Minor fixes to Backbone

code/03_TaxonomicBackbone.Rmd

@@ -51,7 +51,7 @@ library(vegdata)
 ## Read in taxon names from [sPlot](https://www.idiv.de/sdiv/working_groups/wg_pool/splot/splot_database.html) and [TRY](https://www.try-db.org/TryWeb/Home.php)
 
 
-```{r}
+```{r eval=F}
 #import and save splot names from DT table
 DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species_test.csv", 
                             delim="\t", 
@@ -72,7 +72,7 @@ DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species_test.csv",
 
 ```
 Create list of species, and exclude fungi
-```{r}
+```{r eval=T, echo=F}
 ## fungi genera #NOT COMPLETE LIST
 mushroom <- c("Mycena", "Boletus", "Russula","Calocybe","Collybia","Amanita","Amanitopsis","Coprinus",
   "Galerina","Geoglossum","Hebeloma","Hydnum","Lactarius","Leucocarpia","Naucoria","Otidea","Polyporus", 
@@ -87,7 +87,9 @@ mushroom <- c("Mycena", "Boletus", "Russula","Calocybe","Collybia","Amanita","Am
   "Multiclavula","Phaeocollybia","Phellinus","Plectocarpon","Pleospora","Ramariopsis","Reinkella",
   "Roccella","Roccellina","Sigridea","Stereum","Tremella","Tulostoma","Unguiculariopsis" ,
   "Xanthoconium")
+```
 
+```{r eval=F}
 splot.species <- DT0 %>%
   rename(Species.original=`Turboveg2 concept`, Matched.concept=`Matched concept`) %>%
   filter(`Taxon group`!="Mushroom") %>%
@@ -1456,6 +1458,8 @@ Backbone <- Backbone %>%
       dplyr::select(genus, family) %>% 
       distinct() %>% 
       filter(family != "") %>% 
+      group_by(genus) %>%  #There are two genera with multiple attribution to families
+      slice(1) %>% 
       filter(genus %in% Genera_missing$Genus_correct) %>% 
       rename(Genus_correct=genus), 
     by="Genus_correct") %>% 

code/04_buildHeader.Rmd

@@ -12,13 +12,10 @@ output: html_document
 </center>
 
   
-    
-      
-        
 **Timestamp:** `r date()`  
 **Drafted:** Francesco Maria Sabatini  
 **Revised:**  
-**version:**
+**version:** 1.0
 
 This report documents the construction of the header file for sPlot 3.0. It is based on dataset sPlot_3.0.2, received on 24/07/2019 from Stephan Hennekens.