06_builDT - added calculation of relative cover

code/06_buildDT.Rmd

@@ -229,7 +229,7 @@ conflict <- DT1 %>%
 
 Delete all records of fungi
 ```{r}
-DT1f <- DT1 %>% 
+DT1 <- DT1 %>% 
   dplyr::select(-Genus) %>% 
   left_join(DT1 %>% 
               distinct(`Matched concept`) %>% 
@@ -251,12 +251,12 @@ DT1f <- DT1 %>%
   filter(`Taxon group`!="Mushroom")# %>% 
   #dplyr::select(-Genus)
 
-table(DT1f$`Taxon group`, exclude=NULL)
+table(DT1$`Taxon group`, exclude=NULL)
 ```
 
 Check the most frequent species for which we don't have taxon group info
 ```{r, echo=F, eval=F}
-DT1f %>% 
+DT1 %>% 
   filter(`Taxon group` == "Unknown") %>% 
   group_by(Genus) %>% 
   summarize(n=n()) %>% 
@@ -264,15 +264,33 @@ DT1f %>%
     slice(1:40)
 ```
 
-Clean DT and export
+Calculate relative cover per layer per species in each plot
+```{r}
+DT1 <- DT1 %>% 
+  mutate(tmp.cover=ifelse(`Cover code` %in% c("x_BA", "x_IC", "x_SC", "x_IV", "x_RF"), 
+                          x_, `Cover %`)) %>% 
+  left_join(x=., 
+            y={.} %>%
+              group_by(PlotObservationID, Layer) %>% 
+              summarize(tot.cover=sum(tmp.cover)), 
+            by=c("PlotObservationID", "Layer")) %>% 
+  mutate(Relative.cover=tmp.cover/tot.cover)
+              
+            
+```
+
+
+
+
+## Clean DT and export
 ```{r}
 DT2 <- DT1 %>% 
-  dplyr::select(PlotObservationID, Name_short, `Turboveg2 concept`, `Taxon group`, Layer:x_ ) %>% 
-  rename(Species_original=`Turboveg2 concept`, 
-         Species_matched=Name_short,
-         Taxon_group=`Taxon group`, 
-         Cover_perc=`Cover %`, 
-         Cover_code=`Cover code`)
+  dplyr::select(PlotObservationID, Name_short, `Turboveg2 concept`, `Taxon group`, Layer:x_, Relative.cover ) %>% 
+  rename(species_original=`Turboveg2 concept`, 
+         species=Name_short,
+         taxon_group=`Taxon group`, 
+         cover_perc=`Cover %`, 
+         cover_code=`Cover code`)
 ```
 
 The output of the DT table contains `r nrow(DT2)` records, over `r length(unique(DT2$PlotObservationID))` plots. The total number of taxa is `r length(unique(DT2$Species_original))` and `r length(unique(DT2$Species_matched))`, before and after standardization, respectively. Information on the `Taxon group` is available for `r DT2 %>% filter(Taxon_group!="Unknown") %>% distinct(Species_matched) %>% nrow()` standardized species.
@@ -284,5 +302,3 @@ save(DT2, file = "../_output/DT_sPlot3.0.RData")
 ***!!! ADD Explanation of fields!!!***
 
 
-
-!! It seems there are a few species in Name_sPlot_TRY which are duplicated!!! Check in Backbone