usepa/lakemorpho

Calculate metrics about a lake using just its shape

lakemorpho

The purpose of lakemorpho is to provide a suite of tools that can be used to calculate basic lake morphometry metrics from an input SpatialPolygonsDataframe of a lake and a digital elevation model, as a RasterLayer, for the terrain surrounding that lake. These tools are being used to calculate lake morphometry metrics for all "lakepond" waterbodies in the NHDPlus V2.

For a detailed description of the package and its use, see:

Hollister J and Stachelek J. lakemorpho: Calculating lake morphometry metrics in R [version 1; referees: 2 approved]. F1000Research 2017, 6:1718 (doi: 10.12688/f1000research.12512.1)

Metrics Included

lakemorpho calculates the following metrics

• Surface Area
• Shoreline Length
• Shoreline Development
• Maximum Depth
• Mean Depth
• Lake Volume
• Maximum Lake Length
• Mean Lake Width
• Maximum Lake Width
• Major and Minor Axis
• Fetch from a specified bearing

To install

Install version 1.1.0 of lakemorpho from CRAN:

install.packages("lakemorpho")
require(lakemorpho)

Install development version of lakemorpho from GitHub:

install.packages("devtools")
require(devtools)
install_github("USEPA/lakemorpho")
require(lakemorpho)

EPA Disclaimer

The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.

lakemorpho's Issues

update dependencies to include geosphere

lakeSurroundTopo should have error on # of lake check

replace return(warning()) with stop().

License?

Hi Jeff - was wondering if there's a particular reason for the NASA license rather than CC0. The NASA license would prevent someone from using this code in conjunction with other open source code that were not their own original development work. I'm trying to lean toward CC0, myself. https://github.com/USEPA/FRS-getfacilities-samples/blob/master/LICENSE

Out of memory with large rasters/lakes

Reports of out of error memories on larger lakes and larger rasters.

Need to figure out why this is happening and see if I can hack a solution that allows larger datasets with out issue.

Sample data coming from rich

Compare GME geom.polygonfetch with lakeFetch

Might be interesting to see if the geom.polygonfetch command in Geospatial Modelling Environment returns similar results as lakeFetch: http://www.spatialecology.com/gme/geompolygonfetch.htm

calcLakeMetrics example needs to have bearing updated

Lake on Edge in lakeSurroundTopo

Doesn't currently assign this correctly.

Fix reference with umlaut - throwing encoding error on windows

Link F1000 paper here to illustrate package usage?

calc metrics without a raster

I think it would be useful to be able to calcLakeMetrics without supplying a raster. I was only interested in width and length in a recent analysis so I used the following non-ideal solution:

lake_outline_sp <- as(spark_outline, "Spatial")
r <- rasterize(lake_outline_sp, raster(lake_outline_sp))

lake_outline_sp <- spTransform(lake_outline_sp, CRS("+proj=utm +zone=10 +datum=WGS84"))
r <- projectRaster(r, crs = "+proj=utm +zone=10 +datum=WGS84")

lake_lm <- lakeSurroundTopo(lake_outline_sp, r)

calcLakeMetrics(lake_lm, bearing = 45, pointDens = 250)

Try to speed up lakeMaxLength

lakeFetch

update lakeFetch so that it can take any numeric bearing.

Return value

Need more detail on the return values in the documentation. Need to indicate type, units, etc.

add switch to lakeMaxWidth to have line intersect or not the lake max length line

Add input error check on all functions

Once accepted to CRAN - new release and DOI

Add tests

Flexibility on input classes

Many functions don't need elevation. Add in flexiblity so that those can be run directly on sp objects.

lakeMaxWidth not working correctly for lakes with a max length line with negative slope

Complete Vignette

Prior to next release, complete vignette

Try to speed up lakeSurroundTopo

plot.lakeMorpho

Need to add examples and make sure default is working (right parameters and ...)

lakeSurroundTopo input elevation looking for tif: allow tif or RasterLayer as input

Try to speed up lakMaxWidth

revist poitndens - use all points in poly as starting point

pointdens is currently required and samples along the polygon boundary. This is nice because it allows you to control the time it takes to calc the lines. Also a problem becuase it impacts the accuracy of the resultant line if an insufficeint number of points are used. A default value of all points that make up the polygon would be acceptable.

Might be better to switch this to a percentage sample of the polygon points instead of using spsample along the boundary.