Minor changes to Taxonomic Backbone

code/03_TaxonomicBackbone.Rmd

@@ -69,7 +69,6 @@ DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species_test.csv",
                                 x_ = col_double()
                               )
                          ) 
-
 ```
 Create list of species, and exclude fungi
 ```{r eval=T, echo=F}
@@ -167,8 +166,16 @@ knitr::kable(spec.list.TRY.sPlot %>%
 Stripping unwanted characters as well as abbreviation (such as hybrid markers) which would prevent name matching:
 
 ```{r}
+#Ancillary function to change to lower case
+firstup <- function(x) {
+  substr(x, 1, 1) <- toupper(substr(x, 1, 1))
+  x
+}
+
 spec.list.TRY.sPlot <- spec.list.TRY.sPlot %>%
   mutate(OriginalNames=Species) %>%
+  mutate(Species=tolower(Species)) %>%
+  mutate(Species=firstup(Species)) %>%
   dplyr::select(OriginalNames, Species, Source) %>%
   mutate(Species=gsub('*', '', Species, fixed=TRUE)) %>%
   mutate(Species=gsub('cf. ', '', Species, fixed=TRUE)) %>%
@@ -433,11 +440,6 @@ save(tnrs.res.certain, tnrs.res.uncertain, file="../_derived/TNRS_submit/tnrs.it
 ### Manual cleaning, delete subspecies information and rerun match in TNRS
 Many unmatched records do contain subspecies information which could not be retrieved in TNRS, although genus and species seem to be spelled correctly. Also, sometimes the mismatch derives from having the word 'species' or 'sp' at the end of the name. 
 ```{r}
-#Ancillary function to change to lower case
-firstup <- function(x) {
-  substr(x, 1, 1) <- toupper(substr(x, 1, 1))
-  x
-}
 #Manual cleaning
 tnrs.submit.iter2 <- data.frame(old=tnrs.res.uncertain$Name_submitted) %>%
   mutate(new=old) %>%