merge to update branch

.Rbuildignore

@@ -8,3 +8,6 @@
 ^.cache$
 ^inst/pkg-structure$
 ^_pkgdown.yml$
+^\.github$
+^_pkgdown\.yml$
+^pkgdown$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-full.yaml

@@ -0,0 +1,85 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: '4.0'}
+          - {os: windows-latest, r: '4.0'}
+          - {os: ubuntu-16.04,   r: '4.0', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.6', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.5', rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
+          sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
+          sudo apt update
+          sudo apt install r-cran-rstan
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,44 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}

.gitignore

@@ -2,3 +2,5 @@
 .RData
 .Rproj.user
 inst/doc
+.DS_Store
+docs

DESCRIPTION

@@ -7,14 +7,14 @@ Authors@R: c(
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0001-8057-8037")),
-    person("Joel", "Hellewell",
-           email = "[email protected]", 
-           role = c("aut"),
-           comment = c(ORCID = "0000-0003-2683-0849")),
     person(given = "Nikos",
            family = "Bosse",
            role = c("aut"),
            email = "[email protected]"),
+    person("Joel", "Hellewell",
+           email = "[email protected]", 
+           role = c("aut"),
+           comment = c(ORCID = "0000-0003-2683-0849")),
     person("Katharine", "Sherratt", 
            email = "[email protected]", 
            role = c("aut")),  
@@ -24,24 +24,38 @@ Authors@R: c(
     person("Robin", "Thompson", 
            email = "[email protected]", 
            role = c("aut")), 
+    person("Aurelien", "Chateigner", 
+           email = "[email protected]", 
+           role = c("aut")),
+    person("Sylvain", "Mareschal", 
+           email = "[email protected]", 
+           role = c("aut")),
+    person("Andrea", "Rau", 
+           email = "[email protected]", 
+           role = c("aut")),
+    person("Nathalie", "Vialaneix", 
+           email = "[email protected]", 
+           role = c("aut")),
+    person(given = "Michael",
+           family = "DeWitt",
+           role = c("aut"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-8940-1967")),
     person("Sebastian", "Funk", 
             email = "[email protected]", 
             role = c("aut")))
-Description: To forecast the time-varying reproduction number and using this to forecast reported case counts. Includes
+Description: To forecast the time-varying reproduction number and use this to forecast reported case counts. Includes
              tools to evaluate a range of models across samples and time series using proper scoring rules.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Depends: 
     R (>= 3.3.0)
 Imports: 
     scoringutils,
     scoringRules,
-    bsts,
-    fabletools,
-    tsibble,
     purrr,
     furrr,
     magrittr,
@@ -60,7 +74,14 @@ Remotes:
 Suggests: 
     knitr,
     rmarkdown,
+    fabletools,
+    tsibble,
+    forecastHybrid,
     fable,
+    bsts,
     feasts,
-    future.apply
+    future.apply,
+    brms,
+    tidybayes,
+    testthat
 VignetteBuilder: knitr

NAMESPACE

@@ -1,12 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(brms_model)
 export(bsts_model)
 export(compare_models)
 export(compare_timeseries)
 export(draw_from_si_prob)
 export(evaluate_model)
 export(fable_model)
+export(forecastHybrid_model)
 export(forecast_cases)
 export(forecast_rt)
 export(iterative_case_forecast)
@@ -23,10 +25,10 @@ export(summarise_forecast)
 export(summarise_scores)
 importFrom(HDInterval,hdi)
 importFrom(R.utils,withTimeout)
-importFrom(bsts,bsts)
-importFrom(bsts,predict.bsts)
 importFrom(cowplot,theme_cowplot)
+importFrom(data.table,`:=`)
 importFrom(dplyr,arrange)
+importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
@@ -40,8 +42,6 @@ importFrom(dplyr,select_if)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
-importFrom(fabletools,forecast)
-importFrom(fabletools,model)
 importFrom(furrr,future_map)
 importFrom(furrr,future_pmap)
 importFrom(ggplot2,aes)
@@ -67,9 +67,14 @@ importFrom(scoringutils,bias)
 importFrom(scoringutils,interval_score)
 importFrom(scoringutils,pit)
 importFrom(scoringutils,sharpness)
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,rpois)
+importFrom(stats,rt)
+importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(tibble,tibble)
 importFrom(tidyr,expand_grid)
 importFrom(tidyr,gather)
 importFrom(tidyr,spread)
 importFrom(tidyr,unnest)
-importFrom(tsibble,tsibble)

R/brms_model.R

@@ -0,0 +1,76 @@
+#' brms model wrapper
+#'
+#' Allows users to specify a model using the [brms::bf()]  wrapper from `brms`
+#' Note that `brms` and `tidybayes` must both be installed for this
+#' model wrapper to be functional.
+#'
+#' @param y Numeric vector of time points to forecast
+#' @param samples Numeric, number of samples to take.
+#' @param model A `brms` model wrapped in the [brms::bf()] function
+#' @param horizon Numeric, the time horizon over which to predict.
+#' @param n_cores Numeric, the number of cores to use, default of 1
+#' @param n_chains Numeric, the number of chains to use, default of 4
+#' @param n_iter Numeric, the number of iterations in the sampler to use,
+#'     default of 4000
+#' @param ... additional arguments passed to `brms` (e.g. priors or family)
+#' @return A dataframe of predictions (with columns representing the time horizon and rows representing samples).
+#' @export
+#' @importFrom data.table `:=`
+#' @examples \dontrun{
+#'
+#' ## Used on its own
+#' ## Note: More iterations and chains should be used
+#' library(brms)
+#'brms_model(y = EpiSoon::example_obs_rts[1:10, ]$rt,
+#'           model = brms::bf(y ~ gp(time)),
+#'           samples = 10, horizon = 7, n_iter = 40, n_chains = 1, refresh =0)
+#'
+#' ## Used for forecasting
+#' ## Note that the timeout parameter has been increased to allow
+#' ## for the time for the code to be compiled
+#' ## Note: More iterations and chains should be used
+#'
+#' forecast_rt(EpiSoon::example_obs_rts[1:10, ],
+#'             model = function(...){
+#'               brms_model(model = brms::bf(y ~ gp(time)), n_iter = 40, n_chains = 1, ...)},
+#'                    horizon = 7, samples = 10, timeout = 300)
+#'}
+
+brms_model <- function(y = NULL, samples = NULL,
+                       horizon = NULL, model = NULL, n_cores = 1,
+                       n_chains = 4, n_iter = 2000, ...) {
+
+  check_suggests("brms")
+  check_suggests("tidybayes")
+  check_suggests("tsibble")
+
+  ## Make input numeric into correct tsibble format
+  timeseries <- tsibble::tsibble(y = y, time = 1:length(y), index = time)
+
+  ## Fit the model
+  fit <- brms::brm(formula = model, data = timeseries,
+                            chains = n_chains, iter = n_iter,
+                            cores = n_cores, ...)
+
+  # Create Prediction Data Frame
+  dat_new <- data.frame(time = (length(y)+1):(length(y)+horizon))
+
+  prediction <- tidybayes::add_fitted_draws(newdata = dat_new,
+                                            model = fit, n = samples)
+
+  prediction <- dplyr::mutate(prediction, row_id = dplyr::row_number())
+
+  prediction <- dplyr::ungroup(prediction)
+
+  prediction <- data.table::as.data.table(prediction)
+
+  prediction <- data.table::dcast(prediction, row_id~time, value.var = ".value")
+
+  prediction <- prediction[,row_id:=NULL]
+
+  ## Extract samples and tidy format
+  samples <- as.data.frame(prediction)
+
+  return(samples)
+
+}

R/bsts_model.R

@@ -6,8 +6,9 @@
 #' @param horizon Numeric, the time horizon over which to predict.
 #' @return A dataframe of predictions (with columns representing the time horizon and rows representing samples).
 #' @export
-#' @importFrom bsts bsts predict.bsts
-#' @examples
+#' @examples \dontrun{
+#'
+#' library(bsts)
 #'
 #' ## Used on its own
 #' bsts_model(y = EpiSoon::example_obs_rts[1:10, ]$rt,
@@ -21,10 +22,14 @@
 #'                       function(ss, y){
 #'                         bsts::AddAr(ss, y = y, lags = 3)}, ...)},
 #'                     horizon = 7, samples = 10)
+#'}
 bsts_model <- function(y = NULL, samples = NULL,
                        horizon = NULL, model = NULL) {
 
 
+  check_suggests("bsts")
+
+
   model <- model(list(), y)
 
   ## Fit the model
@@ -44,9 +49,4 @@ bsts_model <- function(y = NULL, samples = NULL,
 
   return(samples)
 
-
-
-
-
-
 }