dplyr 1.0.0 compatibility updates (#146)

* Using packrat * Roxygen update * Update drop_na_rows implementation for data.frame * src_sqlite is deprecated * New expect_that behavior * New expect that behavior * rebuild docs * rebuild docs * styler * remove names * Coerce to data.frame
cytomining · May 9, 2020 · de4b433 · de4b433
1 parent c563f85
commit de4b433
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Showing 46 changed files with 171 additions and 93 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,5 @@
 ^LICENSE.md$
 ^CONTRIBUTING.md$
 ^CRAN-RELEASE$
+^packrat/
+^\.Rprofile$
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,6 @@
 .Rhistory
 .RData
 inst/doc
+packrat/lib*/
+packrat
+.Rprofile
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -46,4 +46,4 @@ Suggests:
 VignetteBuilder: knitr
 URL: https://github.com/cytomining/cytominer
 BugReports: https://github.com/cytomining/cytominer/issues
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
diff --git a/R/drop_na_rows.R b/R/drop_na_rows.R
@@ -1,12 +1,12 @@
-utils::globalVariables(c("key", "value", "rowname_temp", "coalesce"))
-#' Drop rows that are \code{NA} in all variables.
+utils::globalVariables(c("key", "value", "rowname_temp", "rowid", "coalesce"))
+#' Drop rows that are \code{NA} in all specified variables.
 #'
-#' \code{drop_na_rows} drops rows that are \code{NA} in all variables.
+#' \code{drop_na_rows} drops rows that are \code{NA} in all specified variables.
 #'
 #' @param population tbl with grouping (metadata) and observation variables.
 #' @param variables character vector specifying observation variables.
 #'
-#' @return \code{population} without rows that have \code{NA} in all variables.
+#' @return \code{population} without rows that have \code{NA} in all specified variables.
 #'
 #' @examples
 #' population <- tibble::tibble(
@@ -26,11 +26,12 @@ utils::globalVariables(c("key", "value", "rowname_temp", "coalesce"))
 drop_na_rows <- function(population, variables) {
   if (is.data.frame(population)) {
     population %>%
-      tibble::rownames_to_column(., var = "rowname_temp") %>%
-      tidyr::gather(key, value, variables) %>%
+      tibble::rowid_to_column() %>%
+      tidyr::pivot_longer(variables) %>%
       dplyr::filter(!is.na(value)) %>%
-      tidyr::spread(key, value) %>%
-      dplyr::select(-rowname_temp)
+      tidyr::pivot_wider(names_from = "name", values_from = "value") %>%
+      dplyr::select(-rowid) %>%
+      dplyr::select(names(population))
   } else {
 
     # Coalesce() must have at least 2 arguments.

diff --git a/R/extract_subpopulations.R b/R/extract_subpopulations.R
@@ -70,7 +70,7 @@ extract_subpopulations <-
         as.matrix())[1, 2]
     }
 
-    data %<>% dplyr::mutate(cluster_id = kmeans_output$cluster)
+    data %<>% dplyr::mutate(cluster_id = unname(kmeans_output$cluster))
     data %<>%
       dplyr::bind_cols(
         purrr::map_df(

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/cytominer-pipeline.html b/docs/articles/cytominer-pipeline.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,7 +1,7 @@
 pandoc: 2.9.2.1
-pkgdown: 1.5.1
+pkgdown: 1.5.0
 pkgdown_sha: ~
 articles:
   cytominer-pipeline: cytominer-pipeline.html
-last_built: 2020-04-29T02:38Z
+last_built: 2020-05-08T23:08Z
 
diff --git a/docs/reference/aggregate.html b/docs/reference/aggregate.html
diff --git a/docs/reference/correlation_threshold.html b/docs/reference/correlation_threshold.html
diff --git a/docs/reference/count_na_rows.html b/docs/reference/count_na_rows.html
diff --git a/docs/reference/covariance.html b/docs/reference/covariance.html
diff --git a/docs/reference/drop_na_columns.html b/docs/reference/drop_na_columns.html
diff --git a/docs/reference/drop_na_rows.html b/docs/reference/drop_na_rows.html
diff --git a/docs/reference/extract_subpopulations.html b/docs/reference/extract_subpopulations.html
diff --git a/docs/reference/generalized_log.html b/docs/reference/generalized_log.html
diff --git a/docs/reference/generate_component_matrix.html b/docs/reference/generate_component_matrix.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/normalize.html b/docs/reference/normalize.html