geoknife
package version r packageVersion('geoknife')
Tools for geo-web processing of gridded data via the Geo Data Portal. geoknife
slices up gridded data according to overlap with irregular features, such as watersheds, lakes, points, etc. The result is subsetted data in plain text, NetCDF, geotiff or other formats.
geoknife
To install the geoknife
from CRAN:
install.packages("geoknife")
library(knitr) opts_chunk$set(fig.path = "inst/", dev='png')
Or to install the current development version of the package:
install.packages("remotes") remotes::install_github('DOI-USGS/geoknife')
Please consider reporting bugs and asking questions on the Issues page: https://github.com/DOI-USGS/geoknife/issues
We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the code of conduct for more information.
The Water Mission Area of the USGS supports the development and maintenance of geoknife
through September 2018, and most likely further into the future. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the geoknife
development team.
geoknife
overviewThe geoknife
package was created to support web-based geoprocessing of large gridded datasets according to their overlap with landscape (or aquatic/ocean) features that are often irregularly shaped. geoknife
creates data access and subsequent geoprocessing requests for the USGS's Geo Data Portal to carry out on a web server. The results of these requests are available for download after the processes have been completed. This type of workflow has three main advantages: 1) it allows the user to avoid downloading large datasets, 2) it avoids reinventing the wheel for the creation and optimization of complex geoprocessing algorithms, and 3) computing resources are dedicated elsewhere, so geoknife
operations do not have much of an impact on a local computer.
geoknife
interacts with a remote server to figure out what types of processing capabilities are available, in addition to seeing what types of geospatial features are already available to be used as an area of interest (commonly, these are user-uploaded shapefiles). Because communication with web resources are central to geoknife
operations, users must have an active internet connection.
The main elements of setting up and carrying out a geoknife
'job' (geojob
) include defining the feature of interest (the stencil
argument in the geoknife
function), the gridded web dataset to be processed (the fabric
argument in the geoknife
function), and the the processing algorithm parameters (the knife
argument in the geoknife
function). The status of the geojob
can be checked with check
, and output can be loaded into a data.frame with result
.
geoknife
do?library(geoknife) # from a single point stencil <- simplegeom(c(-89, 46.23)) # -- or -- # from a collection of named points stencil <- simplegeom(data.frame( 'point1' = c(-89, 46), 'point2' = c(-88.6, 45.2))) # -- or -- #for a state from a web available dataset stencil <- webgeom('state::New Hampshire') stencil <- webgeom('state::New Hampshire,Wisconsin,Alabama') # -- or -- #for HUC8s from a web available dataset stencil <- webgeom('HUC8::09020306,14060009')
# from the prism dataset: fabric <- webdata('prism') # -- or -- # explicitly define webdata from a list: fabric <- webdata(list( times = as.POSIXct(c('1895-01-01','1899-01-01')), url = 'https://cida.usgs.gov/thredds/dodsC/prism_v2', variables = 'ppt')) # modify the times field: times(fabric) <- as.POSIXct(c('2003-01-01','2005-01-01'))
job <- geoknife(stencil, fabric, wait = TRUE) # use existing convienence functions to check on the job: check(job)
see also:
running(job) error(job) successful(job)
data <- result(job) plot(data[,1:2], ylab = variables(fabric))
job <- geoknife(webgeom('state::New Hampshire'), fabric = 'prism', email = 'fake.email@gmail.com')
geoknife
Functions (as of v1.1.5)| Function | Title |
| ------------- |:-------------|
| geoknife
| slice up gridded data according to overlap with feature(s) |
| gconfig
| set or query package settings for geoknife
processing defaults |
| algorithm
| the algorithm of a webprocess
|
| attribute
| the attribute of an webgeom
|
| check
| check status of geojob
|
| download
| download the results of a geojob
|
| error
| convenience function for state of geojob
|
| running
| convenience function for state of geojob
|
| successful
| convenience function for state of geojob
|
| start
| start a geojob
|
| cancel
| cancel a geojob
|
| geom
| the geom of a webgeom
|
| inputs
| the inputs of a webprocess
|
| id
| the process id of a geojob
|
| values
| the values of a webgeom
|
| result
| load the output of a completed geojob
into data.frame |
| variables
| the variables for a webdata
object |
| wait
| wait for a geojob
to complete processing |
| times
| the times of a webdata
object |
| url
| the url of a webdata
, webgeom
, geojob
, or webprocess
|
| version
| the version of a webgeom
or webdata
|
| xml
| the xml of a geojob
|
| query
| query datasets or variables |
geoknife
classes (as of v0.12.0)| Class | Title |
| ------------- |:-------------|
| simplegeom
| a simple geometric class. Extends sp::SpatialPolygons
|
| webgeom
| a web feature service geometry |
| webprocess
| a web processing service |
| webdata
| web data |
| geojob
| a geo data portal processing job |
| datagroup
| a simple class that contains data lists that can be webdata
|
geoknife
need?This version requires httr
, sp
, and XML
. All of these packages are available on CRAN, and will be installed automatically when using the install.packages()
instructions above.
In addition to typical R package checking, a Dockerfile is included in this repository. Once built, it can be run with the following command.
docker build -t geoknife_test . docker run --rm -it -v %cd%:/src geoknife_test /bin/bash -c "cp -r /src/* /check/ && cp /src/.Rbuildignore /check/ && cd /check && Rscript -e 'devtools::build()' && R CMD check --as-cran ../geoknife_*"
For release of the sbtools package, a number of steps are required.
NEWS.md
reflects updates in version.DESCRIPTION
to reflect release version.DISCLAIMER.md
to approved language and rebuild README.Rmd
.DISCLAIMER.md
back to development mode and increment description version.Add the following code to your website.
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