Hotfix

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "multimput: Using Multiple Imputation to Address Missing Data",
-  "version": "0.2.14",
+  "version": "0.2.15",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>Accompanying package for the paper: Working with population totals in the presence of missing data comparing imputation methods in terms of bias and precision. Published in 2017 in the Journal of Ornithology volume 158 page 603–615 (doi:10.1007/s10336-016-1404-9).<\/p>",

CITATION.cff

@@ -32,4 +32,4 @@ identifiers:
   value: 10.5281/zenodo.598331
 - type: url
   value: https://inbo.github.io/multimput/
-version: 0.2.14
+version: 0.2.15

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: multimput
 Title: Using Multiple Imputation to Address Missing Data
-Version: 0.2.14
+Version: 0.2.15
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),

NEWS.md

@@ -1,3 +1,7 @@
+# multimput 0.2.15
+
+* Bugfix in `hurdle_impute()` when selecting single covariates.
+
 # multimput 0.2.14
 
 * In case all imputed values are identical, `model_impute()` only runs a single

R/hurdle_impute.R

@@ -54,23 +54,31 @@
 
   # prepare covariates
   cv_count <- count@Data[
-    , !colnames(count@Data) %in% c(count@Response, count@Minimum)
+    , !colnames(count@Data) %in% c(count@Response, count@Minimum), drop = FALSE
   ]
   cv_presence <- presence@Data[
-    , !colnames(presence@Data) %in% c(presence@Response, presence@Minimum)
+    , !colnames(presence@Data) %in% c(presence@Response, presence@Minimum),
+    drop = FALSE
   ]
   common <- colnames(cv_count)[colnames(cv_count) %in% colnames(cv_presence)]
   common <- common[apply(cv_count[, common] == cv_presence[, common], 2, all)]
   extra_count <- colnames(cv_count)[!colnames(cv_count) %in% common]
   extra_presence <- colnames(cv_presence)[!colnames(cv_presence) %in% common]
-  ren_count <- cv_count[, extra_count[extra_count %in% extra_presence]]
+  ren_count <- cv_count[
+    , extra_count[extra_count %in% extra_presence], drop = FALSE
+  ]
   colnames(ren_count) <- sprintf("count_%s", colnames(ren_count))
-  ren_presence <- cv_presence[, extra_presence[extra_presence %in% extra_count]]
+  ren_presence <- cv_presence[
+    , extra_presence[extra_presence %in% extra_count], drop = FALSE
+  ]
   colnames(ren_presence) <- sprintf("presence_%s", colnames(ren_presence))
   cv <- cbind(
-    cv_count[, common],
-    cv_count[, extra_count[!extra_count %in% extra_presence]], ren_count,
-    cv_presence[, extra_presence[!extra_presence %in% extra_count]],
+    cv_count[, common, drop = FALSE],
+    cv_count[, extra_count[!extra_count %in% extra_presence], drop = FALSE],
+    ren_count,
+    cv_presence[
+      , extra_presence[!extra_presence %in% extra_count], drop = FALSE
+    ],
     ren_presence
   )
   if (nrow(count@Extra) == 0) {
@@ -80,11 +88,16 @@
       count@Extra[[count@Response]], nrow = nrow(count@Extra),
       ncol = ncol(count_resp)
     )
-    ren_count <- count@Extra[, extra_count[extra_count %in% extra_presence]]
+    ren_count <- count@Extra[
+      , extra_count[extra_count %in% extra_presence], drop = FALSE
+    ]
     colnames(ren_count) <- sprintf("count_%s", colnames(ren_count))
     cv_extra <- cbind(
-      count@Extra[, common],
-      count@Extra[, extra_count[!extra_count %in% extra_presence]], ren_count
+      count@Extra[, common, drop = FALSE],
+      count@Extra[
+        , extra_count[!extra_count %in% extra_presence], drop = FALSE
+      ],
+      ren_count
     )
     c(
       extra_presence[!extra_presence %in% extra_count],

R/impute_inla.R

@@ -108,10 +108,8 @@
           prob = hyperpar[[grep("zero-probability", colnames(hyperpar))]],
           size = hyperpar[[grep("size for nbinomial", colnames(hyperpar))]]
         ),
-        .f = function(n, eta, prob, size) {
-          rzinb0(
-            n = length(missing_obs), mu = exp(eta), prob = prob, size = size
-          )
+        .f = function(eta, prob, size, n = length(missing_obs)) {
+          rzinb0(mu = exp(pmin(eta, 20)), prob = prob, size = size, n = n)
         }
       ),
       zeroinflatednbinomial1 = pmap_dfr(
@@ -120,10 +118,8 @@
           prob = hyperpar[[grep("zero-probability", colnames(hyperpar))]],
           size = hyperpar[[grep("size for nbinomial", colnames(hyperpar))]]
         ),
-        .f = function(n, eta, prob, size) {
-          rzinb1(
-            n = length(missing_obs), mu = exp(eta), prob = prob, size = size
-          )
+        .f = function(eta, prob, size, n = length(missing_obs)) {
+          rzinb1(mu = exp(eta), prob = prob, size = size, n = n)
         }
       ),
       zeroinflatedpoisson0 = map2_dfr(

inst/CITATION

@@ -2,12 +2,12 @@ citHeader("To cite `multimput` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.14",
+  title = "multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.15",
   author = c( author = c(person(given = "Thierry", family = "Onkelinx"), person(given = "Koen", family = "Devos"), person(given = "Paul", family = "Quataert"))),
-  year = 2024,
+  year = 2025,
   url = "https://inbo.github.io/multimput/",
   abstract = "Accompanying package for the paper: Working with population totals in the presence of missing data comparing imputation methods in terms of bias and precision. Published in 2017 in the Journal of Ornithology volume 158 page 603–615 (doi:10.1007/s10336-016-1404-9).",
-  textVersion = "Onkelinx, Thierry; Devos, Koen; Quataert, Paul (2024) multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.14. https://inbo.github.io/multimput/",
+  textVersion = "Onkelinx, Thierry; Devos, Koen; Quataert, Paul (2025) multimput: Using Multiple Imputation to Address Missing Data. Version 0.2.15. https://inbo.github.io/multimput/",
   keywords = "missing data, multiple imputation, Rubin",
   doi = "10.5281/zenodo.598331",
 )

multimput.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 67edd119-a857-4812-acf7-b7a36277956a
 
 RestoreWorkspace: Default
 SaveWorkspace: Default