https://github.com/tom-n-walker/uphill-plants-soil-carbon
Revision 05e1672664e587a3808d326d6f78d29ca5e44c01 authored by Tom Walker on 07 September 2021, 14:31:53 UTC, committed by Tom Walker on 07 September 2021, 14:32:33 UTC
1 parent bd5cb92
Tip revision: 05e1672664e587a3808d326d6f78d29ca5e44c01 authored by Tom Walker on 07 September 2021, 14:31:53 UTC
Added all analyses, streamlined pipelines and improved statistical models. Removed data export (all done via drake cache).
Added all analyses, streamlined pipelines and improved statistical models. Removed data export (all done via drake cache).
Tip revision: 05e1672
clean_species_names.R
################################################################################
#### Project: Lowland plant migrations alpine soil C loss
#### Title: Function | Clean species names
#### Author: Tom Walker (thomas.walker@usys.ethz.ch)
#### Date: 26 May 2021
#### ---------------------------------------------------------------------------
clean_species_names <- function(formatted){
# species names
species <- unique(formatted$species)
# call name resolver
resolved <- gnr_resolve(species,
best_match_only = T,
with_canonical_ranks = T)
# take resolved, select, join to data, merge gnr/original names, select
cleaned <- resolved %>%
select(user_supplied_name, accepted_name = matched_name2) %>%
left_join(formatted, ., by = c("species" = "user_supplied_name")) %>%
select(site, grid_id, species, accepted_name, total_cover)
# deal with fuckers
cleaned[cleaned$species == "bare ground", "accepted_name"] <- "bare ground"
cleaned[cleaned$species == "Erigeron-Aster Group", "accepted_name"] <- "unknown"
cleaned[cleaned$species == "Aster-Erigeron Group", "accepted_name"] <- "unknown"
cleaned[cleaned$species == "Sebastian has photo_UKS", "accepted_name"] <- "unknown"
cleaned[cleaned$species == "Grass Group", "accepted_name"] <- "unknown"
cleaned[cleaned$species == "Lychen Group", "accepted_name"] <- "mosses"
cleaned[cleaned$species == "Moos Group", "accepted_name"] <- "mosses"
cleaned[cleaned$species == "CAREXLACCA", "accepted_name"] <- "Carex flacca"
cleaned[cleaned$species == "Baby carlina_UKS", "accepted_name"] <- "Carlina"
# return species table
cleaned <- cleaned %>% select(-species)
return(cleaned)
}
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