Find how taxa changed through the cleaning/filtering/tidying process

Source: R/find_taxa.R

find_taxa does not work hierarchically. For example Eucalyptus will only match genus level records, not species records, such as Eucalyptus leucoxylon.

find_taxa(
  taxa_to_find,
  taxa_cols = c("original_name", "taxa"),
  lutaxa,
  filt_df_prefix = "flor_"
)

Arguments

taxa_to_find

Character. Taxa name to find.

taxa_cols

Character. Name of column(s) across data frames containing taxa information.

lutaxa

Dataframe with column names matching taxa_cols, usually, say, taxonomy$species$lutaxa as a result of make_taxonomy().

filt_df_prefix

Character. Prefix used in each of the data frames created at each step in the filtering process.

Examples



# library(envClean)

# Example taxa
use_taxa <- "Eucalyptus gracilis"

# Set context
context <- c("lat", "long", "month", "year")

# Start
flor_start <- flor_all %>%
  tibble::as_tibble() %>%
  envFunc::add_time_stamp()

# Remove singletons
flor_single <- flor_start %>%
  filter_counts(context = context
                , thresh = 5
                ) %>%
  envFunc::add_time_stamp()

# Just keep most recent contexts
flor_recent <- flor_single %>%
  dplyr::group_by(across(any_of(context[!context %in% c("month", "year")]))) %>%
  dplyr::filter(year == max(year)
                , month == max(month)
                ) %>%
  dplyr::ungroup() %>%
  envFunc::add_time_stamp()

# make_taxonomy
taxa <- make_taxonomy(df = flor_recent)
#> Joining with `by = join_by(original_name)`
#> Error in check_pour_interactive(.slot): No data stored by `potions`
#> ℹ try using `brew()

# bin taxa
flor_taxa <- flor_recent %>%
  bin_taxa(taxonomy = taxa$species)
#> Error: object 'taxa' not found

# distinct over bins
flor_bin <- flor_taxa %>%
  dplyr::distinct(taxa, dplyr::across(tidyselect::any_of(context)))
#> Error: object 'flor_taxa' not found

# How did records of 'taxa' change through the filtering?
# Eucalyptus gracilis
find_taxa("Eucalyptus gracilis"
          , lutaxa = taxa$species$lutaxa
          )
#> Error: object 'taxa' not found

# Chenopodium nutans
find_taxa("Chenopodium nutans"
          , lutaxa = taxa$species$lutaxa
          )
#> Error: object 'taxa' not found