https://github.com/tom-n-walker/uphill-plants-soil-carbon
Revision 0222df8ac72ac241faa8e579969ae1a5bba4fcff authored by tom-n-walker on 08 September 2021, 06:47:11 UTC, committed by GitHub on 08 September 2021, 06:47:11 UTC
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Tip revision: 0222df8ac72ac241faa8e579969ae1a5bba4fcff authored by tom-n-walker on 08 September 2021, 06:47:11 UTC
Update README.md
Update README.md
Tip revision: 0222df8
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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