This project contains the core data management scripts of the USGS Powell Center working group on continental-scale stream metabolism. The resulting data are now published in
Appling, A.P., Read, J.S., Winslow, L.A., Arroita, M., Bernhardt, E.S., Griffiths, N.A., Hall, R.O., Jr., Harvey, J.W., Heffernan, J.B., Stanley, E.H., Stets, E.G., and Yackulic, C.B., 2018, Metabolism estimates for 356 U.S. rivers (2007-2017): U.S. Geological Survey data release. https://doi.org/10.5066/F70864KX.
and described in
Appling, A.P., Read, J.S., Winslow, L.A., Arroita, M., Bernhardt, E.S., Griffiths, N.A., Hall, R.O., Jr., Harvey, J.W., Heffernan, J.B., Stanley, E.H., Stets, E.G., and Yackulic, C.B., 2018. The metabolic regimes of 356 rivers in the United States. Scientific Data, Volume 5, Article 180292. https://doi.org/10.1038/sdata.2018.292.
The workflow is documented and enforced in remake/remake.yml, which can be run with these call in the R console:
setwd('remake')
remake::make()
setwd('..')For development, it may be easiest to run one target from one makefile at a
time. (The 'remake.yml' makefile actually calls several other makefiles, all in
the 'remake' directory.) The function remake_smu, defined in 'remake/build.R',
can help. For example:
source('remake/build.R')
sb_sites <- remake_smu('sb_sites', '1_site_data.yml')
wtr_nwis <- remake_smu('wtr_nwis', '1_timeseries.yml')The main USGS package dependencies for the stream_metab_usa R project are
streamMetabolizer, sbtools,dataRetrieval, geoknife, and mda.streams.
To install, execute the following code chunk.
install.packages(
c("dataRetrieval", "R.utils", "geoknife", "sbtools"),
repos=c("http://owi.usgs.gov/R","http://cran.rstudio.com"),
dependencies=TRUE, type="both")
devtools::install_github("USGS-R/mda.streams")
devtools::install_github("USGS-R/streamMetabolizer")This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at http://www.usgs.gov/visual-id/credit_usgs.html#copyright