay is computed empirically,
+#'   using an iterative algorithm starting from the most recent observations.
+#'   This code was adapted from code written (under an MIT license)
+#'   by the Karlsruhe Institute of Technology RESPINOW
+#'   German Hospitalization Nowcasting Hub.
+#'   Modified from: https://github.com/KITmetricslab/RESPINOW-Hub/blob/7cce3ae2728116e8c8cc0e4ab29074462c24650e/code/baseline/functions.R#L55 #nolint
 #' @param triangle Matrix of the reporting triangle, with rows representing
-#'  the time points of reference and columns representing the delays
+#'   the time points of reference and columns representing the delays
 #' @param max_delay Integer indicating the maximum delay to estimate, in units
-#'  of the delay. The default is to use the whole reporting triangle,
-#'  `ncol(triangle) -1`.
+#'   of the delay. The default is to use the whole reporting triangle,
+#'   `ncol(triangle) -1`.
 #' @param n_history Integer indicating the number of reference dates to be
 #'   used in the estimate of the reporting delay, always starting from the most
 #'   recent reporting delay. The default is to use the whole reporting triangle,

R/handle_neg_vals.R

@@ -1,5 +1,4 @@
 #' Handle negative values in the reporting triangle
-#' @description
 #' Takes in a reporting triangle and returns a matrix in the same format
 #'   as the input triangle, but with negative values of reporting handled via
 #'   passing them to the subsequent days (from longer delay to shorter).

R/validate.R

@@ -1,5 +1,4 @@
 #' Validate triangle
-#' @description
 #' Various checks to make sure that the reporting triangle passed in to
 #'   [get_delay_estimate()] is formatted properly.
 #' @importFrom checkmate assert_class
@@ -57,7 +56,6 @@
 }
 
 #' Validate triangle to nowcast and delay pmf together
-#' @description
 #' Various checks to make sure that the reporting triangle  and the delay pmf
 #'   passed in to [apply_delay()] are formatted properly and compatible
 #' @param triangle Matrix of values with rows indicating the time points and

_pkgdown.yml

@@ -1,6 +1,6 @@
 url: https://baselinenowcast.epinowcast.org/
 template:
-  pacakge: enwtheme
+  package: enwtheme
   math-rendering: mathjax
 
 
@@ -9,8 +9,11 @@ development:
 
 navbar:
   structure:
+    left: [intro, metareference, news]
     right: [search, github, lightswitch]
   components:
+    metareference:
+      text: Reference
 
 home:
   title: Baseline nowcast for right-truncated epidemiological data

codemeta.json

@@ -4,6 +4,7 @@
   "identifier": "baselinenowcast",
   "description": "Provides functions for nowcasting right-truncated epidemiological data, based heavily on the method implemented in https://github.com/KITmetricslab/RESPINOW-Hub/tree/main/code/baseline",
   "name": "baselinenowcast: Baseline nowcast",
+  "relatedLink": "https://baselinenowcast.epinowcast.org",
   "codeRepository": "https://github.com/epinowcast/baselinenowcast/",
   "issueTracker": "https://github.com/epinowcast/baselinenowcast/issues",
   "license": "https://spdx.org/licenses/MIT",
@@ -65,27 +66,32 @@
   "softwareSuggestions": [
     {
       "@type": "SoftwareApplication",
-      "identifier": "dplyr",
-      "name": "dplyr",
+      "identifier": "epinowcast",
+      "name": "epinowcast"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "bookdown",
+      "name": "bookdown",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=dplyr"
+      "sameAs": "https://CRAN.R-project.org/package=bookdown"
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "bookdown",
-      "name": "bookdown",
+      "identifier": "dplyr",
+      "name": "dplyr",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
         "name": "Comprehensive R Archive Network (CRAN)",
         "url": "https://cran.r-project.org"
       },
-      "sameAs": "https://CRAN.R-project.org/package=bookdown"
+      "sameAs": "https://CRAN.R-project.org/package=dplyr"
     },
     {
       "@type": "SoftwareApplication",
@@ -178,13 +184,25 @@
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
-      "version": ">= 4.0.0"
+      "version": ">= 4.1.0"
+    },
+    "2": {
+      "@type": "SoftwareApplication",
+      "identifier": "cli",
+      "name": "cli",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=cli"
     },
     "SystemRequirements": null
   },
-  "fileSize": "4.575KB",
+  "fileSize": "33.639KB",
   "releaseNotes": "https://github.com/epinowcast/baselinenowcast/blob/master/NEWS.md",
-  "readme": "https://github.com/epinowcast/baselinenowcast/blob/main/README.Rmd",
+  "readme": "https://github.com/epinowcast/baselinenowcast/blob/main/README.md",
   "contIntegration": ["https://github.com/epinowcast/baselinenowcast/actions/workflows/R-CMD-check.yaml", "https://app.codecov.io/gh/epinowcast/baselinenowcast"],
   "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#stable"
 }