In environmentalinformatics-marburg/speciesdist: Species distribution analysis

library(data.table)

inpath <- "D:/active/juergen/"
datapath <- paste0(inpath, "data/")
datapath_gbif <- paste0(datapath, "gbif/")
datapath_rdata <- paste0(datapath, "rdata/")
datapath_geo <- paste0(datapath, "geo/")

load(paste0(datapath_rdata, "gibf_02_cleaned_input.Rdata"))
ctry_and_coord <- 
  gbif[, length(which(!is.na(countryCode) & !is.na(decimalLatitude)))]
cnty_and_coord <- 
  gbif[, length(which(is.na(countryCode) & !is.na(decimalLatitude) & 
                        !is.na(county)))]

Check GBIF coordinate information for plausibility

Since actual geolocation is quite relevant for the upcoming analysis, a cross check of geographical coordinates and country/county information will be performed for the 'r ctry_and_coord + cnty_and_coord' datasets which have both information.

cntr <- rgdal::readOGR(paste0(datapath_geo, "world_boundaries.shp"), 
                       layer = "world_boundaries")

Geocode GBIF by country code information

After checking the coordinates for plausibility, missing coordinates will be assigned by country code or county name. The data source for country information is http://www.gadm.org/version2.

First, get the country centroids from the country data layer of GDAM2:

test <- rgdal::readOGR(paste0(datapath_geo, "test.shp"), 
                       layer = "test")




cntr <- rgdal::readOGR(paste0(datapath_geo, "world_boundaries.shp"), 
                       layer = "world_boundaries")
cntr_cent <- calcPolygonCentroids(cntr)

Second, get the county centroids from the country data layer of GDAM2:

county <- rgdal::readOGR(paste0(datapath_geo, "world_boundaries.shp"), 
                       layer = "world_boundaries")
county_cent <- calcPolygonCentroids(county)

Vignette Info

Note the various macros within the vignette setion of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the title field and the \VignetteIndexEntry to match the title of your vignette.

Styles

The html_vignette template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:

output: 
  rmarkdown::html_vignette:
    css: mystyles.css

Figures

The figure sizes have been customised so that you can easily put two images side-by-side.

plot(1:10)
plot(10:1)

You can enable figure captions by fig_caption: yes in YAML:

output:
  rmarkdown::html_vignette:
    fig_caption: yes

Then you can use the chunk option fig.cap = "Your figure caption." in knitr.

More Examples

You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using knitr::kable().

knitr::kable(head(mtcars, 10))

Also a quote using >:

"He who gives up [code] safety for [code] speed deserves neither." (via)

environmentalinformatics-marburg/speciesdist documentation built on May 16, 2019, 7:55 a.m.