Patch the data objects and the script producing them to take into acount the row names

data-raw/data.prep.R

 bacteria = read.csv('data-raw/bacteria.csv',
                           header = TRUE,
+                          row.names = 1,
                           na.strings = 'NA')
 
 eukaryotes = read.csv('data-raw/eukaryotes.csv',
                     header = TRUE,
+                    row.names = 1,
                     na.strings = 'NA')
 
 climat = read.csv('data-raw/climat.csv',
                     header = TRUE,
+                    row.names = 1,
                     na.strings = 'NA')
 
 soil = read.csv('data-raw/soil.csv',
-                  header = TRUE,
-                  na.strings = 'NA')
+                 header = TRUE,
+                 row.names = 1,
+                 na.strings = 'NA')
 
 geography = read.csv('data-raw/geography.csv',
                   header = TRUE,
+                  row.names = 1,
                   na.strings = 'NA')
 
-devtools::use_data(bacteria)
-devtools::use_data(eukaryotes)
-devtools::use_data(climat)
-devtools::use_data(soil)
-devtools::use_data(geography)
+devtools::use_data(bacteria,overwrite = TRUE)
+devtools::use_data(eukaryotes,overwrite = TRUE)
+devtools::use_data(climat,overwrite = TRUE)
+devtools::use_data(soil,overwrite = TRUE)
+devtools::use_data(geography,overwrite = TRUE)