biogeo: Point Data Quality Assessment and Coordinate Conversion

Functions for error detection and correction in point data quality datasets that are used in species distribution modelling. Includes functions for parsing and converting coordinates into decimal degrees from various formats.

Author
Mark Robertson
Date of publication
2016-04-08 10:43:59
Maintainer
Mark P. Robertson <markrobertsonsa@gmail.com>
License
GPL (>= 3)
Version
1.0
URLs

View on CRAN

Man pages

addmainfields
Adds required fields to a dataframe containing coordinates...
alternatives
Determine where an incorrect point record should be placed by...
alternatives2
Determine where an incorrect point record should be placed by...
alternativesenv
Determine where an incorrect point record should be placed by...
biogeo-package
Point data quality assessment and coordinate conversion
checkdatastr
Checks data structure
coord2numeric
Converts coordinates that are factors into numeric values
dat
Species collection records dataset
datm
A dataset for a marine species
dd2dmslat
Convert decimal degree coordinates for latitude into degrees,...
dd2dmslong
Convert decimal degree coordinates for longitude into...
dem
Digital elevation model 10 minute spatial resolution
dms2dd
Converts coordinates in degrees, minutes, seconds into...
dmsabs
Separates a coordinate string into degrees, minutes and...
dmsparse
Parse coordinate strings into separate degree, minute and...
dmsparsefmt
Parse coordinate string using a format string
duplicatesexclude
Exclude duplicate point records per species per grid cell
edat
Species collection records dataset and environmental...
elevcheck
Elevation check
env2stack
Read environmental variable rasters
errorcheck
Identifies errors in a dataset of point records
fieldsmissing
Determines whether any of the required fields are missing...
finddecimals
Find coordinates that are in decimal degrees
fmtcheck
Coordinate string format check
gbifdat
A dataset of records from GBIF
geo2envid
Interactive plot to explore points in geographical and...
geo2envpca
Interactive plot to explore points in geographical and...
getextent
Get the extent of an object
getformat
Get formats of coordinates
getletter
Find letters in coordinates
keepmainfields
Keep main fields in a dataframe.
missingcoords
Finds indices of records in a dataset where the coordinates...
missingvalsexclude
Excludes records with missing values for points
modified
Identify records that were modified between two dates
modifiedtoday
Identify records that were modified today
msk60
msk60
nearestcell
Assigns points that fall into the sea to the centre of the...
outliers
Detects outliers using values extracted from an environmental...
parsecoords
Parse coordinates into separate fields
places
A dataset of localities
plotsetup
Produces devices for plotting
points2shape
Save data to a points shape file
pointsworld
Plots point records on a world map using their latitude and...
precisioncheck
Check the precision of the coordinates
precisionenv
Check precision of records
quickclean
Automated data cleaning
quickrich
Perform error checks and produce richness map
renamefields
Rename particular fields in a dataframe
richness
Produced a species richness map
richnessmap
Map of the number of species or number of records per grid...
rjack
Outlier detection using the Reverse Jackknife
sep
Separate coordinates into degrees, minutes and seconds
speciescount
Count number of records per species
substddmm
Swap degrees and minutes in a coordinate
uniqueformats
List unique coordinate formats
wclim
Returns Worldclim bioclimatic variable names
world
World country polygons

Files in this package

biogeo
biogeo/inst
biogeo/inst/extdata
biogeo/inst/extdata/placestest.csv
biogeo/inst/doc
biogeo/inst/doc/Biogeo_Tutorial.pdf
biogeo/inst/doc/tutorial_biogeo.r
biogeo/NAMESPACE
biogeo/data
biogeo/data/world.rda
biogeo/data/edat.rda
biogeo/data/gbifdat.rda
biogeo/data/msk60.rda
biogeo/data/places.rda
biogeo/data/dat.rda
biogeo/data/datm.rda
biogeo/data/dem.rda
biogeo/data/datalist
biogeo/R
biogeo/R/checkdatastr.R
biogeo/R/plotsetup.R
biogeo/R/dd2dmslat.R
biogeo/R/precisionenv.R
biogeo/R/coord2numeric.R
biogeo/R/dmsparsefmt.R
biogeo/R/uniqueformats.R
biogeo/R/alternatives.R
biogeo/R/outliers.R
biogeo/R/fmtcheck.R
biogeo/R/points2shape.R
biogeo/R/addmainfields.R
biogeo/R/missingvalsexclude.R
biogeo/R/geo2envpca.R
biogeo/R/nearestcell.R
biogeo/R/richnessmap.R
biogeo/R/getformat.R
biogeo/R/geo2envid.R
biogeo/R/sep.R
biogeo/R/finddecimals.R
biogeo/R/dms2dd.R
biogeo/R/precisioncheck.R
biogeo/R/parsecoords.R
biogeo/R/alternativesenv.R
biogeo/R/rjack.R
biogeo/R/elevcheck.R
biogeo/R/renamefields.R
biogeo/R/getextent.R
biogeo/R/env2stack.R
biogeo/R/alternatives2.R
biogeo/R/pointsworld.R
biogeo/R/quickrich.R
biogeo/R/modified.R
biogeo/R/modifiedtoday.R
biogeo/R/dd2dmslong.R
biogeo/R/missingcoords.R
biogeo/R/speciescount.R
biogeo/R/getletter.R
biogeo/R/keepmainfields.R
biogeo/R/dmsparse.R
biogeo/R/duplicatesexclude.R
biogeo/R/errorcheck.R
biogeo/R/richness.R
biogeo/R/quickclean.R
biogeo/R/wclim.R
biogeo/R/dmsabs.R
biogeo/R/fieldsmissing.R
biogeo/R/substddmm.R
biogeo/MD5
biogeo/DESCRIPTION
biogeo/man
biogeo/man/speciescount.Rd
biogeo/man/places.Rd
biogeo/man/pointsworld.Rd
biogeo/man/geo2envpca.Rd
biogeo/man/getextent.Rd
biogeo/man/modifiedtoday.Rd
biogeo/man/getletter.Rd
biogeo/man/substddmm.Rd
biogeo/man/uniqueformats.Rd
biogeo/man/biogeo-package.Rd
biogeo/man/alternativesenv.Rd
biogeo/man/datm.Rd
biogeo/man/rjack.Rd
biogeo/man/quickrich.Rd
biogeo/man/edat.Rd
biogeo/man/missingcoords.Rd
biogeo/man/checkdatastr.Rd
biogeo/man/richnessmap.Rd
biogeo/man/env2stack.Rd
biogeo/man/geo2envid.Rd
biogeo/man/getformat.Rd
biogeo/man/world.Rd
biogeo/man/elevcheck.Rd
biogeo/man/gbifdat.Rd
biogeo/man/plotsetup.Rd
biogeo/man/parsecoords.Rd
biogeo/man/sep.Rd
biogeo/man/duplicatesexclude.Rd
biogeo/man/fieldsmissing.Rd
biogeo/man/dd2dmslong.Rd
biogeo/man/errorcheck.Rd
biogeo/man/addmainfields.Rd
biogeo/man/dmsabs.Rd
biogeo/man/msk60.Rd
biogeo/man/coord2numeric.Rd
biogeo/man/renamefields.Rd
biogeo/man/dat.Rd
biogeo/man/richness.Rd
biogeo/man/quickclean.Rd
biogeo/man/modified.Rd
biogeo/man/fmtcheck.Rd
biogeo/man/precisionenv.Rd
biogeo/man/dmsparse.Rd
biogeo/man/missingvalsexclude.Rd
biogeo/man/finddecimals.Rd
biogeo/man/dem.Rd
biogeo/man/alternatives.Rd
biogeo/man/dms2dd.Rd
biogeo/man/points2shape.Rd
biogeo/man/nearestcell.Rd
biogeo/man/dd2dmslat.Rd
biogeo/man/precisioncheck.Rd
biogeo/man/alternatives2.Rd
biogeo/man/keepmainfields.Rd
biogeo/man/dmsparsefmt.Rd
biogeo/man/outliers.Rd
biogeo/man/wclim.Rd