From 72f87f659d5dd01751b5d2214cc7df28bd9e94ce Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 30 Sep 2019 16:48:07 +0200
Subject: [PATCH] Prepared list of taxa and submitted to TRY
---
code/03_TaxonomicBackbone.Rmd | 26 ++++++++++++++++++++++----
1 file changed, 22 insertions(+), 4 deletions(-)
diff --git a/code/03_TaxonomicBackbone.Rmd b/code/03_TaxonomicBackbone.Rmd
index 46b8612..2980f5a 100644
--- a/code/03_TaxonomicBackbone.Rmd
+++ b/code/03_TaxonomicBackbone.Rmd
@@ -1481,8 +1481,28 @@ save(Backbone, file="../_output/Backbone3.0.RData")
## Export species list to request in TRY
```{r}
-Backbone %>%
- filter(grep(sPlot_TRY,pattern = "S"))
+ToSubmit1 <- Backbone %>%
+ filter(grepl(sPlot_TRY, pattern = "S")) %>%
+ filter(grepl(sPlot_TRY, pattern = "T")) %>%
+ dplyr::select(Name_sPlot_TRY) %>%
+ rename(Name_submit = Name_sPlot_TRY)
+
+## add names from T, which match names from S only after standardization
+ToSubmit2 <- Backbone %>%
+ filter(grepl(sPlot_TRY, pattern = "T")) %>%
+ filter(!grepl(sPlot_TRY, pattern = "S")) %>%
+ filter(Name_sPlot_TRY %in% ((Backbone %>%
+ filter(grepl(sPlot_TRY, pattern = "S")) %>%
+ filter(!grepl(sPlot_TRY, pattern = "T")) %>%
+ dplyr::select(Name_correct) %>%
+ distinct())$Name_correct)) %>%
+ dplyr::select(Name_sPlot_TRY) %>%
+ rename(Name_submit = Name_sPlot_TRY)
+
+ToSubmit <- ToSubmit1 %>%
+ bind_rows(ToSubmit2)
+
+write_csv(ToSubmit, "../_output/Submit_TRY.csv")
```
@@ -1704,5 +1724,3 @@ write_csv(toCheck_manual, path="../_derived/TPL/toCheck_Manual.csv")
```
-
-user@local $ ssh user@idiv-gateway.ufz.de
--
GitLab