speciesRarity: Calculate the rarity of species recorded by a volunteer

In BiologicalRecordsCentre/recorderMetrics: Calculate recorder behaviour metrics for participants of citizen science projects

Description

This function takes in data for a recorder and calculates the recorder's rarity metrics.

Usage

speciesRarity(
  recorder_name,
  data,
  sp_col = "preferred_taxon",
  recorder_col = "recorders"
)

Arguments

recorder_name	the name of the recorder for whom you want to calculate the metrics
data	the data.frame of recording information
sp_col	the name of the column that contains the species names
recorder_col	the name of the column that contains the recorder names

Details

This function examines the rarity of the species that a recorder observes and compares this to the rarity of species recorded across all recorders. First all species are ranked by rarity across all observations from all recorders. These ranks are then scaled to 100 so that the metrics are independent of the number of species in the group. Each observation, in the entire dataset is then assigned a value for the ranked rarity of the species observed and a median is calculated. This median is therefore the median ranked rarity of species observed, where 1 is the most common species and 100 the rarest (ranks are scaled to 100). The median rarity for the individual recorder is calculated in the same way, but using the species' rank values from the overall dataset.

Value

A data.frame with seven columns

• recorder - The name of the recorder, as given in the recorder_name argument

• median_rarity - The median rarity of all observations made by the recorder

• median_diff_rarity - The median rarity of an recorders observations subtracted from the median rarity across all observers. Negative numbers mean a recorder is recording more common species than the population of recorders as a whole. Positive numbers mean the recorder is recording more rare species than the population of recorders as a whole.

• stdev - The standard deviation of the rarity ranks of a recorders observations

• n - The total number of observations made by this recorder

Examples

## Not run: 

# load example data
head(cit_sci_data)

# Run for a single recorder
SR <- speciesRarity(recorder_name = 3007,
                   data = cit_sci_data, 
                   sp_col = 'species',
                   recorder_col = 'recorder')
                   
# Run the metric for all recorders
SR_all <- lapply(unique(cit_sci_data$recorder),
                 FUN = speciesRarity,
                 data = cit_sci_data,
                 sp_col = 'species',
                 recorder_col = 'recorder')

# summarise as one table
SR_all_sum <- do.call(rbind, SR_all)

hist(SR_all_sum$median_diff_rarity, breaks = 20) 

## End(Not run)

BiologicalRecordsCentre/recorderMetrics documentation built on Nov. 10, 2021, 2:03 p.m.