Seabbs/issue80 (#83)

* update to new version of pkgdown

* modify version and update news

* update pkgdown template to new version and make related fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EpiSoon
 Type: Package
 Title: Forecast Cases Using Reproduction Numbers
-Version: 0.3.0
+Version: 0.3.0.1000
 Authors@R: c(
     person(given = "Sam Abbott",
            role = c("aut", "cre"),
@@ -69,22 +69,21 @@ Imports:
     cowplot,
     HDInterval,
     R.utils
-Additional_repositories: 
-    https://epiforecasts.io/drat/
 Remotes:
     nikosbosse/stackr
 Suggests: 
     knitr,
     rmarkdown,
+    fable,
     fabletools,
     tsibble,
     forecastHybrid,
     forecast,
     fable,
-    bsts,
     feasts,
     future.apply,
     stackr,
+    bsts,
     brms,
     tidybayes,
     testthat

NAMESPACE

@@ -43,6 +43,7 @@ importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_at)
 importFrom(dplyr,group_split)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
@@ -54,7 +55,6 @@ importFrom(dplyr,select_if)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
-importFrom(dplyr,vars)
 importFrom(furrr,furrr_options)
 importFrom(furrr,future_map)
 importFrom(furrr,future_pmap)

NEWS.md

@@ -1,7 +1,13 @@
+# EpiSoon 0.3.1
+
+* Updated all GitHub Actions
+* Updated `tidyverse` code usage to account for depreciation.
+* Updated `pkgdown` site to use `pkgdown` 2.0.0.
+
 # EpiSoon 0.3.0
 
 * Reviewed and updated all tooling and examples
-* Added documentation 
+* Added documentation
 * Bugs squashed.
 
 # EpiSoon 0.2.0

_pkgdown.yml

@@ -1,28 +1,22 @@
 url: epiforecasts.io/EpiSoon/
 template:
+  bootstrap: 5
+  opengraph:
+    twitter:
+      creator: "@seabbs"
+      site: "@epiforecasts"
+      card: summary_large_image
   params:
     bootswatch: lumen
 
 development:
-  mode: release
-
-navbar:
-  type: inverse 
-  left:
-    - text: "Home"
-      href: index.html
-    - text: "Getting started"
-      href: articles/introduction.html
-    - text: News
-      href: news/index.html
-    - icon: fa-file-code-o
-      text: "Functions"
-      href: reference/index.html
-  right:
-    - icon: fa-github
-      href: https://github.com/epiforecasts/EpiSoon
-
+  mode: auto
 
+authors:
+  Sam Abbott:
+    href: "https://www.samabbott.co.uk/"
+  Sebastian Funk: 
+    href: "https://www.lshtm.ac.uk/aboutus/people/funk.sebastian"
 
 reference:
   - title: Analysis wrappers
@@ -34,6 +28,7 @@ reference:
   - title: Forecast
     desc: Forecasting tools
     contents:
+      - forecast_model
       - forecast_rt
       - forecast_cases
       - forecast_cases_directly
@@ -69,6 +64,7 @@ reference:
     desc: Tools to plot forecasts
     contents:
       - plot_forecast
+      - plot_compare_timeseries
       - plot_forecast_evaluation
       - plot_scores
   - title: Example datasets

vignettes/introduction.Rmd

@@ -2,7 +2,7 @@
 title: "Getting started"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{introduction}
+  %\VignetteIndexEntry{Getting started}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -45,9 +45,15 @@ EpiSoon::example_obs_rts
 
 * Fit a `bsts` model and produce a Rt forecast. Any appropriately wrapped model can be used (see `bsts_model` and `fable_model` for an examples).
 ```{r}
-rt_forecast <- forecast_rt(EpiSoon::example_obs_rts[1:10, ],
-                       model = function(...){EpiSoon::bsts_model(model = function(ss, y){bsts::AddAutoAr(ss, y = y, lags = 10)}, ...)},
-                       horizon = 21, samples = 10)
+rt_forecast <- forecast_rt(
+  EpiSoon::example_obs_rts[1:10, ],
+  model = function(...) {
+    EpiSoon::bsts_model(
+      model = function(ss, y) {
+        bsts::AddAutoAr(ss, y = y, lags = 10)}, ...)
+      },
+      horizon = 21, samples = 10
+)
 
 rt_forecast
 ```
@@ -97,8 +103,10 @@ EpiSoon::example_serial_interval
 * Forecast cases (using the case data on which the observed Rt estimates were based)
 
 ```{r}
-case_forecast <- forecast_cases(EpiSoon::example_obs_cases, rt_forecast,
-                                serial_interval = EpiSoon::example_serial_interval)
+case_forecast <- forecast_cases(
+  EpiSoon::example_obs_cases, rt_forecast,
+  serial_interval = EpiSoon::example_serial_interval
+)
 
 case_forecast
 ```