import INLA instead of suggesting it

DESCRIPTION

@@ -25,6 +25,7 @@ Imports:
     assertthat,
     digest,
     dplyr,
+    INLA (>= 22.01.19),
     lme4,
     methods,
     mvtnorm,
@@ -35,7 +36,6 @@ Imports:
     tidyselect
 Suggests:
     ggplot2,
-    INLA (>= 22.01.19),
     knitr,
     MASS,
     mgcv,

NAMESPACE

@@ -12,7 +12,10 @@ exportClasses(rawImputed)
 exportMethods(aggregate_impute)
 exportMethods(impute)
 exportMethods(model_impute)
+importClassesFrom(INLA,inla)
 importClassesFrom(lme4,glmerMod)
+importFrom(INLA,inla.hyperpar.sample)
+importFrom(INLA,inla.posterior.sample)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_name)
 importFrom(assertthat,is.count)
@@ -43,7 +46,6 @@ importFrom(methods,setClassUnion)
 importFrom(methods,setGeneric)
 importFrom(methods,setIs)
 importFrom(methods,setMethod)
-importFrom(methods,setOldClass)
 importFrom(methods,setValidity)
 importFrom(methods,validObject)
 importFrom(mvtnorm,rmvnorm)

R/import_s3_classes.R

@@ -1,6 +1,3 @@
-#' @importFrom methods setOldClass
-setOldClass("inla")
-
 #' The `maybeInla` class
 #'
 #' A superclass holding either `NULL` or an object of the `inla` class.
@@ -9,6 +6,7 @@ setOldClass("inla")
 setClassUnion("maybeInla", "NULL")
 
 #' @importFrom methods getClassDef setIs
+#' @importClassesFrom INLA inla
 .onLoad <- function(...) {
   if (requireNamespace("INLA", quietly = TRUE)) {
     setIs("inla", "maybeInla", classDef = getClassDef("inla", package = "INLA"))

R/impute_inla.R

@@ -1,6 +1,7 @@
 #' @rdname impute
 #' @importFrom assertthat assert_that is.count
 #' @importFrom dplyr coalesce
+#' @importFrom INLA inla.hyperpar.sample inla.posterior.sample
 #' @importFrom methods new setMethod
 #' @importFrom purrr map map_dfr map2_dfr pmap_dfr
 #' @importFrom stats plogis qpois rgamma rnorm rpois setNames
@@ -59,16 +60,15 @@ setMethod(
 
     ifelse(is.null(model$model.spde2.blc), "Predictor:%i", "APredictor:%i") |>
       sprintf(missing_obs) -> missing_obs
-    assert_that(requireNamespace("INLA", quietly = TRUE))
     assert_that(requireNamespace("sn", quietly = TRUE))
-    samples <- INLA::inla.posterior.sample(
+    samples <- inla.posterior.sample(
       n = n_imp, result = model, seed = seed, num.threads = num_threads,
       parallel.configs = parallel_configs
     )
     map(samples, "latent") |>
       map(`[`, missing_obs, 1) |>
       setNames(paste0("sim_", seq_len(n_imp))) -> latent
-    INLA::inla.hyperpar.sample(n = n_imp, result = model) |>
+    inla.hyperpar.sample(n = n_imp, result = model) |>
       as.data.frame() -> hyperpar
     if (
       model$.args$family == "zeroinflatednbinomial0" &&

checklist.yml

@@ -1,19 +1,19 @@
 description: Configuration file for checklist::check_pkg()
 package: yes
 allowed:
-  warnings: []
-  notes:
-  - motivation: INLA not on CRAN
+  warnings:
+  - motivation: INLA is required and not available on CRAN.
     value: |-
-      checking CRAN incoming feasibility ... NOTE
+      checking CRAN incoming feasibility ... WARNING
       Maintainer: 'Thierry Onkelinx <thierry.onkelinx@inbo.be>'
 
       New submission
 
-      Suggests or Enhances not in mainstream repositories:
+      Strong dependencies not in mainstream repositories:
         INLA
       Availability using Additional_repositories specification:
         INLA   yes   https://inla.r-inla-download.org/R/stable
+  notes: []
 required:
 - CITATION
 - DESCRIPTION
@@ -22,6 +22,7 @@ required:
 - codemeta
 - documentation
 - filename conventions
+- folder conventions
 - license
 - lintr
 - repository secret