underhill_smoother: Fit the underhill smoother to a reporting rate distribution

In davidclarance/africabirdmap: Functions to clean, analyze and plot Africa Bird Map data.

Description

Fit the underhill smoother (put reference here) to reporting rate distribution over pentades.The underhill smoother is a locally weighted binomial general linear model using a logit link, where the weights are generated using a exponential distribution.

Usage

underhill_smoother(raw_data, species_id, start_month = 7,
  selected_area = "Kenya", selection_type = "Country", pentade_window,
  first_pentade = 1, last_pentade = 73)

Arguments

raw_data	Data for a species extracted uing 'extract_data()'. The StartDate column should be of type 'date'.
species_id	The species_id for which data is extracted. A complete list of species name and ids are available on the Kenya Bird Map website.
start_month	The month to start the pentades from. Default is 7.
selected_area	Either a pentad (eg: 0105_3930), country (eg: Kenya), county (eg: Kitui) or province (eg: rift valley). Lists of the same can be applied as well. For instance, for multiple pentads you could use, c('0105_3930', '0110c3620').
selection_type	Can take either of the four values: 'Pentad', 'Country', 'County' or 'Province'.
pentade_window	The number of pentades on either side of the target day to give the weights to.
first_pentade	The starting value of the pentades. Default is 1.
last_pentade	The last value of the pentades. Default is 73.

Details

• Pentades are blocks of 5 consecutive days. The implementation measures pentades from a defined month 'start_month'. This implementation needs review and should not be considered final.

• For a full list of all possible values for selection_area, run 'View(africabirdmap::pentads_geographical_features)' in the console.

Value

A dataframe where each row is a pentade with the 'fit' values, the standard errors ('se'), the 'reporting_rates' and its associated inputs. Ignore the various date columns as those are only meant to be used in graphs.

Examples

## Not run: 


underhill_smoother(raw_data, species_id, start_month = 7, pentade_window, first_pentade = 1, last_pentade = 73)


## End(Not run)

davidclarance/africabirdmap documentation built on Sept. 3, 2019, 12:34 p.m.