Merge pull request #33 from inbo/dplyr-update

Dplyr update
inbo · Jul 13, 2017 · d32a889 · d32a889
2 parents 65263e9 + 5327b5a
commit d32a889
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Showing 16 changed files with 34 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,24 +1,24 @@
 Package: multimput
 Type: Package
 Title: Using Multiple Imputation to Address Missing Data
-Version: 0.2.6
-Date: 2017-01-20
+Version: 0.2.7
+Date: 2017-07-13
 Authors@R: c(person("Thierry", "Onkelinx", role = c("aut", "cre"), email = "thierry.onkelinx@inbo.be"),
   person("Koen", "Devos", role = "aut"),
   person("Paul", "Quataert", role = "aut"))
 Description: Accompaning package for the paper: "Working with population totals
     in the presence of with missing data".
 License: GPL-3 | file LICENSE
-URL: http://dx.doi.org/10.5281/zenodo.48423
+URL: https://doi.org/10.5281/zenodo.598331
+BugReports: https://github.com/inbo/multimput/issues
 Depends:
-    dplyr,
     R (>= 3.0.0)
 Imports:
+    dplyr,
     methods,
     tibble,
     tidyr,
     assertthat,
-    MASS,
     lme4,
     mvtnorm,
     digest
@@ -29,11 +29,12 @@ Suggests:
     ggplot2,
     mgcv,
     knitr,
-    plyr,
+    MASS,
     rmarkdown
+Remotes: inbo/INLA
 Roxygen: list(wrap = FALSE)
 LazyData: TRUE
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
 Collate:
     'rawImputed_class.R'
     'aggregate_impute.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,7 +11,6 @@ exportClasses(rawImputed)
 exportMethods(aggregate_impute)
 exportMethods(impute)
 exportMethods(model_impute)
-import(dplyr)
 importClassesFrom(lme4,glmerMod)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_name)
@@ -28,17 +27,20 @@ importFrom(dplyr,mutate_)
 importFrom(dplyr,n)
 importFrom(dplyr,select_)
 importFrom(dplyr,semi_join)
+importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise_)
-importFrom(dplyr,summarise_each_)
+importFrom(dplyr,summarise_at)
 importFrom(dplyr,transmute_)
 importFrom(dplyr,ungroup)
+importFrom(dplyr,vars)
 importFrom(methods,new)
 importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,setOldClass)
 importFrom(methods,setValidity)
 importFrom(mvtnorm,rmvnorm)
+importFrom(stats,aggregate)
 importFrom(stats,as.formula)
 importFrom(stats,model.matrix)
 importFrom(stats,na.omit)

diff --git a/R/aggregate_impute.R b/R/aggregate_impute.R
@@ -30,8 +30,7 @@ setMethod(
 #' @importFrom methods setMethod
 #' @importFrom assertthat assert_that
 #' @importFrom tidyr spread_
-#' @import dplyr
-#' @importFrom dplyr %>% group_by_ summarise_each_ funs mutate_ bind_rows ungroup select_ filter_ n semi_join
+#' @importFrom dplyr %>% group_by_ summarise_at funs vars mutate_ bind_rows ungroup select_ filter_ n semi_join starts_with
 #' @importFrom methods new
 #' @importFrom stats setNames na.omit
 #' @importFrom digest sha1
@@ -110,7 +109,7 @@ setMethod(
         )
         data %>%
           group_by_(.dots = grouping) %>%
-          summarise_each_(funs = funs(fun), vars = response) %>%
+          summarise_at(.funs = funs(fun), .vars = vars(response)) %>%
           mutate_(Imputation = ~sprintf("Imputation%04i", i))
       }
     ) %>%

diff --git a/R/import_S3_classes.R b/R/import_S3_classes.R
@@ -1,3 +1,8 @@
+#' inla
+#'
+#' the inla class is defined in the INLA package
+#' @name inla-class
+#' @seealso \link[INLA]{inla}
 #' @importFrom methods setOldClass
 #' @exportClass inla
 setOldClass("inla")
diff --git a/man/aggregate_impute.Rd b/man/aggregate_impute.Rd
diff --git a/man/generateData.Rd b/man/generateData.Rd
diff --git a/man/impute.Rd b/man/impute.Rd
diff --git a/man/inla-class.Rd b/man/inla-class.Rd
diff --git a/man/missingAtRandom.Rd b/man/missingAtRandom.Rd
diff --git a/man/missingCurrentCount.Rd b/man/missingCurrentCount.Rd
diff --git a/man/missingObserved.Rd b/man/missingObserved.Rd
diff --git a/man/missingVolunteer.Rd b/man/missingVolunteer.Rd
diff --git a/man/model_impute.Rd b/man/model_impute.Rd
diff --git a/man/waterfowl.Rd b/man/waterfowl.Rd
diff --git a/tests/testthat/test_bbb_aggregate_impute.R b/tests/testthat/test_bbb_aggregate_impute.R
@@ -108,7 +108,7 @@ describe("aggregate_impute", {
     )
     expect_error(
       aggregate_impute(imputed, grouping = "junk", fun = sum),
-      "unknown.*junk"
+      "((junk){1}.*(unknown){1}|(unknown){1}.*(junk){1})"
     )
     expect_error(
       aggregate_impute(imputed, grouping = imputed),

diff --git a/vignettes/child/details.Rmd b/vignettes/child/details.Rmd
@@ -317,6 +317,7 @@ model.better <- model_impute(
 )
 model.complete <- extractor.logindex(model.complete)
 colnames(model.complete) <- c("Estimate", "SE")
+library(dplyr)
 model.complete <- model.complete %>%
   as.data.frame() %>%
   mutate(