fix various tidyverse warnings

jasenfinch · Sep 12, 2023 · d5b7e56 · d5b7e56
1 parent fb1fb61
commit d5b7e56
Showing 5 changed files with 13 additions and 10 deletions.
diff --git a/R/modelling-plots.R b/R/modelling-plots.R
@@ -457,7 +457,7 @@ setMethod('plotMDS',
                 mds_dimensions <- mds_dimensions %>%
                   bind_cols(x %>%
                               sinfo() %>%
-                              select(label))
+                              select(all_of(label)))
               }
             }
 

diff --git a/R/occupancy.R b/R/occupancy.R
@@ -164,7 +164,10 @@ setMethod('occupancy',signature = 'AnalysisData',
               full_join(clsSize %>%
                           select(Class,Frequency) %>%
                           rename(!!cls := Class) %>%
-                          mutate(dummy = 1),by = 'dummy') %>%
+                          mutate(dummy = 1),
+                        by = 'dummy',
+                        relationship = "many-to-many"
+                        ) %>%
               select(!!cls,Feature,N,`Class total` = Frequency,Occupancy) %>% 
               drop_na(Feature)
             occ <- occ %>%

diff --git a/R/plotFeature.R b/R/plotFeature.R
@@ -58,7 +58,7 @@ setMethod('plotFeature',
             i <- sinfo(analysis)
 
             i <- i %>%
-              select(!!cls,Label = label)
+              select(!!cls,Label = !!label)
 
             if (!is.null(label)) {
               d <- d %>%

diff --git a/R/randomForest-classification.R b/R/randomForest-classification.R
@@ -28,7 +28,7 @@ classificationMetrics <- function(model){
   }
 
   roc <- predictions %>% 
-    roc_auc(obs,estimate)
+    roc_auc(obs,all_of(estimate))
 
   bind_rows(
     acc_kap,

diff --git a/R/univariate.R b/R/univariate.R
@@ -86,14 +86,14 @@ setMethod('anova',signature = 'AnalysisData',
                     pc <- str_split(.x,'~')[[1]]
 
                     pad <- removeClasses(x,pred,classes = sinfo(x) %>%
-                                           select(pred) %>%
+                                           select(all_of(pred)) %>%
                                            unlist() %>%
                                            unique() %>%
                                            .[!(. %in% pc)])
 
                     response <- pad %>%
                       sinfo() %>%
-                      select(pred) %>%
+                      select(all_of(pred)) %>%
                       unlist() %>%
                       factor()
 
@@ -197,14 +197,14 @@ setMethod('ttest',signature = 'AnalysisData',
                     pc <- str_split(.x,'~')[[1]]
 
                     pad <- removeClasses(x,pred,classes = sinfo(x) %>%
-                                           select(pred) %>%
+                                           select(all_of(pred)) %>%
                                            unlist() %>%
                                            unique() %>%
                                            .[!(. %in% pc)])
 
                     response <- pad %>%
                       sinfo() %>%
-                      select(pred) %>%
+                      select(all_of(pred)) %>%
                       unlist() %>%
                       factor()
 
@@ -282,7 +282,7 @@ setMethod('linearRegression',signature = 'AnalysisData',
                    returnModels = FALSE){
             indep <- x %>%
               sinfo() %>%
-              select(cls)
+              select(all_of(cls))
 
             if (FALSE %in% 
                 (map_chr(indep,class) %in% c('integer','numeric'))) {
@@ -299,7 +299,7 @@ setMethod('linearRegression',signature = 'AnalysisData',
                 i <- .
 
                 pred <- indep %>%
-                  select(i) %>%
+                  select(all_of(i)) %>%
                   unlist()
 
                 d %>%