RuHere (version 1.0.1)

fix_states: Identify and correct coordinates based on state information

Description

This function identifies and correct inverted and transposed coordinates based on state information.

Usage

fix_states(
  occ,
  long = "decimalLongitude",
  lat = "decimalLatitude",
  state_column,
  correct_state = "correct_state",
  distance = 5,
  progress_bar = FALSE,
  verbose = TRUE
)

Value

The original occ data.frame with the coordinates in the long and lat

columns corrected, and an additional column (state_issues) indicating whether the coordinates are:

• correct: the record falls within the assigned state;

• inverted: longitude and/or latitude have reversed signs;

• swapped: longitude and latitude are transposed (i.e., each appears in the other's column). incorrect: the record falls outside the assigned state and could not be corrected.

Arguments

occ

(data.frame) a dataset with occurrence records, preferably with state information checked using state_countries().

long

(character) column name with longitude. Default is 'decimalLongitude'.

lat

lat (character) column name with latitude. Default is 'decimalLatitude'.

state_column

(character) name of the column containing the state information.

correct_state

(character) name of the column with logical value indicating whether each record falls within the state specified in the metadata. Default is 'correct_state'. See details.

distance

(numeric) maximum distance (in kilometers) a record can fall outside the state assigned in the state_column. Default is 5.

progress_bar

(logical) whether to display a progress bar during processing. If TRUE, the 'pbapply' package must be installed. Default is FALSE.

verbose

(logical) whether to print messages about function progress. Default is TRUE.

Details

The function checks and corrects coordinate errors in occurrence records by testing whether each point falls within the expected state polygon (from RuHere’s internal world map).

The input occurrence data must contain a column (specified in the correct_state argument) with logical values indicating which records to check and fix — only those marked as FALSE will be processed. This column can be obtained by running the check_states() function.

It runs a series of seven tests to detect common issues such as inverted signs or swapped latitude/longitude values. Inverted coordinates have their signs flipped (e.g., -45 instead of 45), placing the point in the opposite hemisphere, while swapped coordinates have latitude and longitude values exchanged (e.g., -47, -15 instead of -15, -47).

For each test, state borders are buffered by distance km to account for minor positional errors.

The type of issue (or "correct") is recorded in a new column, state_issues. Records that match their assigned state after any correction are updated accordingly, while remaining mismatches are labeled "incorrect".

This function can be used internally by check_states() to automatically identify and fix common coordinate errors.

Examples

# Load example data
data("occurrences", package = "RuHere") # Import example data
# Subset records of Araucaria
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Standardize country names
occ_country <- standardize_countries(occ = occ,
                                     return_dictionary = FALSE)

# Standardize state names
occ_state <- standardize_states(occ = occ_country,
                                country_column = "country_suggested",
                                return_dictionary = FALSE)

# Check whether records fall within the assigned states
occ_states_checked <- check_states(occ = occ_state,
                                   state_column = "state_suggested")

# Fix records with incorrect or misassigned states
occ_states_fixed <- fix_states(occ = occ_states_checked,
                               state_column = "state_suggested")