From b99e8124d9c6531da670e6165403166e5e226b82 Mon Sep 17 00:00:00 2001 From: Francesco Sabatini <francesco.sabatini@idiv.de> Date: Thu, 1 Aug 2019 00:38:19 +0200 Subject: [PATCH] Added chunk to 03_backbone to assist manual check of unresolved names --- code/03_TaxonomicBackbone.Rmd | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/code/03_TaxonomicBackbone.Rmd b/code/03_TaxonomicBackbone.Rmd index 7d82365..21d120a 100644 --- a/code/03_TaxonomicBackbone.Rmd +++ b/code/03_TaxonomicBackbone.Rmd @@ -1297,6 +1297,32 @@ nrow(unique(Backbone$Family.correct)) sessionInfo() ``` +```{r, eval=F, echo=F} +toCheck_manual <- read_csv("../_derived/TPL/tpl.ncbi.uncertain.csv") +load("../_output/Backbone3.0.RData") + +toCheck_manual <- toCheck_manual %>% + rename(Name_string_corr2=Taxon) %>% + left_join(Backbone %>% + dplyr::select(Name_sPlot_TRY:sPlot_TRY), + by="Name_string_corr2") %>% + left_join(DT0 %>% + rename(Name_sPlot_TRY=`Matched concept`) %>% + dplyr::select(Name_sPlot_TRY) %>% + group_by(Name_sPlot_TRY) %>% + summarize(count=n()), + by="Name_sPlot_TRY") %>% + left_join(DT0 %>% + rename(Name_sPlot_TRY=`Matched concept`) %>% + dplyr::select(Name_sPlot_TRY, Taxonomy) %>% + distinct(Name_sPlot_TRY, .keep_all=T), + by="Name_sPlot_TRY" + ) + +write_csv(toCheck_manual, path="../_derived/TPL/toCheck_Manual.csv") + +``` +user@local $ ssh user@idiv-gateway.ufz.de \ No newline at end of file -- GitLab