getVecOcc: Download Vector Occurrence points from the MAP database...

In malariaAtlas: An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'

Download Vector Occurrence points from the MAP database getVecOcc downloads all publicly available vector occurrence points for a specified country (or countries) and returns this as a dataframe. country and ISO refer to countries and a lower-level administrative regions such as French Guiana.

Description

Download Vector Occurrence points from the MAP database getVecOcc downloads all publicly available vector occurrence points for a specified country (or countries) and returns this as a dataframe. country and ISO refer to countries and a lower-level administrative regions such as French Guiana.

Usage

getVecOcc(
  country = NULL,
  ISO = NULL,
  continent = NULL,
  species = "all",
  extent = NULL,
  start_date = NULL,
  end_date = NULL,
  version = NULL
)

Arguments

country	string containing name of desired country, e.g. c("Country1", "Country2", ...) OR = "ALL". (Use one of country OR ISO OR continent, not combined)
ISO	string containing ISO3 code for desired country, e.g. c("XXX", "YYY", ...) OR = "ALL". (Use one of country OR ISO OR continent, not combined)
continent	string containing continent (one of "Africa", "Americas", "Asia", "Oceania") for desired data, e.g. c("continent1", "continent2", ...). (Use one of country OR ISO OR continent, not combined)
species	string specifying the Anopheles species for which to find vector occurrence points, options include: "Anopheles...." OR "ALL"
extent	an object specifying spatial extent within which PR data is desired, as returned by sf::st_bbox(). - the first column has the minimum, the second the maximum values; rows 1 & 2 represent the x & y dimensions respectively (matrix(c("xmin", "ymin","xmax", "ymax"), nrow = 2, ncol = 2, dimnames = list(c("x", "y"), c("min", "max"))))
start_date	string object representing the lower date to filter the vector occurrence data by (inclusive)
end_date	string object representing the upper date to filter the vector occurrence data by (exclusive)
version	(optional) The vector points dataset version to use. If not provided, will just use the most recent version of vector points data. (To see available version options, use listVecOccPointVersions)

Value

getVecOcc returns a dataframe containing the below columns, in which each row represents a distinct data point/ study site.

1. COLUMNNAME description of contents

2. COLUMNNAME description of contents

3. COLUMNNAME description of contents

See Also

autoplot method for quick mapping of Vector occurrence point locations (autoplot.vector.points).

Examples

# Download vector occurrence data for Brazil and map the locations using autoplot.vector.points
## Not run: 
Brazil_vec <- getVecOcc(country = "Brazil")
autoplot(Brazil_vec)

# Download vector data for Madagascar and map the locations using autoplot
Madagascar_vec <- getVecOcc(ISO = "MDG", species = "All")
autoplot(Madagascar_vec)

# Subset by extent.
extent_vec <- getVecOcc(extent = matrix(c(100,13,110,18), nrow = 2), species = 'all')

## End(Not run)

malariaAtlas documentation built on Oct. 27, 2023, 9:07 a.m.