Feature missing reference dates

.Rbuildignore

@@ -16,5 +16,6 @@
 ^vignettes/precompile.R$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^codemeta\.json$
 ^CONTRIBUTING\.md$
-^inst/make_hexsticker\.R$
+^inst/make_hexsticker\.R$

.github/workflows/R-CMD-check.yaml

@@ -107,7 +107,7 @@ jobs:
         run: |
           print(list.files("C:/rtools42"))
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2)
+          cmdstanr::install_cmdstan(cores = 2, version = "2.29.0")
         shell: Rscript {0}
 
       - name: Session info

.github/workflows/codemeta.yaml

@@ -0,0 +1,25 @@
+on:
+  push:
+    paths:
+      - DESCRIPTION
+      - .github/workflows/codemeta.yml
+
+name: Render codemeta
+jobs:
+  render:
+    name: Render codemeta
+    runs-on: macOS-latest
+    if: "!contains(github.event.head_commit.message, 'cm-skip')"
+    steps:
+      - uses: actions/checkout@v1
+      - uses: r-lib/actions/setup-r@v2
+      - name: Install remotes
+        run: Rscript -e 'install.packages("remotes")'
+      - name: Install codemetar
+        run: Rscript -e 'remotes::install_local(dependencies = c("Imports", "Depends"))'
+      - name: Render codemeta
+        run: Rscript -e 'codemetar::write_codemeta()'
+      - name: Commit results
+        run: |
+          git commit codemeta.json -m 'Re-build codemeta.json' || echo "No changes to commit"
+          git push https://${{github.actor}}:${{secrets.GITHUB_TOKEN}}@github.com/${{github.repository}}.git HEAD:${{ github.ref }} || echo "No changes to commit"

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, develop]
     tags: ['*']
 
 name: pkgdown

.github/workflows/test-coverage.yaml

@@ -53,7 +53,7 @@ jobs:
         run: |
           print(list.files("C:/rtools42"))
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2)
+          cmdstanr::install_cmdstan(cores = 2, version = "2.29.0")
         shell: Rscript {0}
 
       - name: Install package

.gitignore

@@ -13,4 +13,4 @@ cache
 .Rproj.user
 *.Rproj
 !inst/extdata/*.rds
-pkgdown
+pkgdown

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.1
+    rev: v0.3.2
     hooks: 
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]    

CONTRIBUTING.md

@@ -32,17 +32,18 @@ External code contributions are extremely helpful and appreciated. Here are the
 
 1. Prior to contribution, please propose your idea in a [new issue thread](https://github.com/epiforecasts/epinowcast/issues) so you and the reviewer can define the intent and scope of the work.
 2. [Fork the repository](https://help.github.com/articles/fork-a-repo/).
-3. Follow the [GitHub flow](https://guides.github.com/introduction/flow/index.html) to create a new branch, add commits, and open a pull request.
+3. Follow the [GitHub flow](https://guides.github.com/introduction/flow/index.html) to create a new branch, add commits, and open a pull request. 
 4. Discuss your code with the reviewer in the pull request thread.
 5. If everything looks good, the reviewer will merge your code into the project.
 
 Please also follow these additional guidelines.
 
+* We use a `develop`/ `main` workflow so please target major changes to the `develop` branch and minor changes to the `main` branch. If unclear please ask when opening the initial issue proposing the change.
 * Respect the architecture and reasoning of the package. Depending on the scope of your work, you may want to read the design documents (package vignettes).
 * In general we aim to use `data.table` to manipulate data. However, if this is a barrier to contributing please use tools you are familiar with and raise this in your pull request. The reviewer will then work with you to refactor your contribution or if appropriate add the dependencies you require.
 * If possible, keep contributions small enough to easily review manually. It is okay to split up your work into multiple pull requests.
 * Format your code according to the [tidyverse style guide](https://style.tidyverse.org/) and check your formatting with the `lint_package()` function from the [`lintr`](https://github.com/jimhester/lintr) package.
 * Check code coverage with `covr::package_coverage()`. Automated tests should cover all the new or changed functionality in your pull request.
 * Run overall package checks with `devtools::check()` and `goodpractice::gp()`
 * Describe your contribution in the project's [`NEWS.md`](https://github.com/epiforecasts/epinowcast/blob/main/NEWS.md) file. Be sure to mention relevant GitHub issue numbers and your GitHub name as done in existing news entries.
-* If you feel your contribution is substantial enough for official author or contributor status, please add yourself to the `Authors@R` field of the [`DESCRIPTION`](https://github.com/ropensci/jagstargets/blob/main/DESCRIPTION) file. In general, we consider any contribution sufficient for contributor status and several minor or a single major contribution sufficient for author status.
+* If you feel your contribution is substantial enough for author or contributor status, please add yourself to the `Authors@R` field of the [`DESCRIPTION`](https://github.com/ropensci/jagstargets/blob/main/DESCRIPTION) file. In general, we consider any contribution sufficient for contributor status and several minor or a single major contributions sufficient for author status. If planning on writing a paper or similar about your package extension please note this in your contribution and feel free to suggest how you would like this to be managed.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epinowcast
 Title: Hierarchical Nowcasting of Right Censored Epidemiological Counts
-Version: 0.0.7
+Version: 0.1.0.1000
 Authors@R:
   c(person(given = "Sam Abbott",
            role = c("aut", "cre"),
@@ -11,6 +11,10 @@ Authors@R:
              role = "aut",
              email = "adrian.lison@bsse.ethz.ch",
              comment = c(ORCID = "0000-0002-6822-8437")),
+    person(given = "Sebastian",
+                family = "Funk",
+                role = "aut",
+                email = "sebastian.funk@lshtm.ac.uk"),
     person(given = "Michael",
              family = "DeWitt",
              role = "ctb",
@@ -35,6 +39,7 @@ Imports:
     cmdstanr,
     data.table,
     lubridate,
+    lme4,
     ggplot2,
     posterior,
     purrr,

NAMESPACE

@@ -12,15 +12,19 @@ export(enw_as_data_list)
 export(enw_assign_group)
 export(enw_construct_data)
 export(enw_dates_to_factors)
+export(enw_delay_filter)
+export(enw_delay_metadata)
 export(enw_design)
 export(enw_effects_metadata)
 export(enw_example)
 export(enw_extend_date)
-export(enw_filter_obs)
+export(enw_filter_reference_dates)
+export(enw_filter_report_dates)
 export(enw_formula)
 export(enw_formula_as_data_list)
 export(enw_inits)
 export(enw_latest_data)
+export(enw_manual_formula)
 export(enw_metadata)
 export(enw_model)
 export(enw_new_reports)
@@ -42,20 +46,19 @@ export(enw_priors_as_data_list)
 export(enw_quantiles_to_long)
 export(enw_reporting_triangle)
 export(enw_reporting_triangle_to_long)
-export(enw_retrospective_data)
 export(enw_sample)
 export(enw_score_nowcast)
 export(enw_summarise_samples)
 export(epinowcast)
-export(expose_stan_fns)
+export(re)
+export(rw)
 import(cmdstanr)
 import(data.table, except = transpose)
 import(ggplot2)
 importFrom(cmdstanr,cmdstan_model)
 importFrom(data.table,":=")
 importFrom(data.table,.N)
 importFrom(data.table,.SD)
-importFrom(data.table,as.IDate)
 importFrom(data.table,as.data.table)
 importFrom(data.table,copy)
 importFrom(data.table,data.table)
@@ -65,9 +68,12 @@ importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
 importFrom(data.table,setcolorder)
+importFrom(data.table,setnafill)
 importFrom(data.table,setnames)
 importFrom(data.table,setorderv)
 importFrom(data.table,shift)
+importFrom(lme4,findbars)
+importFrom(lme4,nobars)
 importFrom(posterior,default_convergence_measures)
 importFrom(posterior,mad)
 importFrom(posterior,quantile2)
@@ -76,6 +82,7 @@ importFrom(purrr,map)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
 importFrom(purrr,reduce)
+importFrom(purrr,transpose)
 importFrom(rstan,expose_stan_functions)
 importFrom(rstan,stanc)
 importFrom(scales,comma)

NEWS.md

@@ -1,3 +1,32 @@
+# epinowcast 0.1.0
+
+This is a major release and contains multiple breaking changes. If needing the old interface please install `0.0.7` from GitHub. A major focus of this release has been improving the user experience with an increase in modularity, development of a flexible and full featured formula interface, and hopefully future proofing as far as possible. For ease, we have stratified changes below into interface, package, documentation, and model changes.
+
+## Interface
+
+* A fully featured and flexible formula interface has been added that allows the specification of fixed effects, `lme4` random effects, and random walks. See [#27](https://github.com/epiforecasts/epinowcast/pull/27) by [@seabbs](https://github.com/seabbs).
+
+## Package
+
+* A new helper function `enw_delay_metadata()` has been added. This produces metadata about the delay distribution vector that may be helpful in future modelling. This prepares the way for [#4](https://github.com/epiforecasts/epinowcast/issues/4) where this data frame will be combined with the reference metadata in order to build non-parametric hazard reference and delay based models. In addition to adding this function, it has also been added to the output of `enw_preprocess_data()` in order to make the metadata readily available to end-users. See [#80](https://github.com/epiforecasts/epinowcast/pull/80) by [@seabbs](https://github.com/seabbs).
+* Two new helper functions `enw_filter_reference_dates()` and `enw_filter_report_dates()` have been added. These replace `enw_retrospective_data()` but allow users to similarly construct retrospective data. Splitting these functions out into components also allows for additional use cases that were not previously possible. See [#82](https://github.com/epiforecasts/epinowcast/pull/82) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).
+* The internal grouping variables have been refactored to reduce the chance of clashes with columns in the data frames supplied by the user. There will also be an error thrown in case of a variable clash, making preprocessing safer. See [#102](https://github.com/epiforecasts/epinowcast/pull/102) by [@adrian-lison](https://github.com/adrian-lison) and [@seabbs](https://github.com/seabbs), which solves [#99](https://github.com/epiforecasts/epinowcast/issues/99).
+
+## Model
+
+* Added support for parametric exponential delay distributions (note that this is comparable to an intercept-only non-parametric hazard model) and potentially no parametric delay (though this will currently throw an error due to the lack of appropriate non-parametric hazard). See [#84](https://github.com/epiforecasts/epinowcast/pull/84) by [@seabbs](https://github.com/seabbs).
+* Update the expectation random walk model to use a more efficient `cumulative_sum` implementation suggested by [@adrian-lison](https://github.com/adrian-lison) in [#98](https://github.com/epiforecasts/epinowcast/issues/98)]. See [#103](https://github.com/epiforecasts/epinowcast/pull/103/) by [@seabbs](https://github.com/seabbs).
+
+## Documentation
+
+* The model descriptipn has been updated to reflect the currently implemented model and to improve readability. The use use of reference and report date nomenclature has also been standardised across the package. See [#71](https://github.com/epiforecasts/epinowcast/pull/71) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).
+
+## Internals
+
+* Array declarations in the stan model have been updated. To maintain compatibility with [expose_stan_fns()] (which itself depends on `rstan`), additional functionality has been added to parse stan code in this function. See [#74](https://github.com/epiforecasts/epinowcast/issues/74), [#85](https://github.com/epiforecasts/epinowcast/pull/85#issuecomment-1172010003), and [#93](https://github.com/epiforecasts/epinowcast/pull/93) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).
+* Remove spurious warnings due to missing initial values for optional parameters. See [#76](https://github.com/epiforecasts/epinowcast/issues/75) by [@sbfnk](https://github.com/sbfnk) and [@seabbs](https://github.com/seabbs).
+
+
 # epinowcast 0.0.7
 
 * Adds additional quality of life data processing so that the maximum number (`max_confirm`) of notifications is available in every row (for both cumulative and incidence notifications) and the cumulative and daily empirical proportion reported are calculated for the user during pre-processing (see [#62](https://github.com/epiforecasts/epinowcast/pull/62) by [@seabbs](https://github.com/seabbs)). 

R/check.R

@@ -19,3 +19,59 @@ check_quantiles <- function(posterior, req_probs = c(0.5, 0.95, 0.2, 0.8)) {
   }
   return(invisible(NULL))
 }
+
+#' Check Report and Reference Dates are present
+#'
+#' @param obs An observation data frame containing \code{report_date} and
+#' \code{reference_date} columns.
+#'
+#' @return Returns the input data.frame with dates converted to date format
+#' if not already.
+#'
+#' @importFrom data.table as.data.table copy
+#' @family check
+check_dates <- function(obs) {
+  obs <- data.table::as.data.table(obs)
+  obs <- data.table::copy(obs)
+  if (is.null(obs$reference_date) && is.null(obs$report_date)) {
+    stop(
+      "Both reference_date and report_date must be present in order to use this
+      function"
+    )
+  } else if (is.null(obs$reference_date)) {
+    stop("reference_date must be present")
+  } else if (is.null(obs$report_date)) {
+    stop("report_date must be present")
+  }
+  obs[, report_date := as.IDate(report_date)]
+  obs[, reference_date := as.IDate(reference_date)]
+  return(obs[])
+}
+
+#' Check Observations for reserved grouping variables
+#'
+#' @param obs An observation data frame that does not contain `.group`,
+#' `.old_group`, or `.new_group` as these are reserved variables.
+#'
+#' @return NULL
+#'
+#' @family check
+check_group <- function(obs) {
+  if (!is.null(obs$.group)) {
+    stop(
+      ".group is a reserved variable and must not be present in the input
+       data"
+    )
+  } else if (!is.null(obs$.new_group)) {
+    stop(
+      ".new_group is a reserved variable and must not be present in the input
+       data"
+    )
+  } else if (!is.null(obs$.old_group)) {
+    stop(
+      ".old_group is a reserved variable and must not be present in the input
+       data"
+    )
+  }
+  return(invisible(NULL))
+}

R/epinowcast-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+#' @aliases epinowcast-package NULL
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/epinowcast.R

@@ -21,10 +21,10 @@
 #' @export
 epinowcast <- function(pobs,
                        reference_effects = epinowcast::enw_formula(
-                         pobs$metareference[[1]]
+                         ~1, pobs$metareference[[1]]
                        ),
                        report_effects = epinowcast::enw_formula(
-                         pobs$metareport[[1]]
+                         ~1, pobs$metareport[[1]]
                        ),
                        priors = epinowcast::enw_priors(),
                        distribution = "lognormal",