Initialize salt-marsh-mapping with user parameters

Reads user-set parameters for package saltmarsh.

Usage

init()

Details

User parameters are set in two distinct locations:

1. The initialization file, in the user's home directory, ~/saltmarsh.yml. This file should contain five lines:

   basedir: c:/Work/etc/saltmarsh
parsdir: pars
parsfile: pars.yml
scratchdir: c:/Work/etc/saltmarsh/data/scratch
   

   a. basedir points to the base directory

   b. parsdir is the parameters subdirectory. It should be pars unless you have a good reason to change it.

   c. parsfile points to the main parameter file. It should be pars.yml.

   d. scratchdir points to the scratch drive, where the cache directory will be located. See notes on caching, below.

2. Everything else, in <basedir>/<parsdir>. The primary parameter file is pars.yml, which points to other parameters (such as sites.txt).

These parameters include:

• sites the name of the sites file, sites.txt by default

• classes the name of the classes file, classes.txt by default

• dirs alternative names for various subdirectories. The directories will keep the standard structure–you can change names here but not paths.

• gather a block of parameters for gather()

This approach splits the user- and platform-dependent parameters (saltmarsh.yml) from parameters that are likely to be shared among users and across platforms (those in parsdir). It allows multiple users on a shared machine (such as Unity cluster) to set user-specific parameters if need be, while sharing other parameters.

This function reads the user parameters and adds them to the environment the with all parameters. It is automatically run upon loading the package, and may be rerun by the user if parameter files are changed.

You can change standard directory names (data, models, gis, flights, field, shapefiles, samples, predicted, and cache) by setting each within a dirs: block in pars.yml. Directories default to standard names, which is usually what you want.

To change parameters on the fly, you can set the components of the. If you change any elements of dirs, you'll have to run set_dirs() afterwards. Note that parameters changed on the fly will only persist until the next call to init(), which can be called on demand but also happens automatically when the package is loaded.

For example:

the$sites <- 'newsites'
the$dirs$cache <- 'newcache'
the$dirs$samples <- 'samples99'
set_dirs()

Notes on caching. A cache directory is required when sourcedrive = google or sftp. The cache directory should be larger than the total amount of data processed–this code isn't doing any quota management. This is not an issue when using a scratch drive on Unity, as the limit is 50 TB. There's no great need to carry over cached data over long periods, as downloading from Google or SFTP to Unity is very fast. Be polite and release the scratch workspace when you're done. See comments in get_file() for more notes on caching.