malariaAtlas (version 0.0.4)

getRaster: Download Rasters produced by the Malaria Atlas Project

Description

getRaster downloads publicly available MAP rasters for a specific surface & year, clipped to a provided bounding box or shapefile.

Usage

getRaster(surface = "Plasmodium falciparum PR2-10", shp = NULL,
  extent = NULL, file_path = tempdir(), year = as.list(rep(NA,
  length(surface))), vector_year = NULL)

Arguments

surface

string containing 'title' of desired raster(s), e.g. c("raster1", "raster2"). Defaults to "PfPR2-10" - the most recent global raster of PfPR 2-10. Check listRaster to find titles of available rasters.

shp

SpatialPolygon(s) object of a shapefile to use when clipping downloaded rasters. (use either shp OR extent; if neither is specified global raster is returned).

extent

2x2 matrix specifying the spatial extent within which raster data is desired, as returned by sp::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")))) (use either shp OR extent; if neither is specified global raster is returned).

file_path

string specifying the directory to which working files will be downloaded. Defaults to tempdir().

year

default = rep(NA, length(surface)) (use NA for static rasters); for time-varying rasters: if downloading a single surface for one or more years, year should be a string specifying the desired year(s). if downloading more than one surface, use a list the same length as surface, providing the desired year-range for each time-varying surface in surface or NA for static rasters.

vector_year

default = NULL for vector occurence rasters, the desired version as prefixed in raster_code returned using available_rasters. By default (NULL) returns the most recent raster version )

Value

getRaster returns a RasterLayer (if only a single raster is queried) or RasterStack (for multiple rasters) for the specified extent.

See Also

autoplot_MAPraster

to quickly visualise rasters downloded using getRaster.

as.MAPraster

to convert RasterLayer/RasterStack objects into a 'MAPraster' object (data.frame) for easy plotting with ggplot.

autoplot.MAPraster

to quickly visualise MAPraster objects created using /codeas.MAPraster.

Examples

# NOT RUN {
# Download PfPR2-10 Raster for Madagascar in 2015 and visualise this immediately.
# }
# NOT RUN {
MDG_shp <- getShp(ISO = "MDG", admin_level = "admin0")
MDG_PfPR2_10 <- getRaster(surface = "Plasmodium falciparum PR2-10", shp = MDG_shp, year = 2015)
autoplot_MAPraster(MDG_PfPR2_10)

# Download global raster of G6PD deficiency from Howes et al 2012.
G6PDd_global <- getRaster(surface = "G6PD Deficiency Allele Frequency")
autoplot_MAPraster(G6PDd_global)

# Download a temporal raster by range
MDG_PfPR2_10_range <- getRaster(surface = "Plasmodium falciparum PR2-10", 
                                shp = MDG_shp, year = 2012:2015)

# Download a mix of rasters
MDG_rasters <- getRaster(surface = c("Plasmodium falciparum PR2-10", 
                                     'Plasmodium falciparum Incidence', 
                                     'Plasmodium falciparum Support'),
                         shp = MDG_shp, year = list(2009:2012, 2005:2007, NA))
p <- autoplot_MAPraster(MDG_rasters)

# }
# NOT RUN {
# }