From 4a51db3cbdca48c47016f16024eaa6cb10363f2e Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 4 Mar 2020 20:07:50 +0100
Subject: [PATCH] 06_builDT - added calculation of relative cover
---
code/06_buildDT.Rmd | 40 ++++++++++++++++++++++++++++------------
1 file changed, 28 insertions(+), 12 deletions(-)
diff --git a/code/06_buildDT.Rmd b/code/06_buildDT.Rmd
index 26f642a..4e3df55 100644
--- a/code/06_buildDT.Rmd
+++ b/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
--
GitLab