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Summarize flags

Source: R/summarize_flags.R
summarize_flags.Rd

This functions returns a dataframe and a bar plot summarizing the number of records flagged by each flagging function.

Usage

summarize_flags(
  occ = NULL,
  flagged_dir = NULL,
  output_format = ".gz",
  flags = "all",
  additional_flags = NULL,
  names_additional_flags = NULL,
  plot = TRUE,
  show_unflagged = TRUE,
  occ_unflagged = NULL,
  fill = "#0072B2",
  sort = TRUE,
  decreasing = TRUE,
  add_n = TRUE,
  size_n = 3.5,
  theme_plot = ggplot2::theme_minimal(),
  ...
)

Arguments

occ

(data.frame or data.table) a dataset containing occurrence records that has been processed by one or more flagging functions. See Details for available flag types.

flagged_dir

(character) optional path to a directory containing files with flagged records saved using the remove_flagged() function. Default is NULL.

output_format

(character) output format used to read the removed records. Options are ".csv" or ".gz". Only used when flagged_dir is not NULL. Default is ".gz".

flags

(character) the flags to be summarized. Use "all" to display all available flags. See Details for all options. Default is "all".

additional_flags

(character) an optional named character vector with the names of additional logical columns to be used as flags. Default is NULL.

names_additional_flags

(character) an optional different name to the flag provided in additional_flags to be shown in the map. Only applicable if additional_flags is not NULL.

plot

(logical) whether to return a ggplot2 bar plot showing the number of flagged records. Default is TRUE.

show_unflagged

(logical) whether to include the number of unflagged records in the plot. Default is TRUE.

occ_unflagged

(data.frame or data.table) an optional dataset containing unflagged occurrence records. Only applicable if occ is NULL and show_unflagged is TRUE.

fill

(character) fill color for the bar plot. Default is "#0072B2".

sort

(logical) whether to sort bars according to the number of records. Default is TRUE.

decreasing

(logical) whether to sort bars in decreasing order (flags with more records appear at the top of the plot). Default is TRUE.

add_n

(logical) whether to display the number of flagged records on the bars. Default is TRUE.

size_n

(numeric) size of the text showing the number of records. Only used when add_n = TRUE. Default is 3.5.

theme_plot

(theme) a ggplot2 theme object. Default is ggplot2::theme_minimal().

...

additional arguments passed to ggplot2::theme().

Value

If plot = TRUE, a list with two elements:

df_summary

A data frame summarizing the number of records per flag.

plot_summary

A ggplot2 object showing the summary as a bar plot.

If plot = FALSE, only the summary data frame is returned.

Details

This function expects an occurrence dataset that has already been processed by one or more flagging routines from RuHere or related packages such as CoordinateCleaner. Any logical column in occ can be used as a flag.

The following built-in flag names are recognized: From RuHere: correct_country, correct_state, cultivated, florabr, faunabr, wcvp, iucn, bien, duplicated, thin_geo, thin_env, consensus

From CoordinateCleaner: .val, .equ, .zer, .cap, .cen, .sea, .urb, .otl, .gbf, .inst, .aohi

Users may also supply additional logical columns using additional_flags, optionally providing alternative display names (names_additional_flags) and colors (col_additional_flags).

Examples

# Load example data
data("occ_flagged", package = "RuHere")
# Summarize flags
sum_flags <- summarize_flags(occ = occ_flagged)
# Plot
sum_flags$plot_summary