Merge pull request #41 from inbo/0.2.11

0.2.11

.github/workflows/check_on_different_r_os.yml

@@ -64,6 +64,7 @@ jobs:
           Rscript -e "remotes::install_github('r-hub/sysreqs')"
           sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
           sudo -s eval "$sysreqs"
+          sudo apt-get install -y libcurl4-openssl-dev
 
       - name: Install dependencies
         run: |

.zenodo.json

@@ -1,7 +1,7 @@
 {
   "title": "multimput: Using Multiple Imputation to Address Missing Data",
-  "version": "0.2.10",
-  "description": "Accompaning package for the paper: \"Working with population totals in the presence of with missing data\".",
+  "version": "0.2.11",
+  "description": "Accompanying package for the paper: \"Working with population totals in the presence of with missing data\".",
   "creators": [
     {
       "name": "Onkelinx, Thierry",
@@ -34,5 +34,6 @@
       "type": "ContactPerson",
       "orcid": "https://orcid.org/0000-0001-8804-4216"
     }
-  ]
+  ],
+  "language": "eng"
 }

CITATION.cff

@@ -17,11 +17,13 @@ contact:
 - email: [email protected]
   name: Research Institute for Nature and Forest
 title: 'multimput: Using Multiple Imputation to Address Missing Data'
-version: 0.2.10
-abstract: 'Accompaning package for the paper: "Working with population totals in the
-  presence of with missing data".'
+version: 0.2.11
+abstract: 'Accompanying package for the paper: "Working with population totals in
+  the presence of with missing data".'
 license: GPL-3.0
 type: software
 doi: 10.5281/zenodo.598331
 repository-code: https://github.com/inbo/multimput
-identifiers: []
+identifiers:
+- type: url
+  value: https://inbo.github.io/multimput/

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: multimput
 Title: Using Multiple Imputation to Address Missing Data
-Version: 0.2.10
+Version: 0.2.11
 Authors@R: c(
     person("Thierry", "Onkelinx", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216")),
@@ -11,11 +11,11 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-6894-9402")),
     person("Research Institute for Nature and Forest", , , "[email protected]", role = c("cph", "fnd"))
   )
-Description: Accompaning package for the paper: "Working with population
+Description: Accompanying package for the paper: "Working with population
     totals in the presence of with missing data".
 License: GPL-3
 URL: https://doi.org/10.5281/zenodo.598331,
-    https://github.com/inbo/multimput
+    https://github.com/inbo/multimput, https://inbo.github.io/multimput/
 BugReports: https://github.com/inbo/multimput/issues
 Depends:
     R (>= 3.0.0)
@@ -41,8 +41,9 @@ Suggests:
     testthat
 VignetteBuilder: 
     knitr
-Additional_repositories: https://inla.r-inla-download.org/R/testing
+Additional_repositories: https://inla.r-inla-download.org/R/stable
 Encoding: UTF-8
+Language: en-GB
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.2

NAMESPACE

@@ -11,7 +11,7 @@ export(missing_current_count)
 export(missing_observed)
 export(missing_volunteer)
 exportClasses(aggregatedImputed)
-exportClasses(inla)
+exportClasses(maybeInla)
 exportClasses(rawImputed)
 exportMethods(aggregate_impute)
 exportMethods(impute)
@@ -39,9 +39,12 @@ importFrom(dplyr,summarise_at)
 importFrom(dplyr,transmute)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
+importFrom(methods,getClassDef)
 importFrom(methods,new)
 importFrom(methods,setClass)
+importFrom(methods,setClassUnion)
 importFrom(methods,setGeneric)
+importFrom(methods,setIs)
 importFrom(methods,setMethod)
 importFrom(methods,setOldClass)
 importFrom(methods,setValidity)

NEWS.md

@@ -1,3 +1,8 @@
+# multimput 0.2.11
+
+* Vignette runs without INLA.
+  Required to make the package build on https://inbo.r-universe.dev
+
 # multimput 0.2.10
 
 * Use checklist infrastructure. 

R/aggregate_impute.R

@@ -1,5 +1,5 @@
 #' Aggregate an imputed dataset
-#' @param object A rawImputed object.
+#' @param object A `rawImputed` object.
 #' @param grouping A vector of variables names to group the aggregation on.
 #' @param fun The function to aggregate.
 #' @param filter

R/aggregated_imputed_class.R

@@ -1,9 +1,9 @@
-#' The aggregatedImputed class
+#' The `aggregatedImputed` class
 #' Holds an aggregated imputation data set
 #' @section Slots:
 #'   \describe{
 #'    \item{`Covariate`}{A data.frame with the covariates.}
-#'    \item{`Imputation`}{A matrix wih aggregated imputed values.}
+#'    \item{`Imputation`}{A matrix with aggregated imputed values.}
 #'   }
 #' @name aggregatedImputed-class
 #' @rdname aggregatedImputed-class

R/generate_data.R

@@ -1,6 +1,6 @@
 #' Generate simulated data
 #'
-#' Generate data for a regural monitoring design.
+#' Generate data for a regular monitoring design.
 #' The counts follow a negative binomial distribution with given size parameters
 #' and the true mean mu depending on a year, period and site effect.
 #' All effects are independent from each other and have, on the log-scale, a
@@ -15,7 +15,7 @@
 #' Defaults to `FALSE`.
 #' @param site_factor Convert site to a factor.
 #' Defaults to `FALSE`.
-#' @param trend The longterm linear trend on the log-scale.
+#' @param trend The long-term linear trend on the log-scale.
 #' @param sd_rw_year The standard deviation of the year effects on the
 #' log-scale.
 #' @param amplitude_period The amplitude of the periodic effect on the

R/import_s3_classes.R

@@ -1,8 +1,16 @@
-#' inla
-#'
-#' the inla class is defined in the INLA package
-#' @name inla-class
-#' @seealso \link[INLA]{inla}
 #' @importFrom methods setOldClass
-#' @exportClass inla
 setOldClass("inla")
+
+#' The `maybeInla` class
+#'
+#' A superclass holding either `NULL` or an object of the `inla` class.
+#' @importFrom methods setClassUnion
+#' @exportClass maybeInla
+setClassUnion("maybeInla", "NULL")
+
+#' @importFrom methods getClassDef setIs
+.onLoad <- function(...) {
+  if (requireNamespace("INLA", quietly = TRUE)) {
+    setIs("inla", "maybeInla", classDef = getClassDef("inla", package = "INLA"))
+  }
+}

R/impute_inla.R

@@ -23,11 +23,12 @@
 #' using `B:0` threads.
 setMethod(
   f = "impute",
-  signature = signature(model = "inla"),
+  signature = signature(model = "maybeInla"),
   definition = function(
     model, ..., seed = 0L, num_threads = NULL, parallel_configs = TRUE,
     n_imp = 19
   ) {
+    assert_that(!is.null(model), msg = "model should be an inla object")
     check_old_names(..., old_names = c(n_imp = "n.imp"))
     assert_that(is.count(n_imp))
     assert_that(
@@ -85,7 +86,7 @@ setMethod(
         .y = hyperpar[[grep("size for the nbinomial", colnames(hyperpar))]]
       ),
       poisson = map_dfr(
-        .x = latent, .f = rpois, n = length(missing_obs)
+        .x = latent, .f = ~rpois(n = length(missing_obs), lambda = exp(.x))
       ),
       stop(
         "Imputations from the '", model$.args$family, "' family not yet defined.

R/raw_imputed_class.R

@@ -1,12 +1,12 @@
-#' The rawimputed class
+#' The `rawImputed` class
 #' Holds a dataset and imputed values
 #' @section Slots:
 #'   \describe{
 #'    \item{`Data`}{A data.frame with the data.}
 #'    \item{`Response`}{A character holding the name of the response variable.}
 #'    \item{`Minimum`}{An optional character holding the name of the variable
 #'    with the minimum.}
-#'    \item{`Imputation`}{A matrix wih imputed values.}
+#'    \item{`Imputation`}{A matrix with imputed values.}
 #'   }
 #' @name rawImputed-class
 #' @rdname rawImputed-class

README.md

@@ -1,5 +1,5 @@
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing-1)
+[![Life cycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing-1)
 [![License](http://img.shields.io/badge/license-GPL--3-blue.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)
 [![Release](https://img.shields.io/github/release/qubyte/rubidium.svg)](https://github.com/inbo/multimput/releases)
 [![check package](https://github.com/inbo/multimput/actions/workflows/check_on_branch.yml/badge.svg)](https://github.com/inbo/multimput/actions/workflows/check_on_branch.yml)
@@ -15,7 +15,7 @@
 ## Rationale
 
 The `multimput` package was originally intended to provide the data and code to replicate the results of Onkelinx, Devos, and Quataert (2016). 
-This paper is freely available at <http://dx.doi.org/10.1007/s10336-016-1404-9>. 
+This paper is freely available at http://dx.doi.org/10.1007/s10336-016-1404-9. 
 The functions were all rewritten to make them more user-friendly and more generic. 
 In order to make the package more compact, we removed the original code and data starting for version 0.2.6. 
 However both the original code and data remain available in [the older releases](https://github.com/inbo/multimput/releases).
@@ -30,13 +30,13 @@ This package requires the `INLA` package.
 You need to install it with `install.packages("INLA", repos = "https://inla.r-inla-download.org/R/stable")`. 
 If this fails you can use `remotes::install_github("inbo/INLA")`. 
 Note that the latter is just a read-only mirror which is infrequently updated. 
-Hence installing `INLA` from <https://inla.r-inla-download.org> is highly recommended.
+Hence installing `INLA` from https://inla.r-inla-download.org is highly recommended.
 
 Once `INLA` is installed, you can install `multimput` using the `remotes` package: `remotes::install_github("inbo/multimput", build_vignettes = TRUE)`). 
 To view the vignette use `vignette("Impute", package = "multimput")`. 
 The vignette is also available at https://inbo.github.io/multimput/articles/impute.html
 
-A docker image with all the required dependencies is available from <https://hub.docker.com/r/inbobmk/multimput/>.
+A docker image with all the required dependencies is available from https://hub.docker.com/r/inbobmk/multimput/.
 Use `docker pull inbobmk/multimput` to get it.
 
 ## Folder structure

checklist.yml

@@ -13,7 +13,7 @@ allowed:
       Suggests or Enhances not in mainstream repositories:
         INLA
       Availability using Additional_repositories specification:
-        INLA   yes   https://inla.r-inla-download.org/R/testing
+        INLA   yes   https://inla.r-inla-download.org/R/stable
 citation_roles:
 - aut
 - cre

inst/CITATION

@@ -2,12 +2,12 @@ citHeader("To cite `multimput` in publications please use:")
 # begin checklist entry
 citEntry(
   entry = "Manual",
-  title = "multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.10",
+  title = "multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.11",
   author = c(person(given = "Thierry", family = "Onkelinx"), person(given = "Koen", family = "Devos"), person(given = "Paul", family = "Quataert")),
   year = 2022,
   url = "https://doi.org/10.5281/zenodo.598331",
-  abstract = "Accompaning package for the paper: \"Working with population totals in the presence of with missing data\".",
-  textVersion = "Onkelinx, Thierry; Devos, Koen; Quataert, Paul (2022) multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.10. https://doi.org/10.5281/zenodo.598331, https://github.com/inbo/multimput",
+  abstract = "Accompanying package for the paper: \"Working with population totals in the presence of with missing data\".",
+  textVersion = "Onkelinx, Thierry; Devos, Koen; Quataert, Paul (2022) multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.11. https://doi.org/10.5281/zenodo.598331, https://github.com/inbo/multimput, https://inbo.github.io/multimput/",
   doi = "10.5281/zenodo.598331",
 )
 # end checklist entry

inst/WORDLIST

@@ -0,0 +1,2 @@
+Codecov
+INLA

multimput.Rproj

@@ -17,6 +17,7 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
+PackageCleanBeforeInstall: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace