malariaAtlas_PR: Occurrence module: malariaAtlas_PR
In zoonproject/modules: Species Distribution Modelling Code Modules for the ZOON Package

Description Usage Arguments Version Date submitted Data type Author(s) References See Also

Occurrence module to collect malaria parasite rate data from the Malaria Atlas Project database.

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malariaAtlas_PR(country = NULL, ISO = "HND", extent = NULL,
  species = "Pf", standardise = c(2, 10), PA = TRUE, year = NULL,
  fold = 1)

`country`	Character vector containing names of desired countries, e.g. c("Country1", "Country2", ...) OR = "ALL" (use exactly one of country, ISO and extent).
`ISO`	Character vector containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...) OR = "ALL" (use exactly one of country, ISO and extent).
`extent`	Numeric vector containing bounding box values for desired area. In the order xmin, xman, ymin, ymax. (use exactly one of country, ISO and extent).
`species`	'Pf' or 'Pv' for P. falciparum or P. vivax respectively.
`standardise`	Length two integer vector giving the age range to standardise all the points to. The original surveys were conducted on different age ranges but this affects PR, so typically they should be standardised. If PA is TRUE, the sample size will be kept the same and the number of positives will be rounded. If NULL, no standardisation will be performed.
`PA`	Should the data be transformed from parasite rate and examined data to presence absence data? Many modules only work with presence absence data so this TRUE aids compatibility. However, the amount of data will often be very large with FALSE. A single country may have 50,000 presence absence data points.
`year`	Vector of years for which to keep data. NULL keeps all years.
`fold`	Control the validation. If 0, all data is validation data. If 1, all data is training data.

1.0

2018-04-19

presence/absence, proportion

Tim Lucas, timcdlucas@gmail.com

Smith, D. L. et al. Standardizing estimates of the Plasmodium falciparum parasite rate. Malaria Journal 6, 131 (2007).

Gething, Peter W., et al. "A long neglected world malaria map: Plasmodium vivax endemicity in 2010." PLoS neglected tropical diseases 6.9 (2012): e1814.

malariaAtlas::getPR

Other occurrence: AnophelesPlumbeus, CWBZimbabwe, CarolinaWrenPA, CarolinaWrenPO, LocalOccurrenceDataFrame, LocalOccurrenceData, Lorem_ipsum_UK, NATrees, NaiveRandomPresenceAbsence, NaiveRandomPresence, SpOcc, SugarMaple, UKAnophelesPlumbeus