From 10939a30edb6d7db7d6ed9839593bd549fd8cfbe Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 4 Mar 2020 16:44:37 +0100
Subject: [PATCH] Minor fixes to Backbone
---
code/03_TaxonomicBackbone.Rmd | 8 ++++++--
code/04_buildHeader.Rmd | 5 +----
2 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/code/03_TaxonomicBackbone.Rmd b/code/03_TaxonomicBackbone.Rmd
index b7cf96e..d58c2a8 100644
--- a/code/03_TaxonomicBackbone.Rmd
+++ b/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") %>%
diff --git a/code/04_buildHeader.Rmd b/code/04_buildHeader.Rmd
index 5e7c11c..02b6fb5 100644
--- a/code/04_buildHeader.Rmd
+++ b/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.
--
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