geoknife package version 1.6.10

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.

Installing geoknife

To install the geoknife from CRAN:

install.packages("geoknife")

Or to install the current development version of the package:

install.packages("remotes")
remotes::install_github('DOI-USGS/geoknife')

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page: https://github.com/DOI-USGS/geoknife/issues

Code of Conduct

We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the code of conduct for more information.

Package Support

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 overview

The 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.

What can geoknife do?

Define a stencil that represents the geographic region to slice out of the data

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')

Define a fabric that represents the underlying data

# 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'))

Create the processing job that will carry out the subsetting/summarization task

job <- geoknife(stencil, fabric, wait = TRUE)

# use existing convienence functions to check on the job:
check(job)

## $status
## [1] "Process successful"
## 
## $URL
## [1] "https://labs.waterdata.usgs.gov:443/gdp-process-wps/RetrieveResultServlet?id=3362d55f-6d35-4e21-baf6-51a2583bc8bdOUTPUT"
## 
## $statusType
## [1] "ProcessSucceeded"
## 
## $percentComplete
## [1] "100"

see also:

running(job)
error(job)
successful(job)

Plot the results

data <- result(job)
plot(data[,1:2], ylab = variables(fabric))

Use an email to listen for process completion

job <- geoknife(webgeom('state::New Hampshire'), fabric = 'prism', email = '[email protected]')

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

What libraries does 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.

Check Notes:

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_*"

Release Procedure

For release of the sbtools package, a number of steps are required.

1. Ensure all checks pass and code coverage is adequate.
2. Ensure NEWS.md reflects updates in version.
3. Update DESCRIPTION to reflect release version.
4. Convert DISCLAIMER.md to approved language and rebuild README.Rmd.
5. Create release candidate branch and commit release candidate.
6. Build source package and upload to CRAN.
7. Once accepted to CRAN, tag release candidate branch an push to repositories.
8. Change DISCLAIMER.md back to development mode and increment description version.
9. Merge release candidate and commit.
10. Open PR/MR in development state.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.