Closed adamdsmith closed 8 years ago
This is great. Can you also add some tests to inst/unitTests/?
Sure. I've not done them before, so your patience is appreciated. Do you want one for each class of unmarkedFit?
Just one test would be fine. Ideally, the test should only take a few seconds to run, so consider doing it on an occu fit. The entire suite of tests can be run using: source("runTests.R")
. Thanks again.
Hope this test is sufficient. I have not tested the parallel application on Mac/Linux, but it should work.
hi Adam, Thanks for this! I'll try to do the merge this week and then test it out myself (in meetings all day between now and Thursday morning, so probably end of the week) regards andy
On Mon, Nov 16, 2015 at 9:03 AM, Adam Smith notifications@github.com wrote:
Hope this test is sufficient. I have not tested the parallel application on Mac/Linux, but it should work.
— Reply to this email directly or view it on GitHub https://github.com/rbchan/unmarked/pull/86#issuecomment-157037909.
Thanks Adam. Merged now.
I've added the capability to generate bootstrapped test statistics on multiple cores using package
parallel
. Parallel computation is the default option so long as more than two cores are present on the machine (parboot
uses nCores - 1) and the requested number of simulations is >= 100 (the approximate point at which parallel computation is advantageous).I've tested it successfully on the following
unmarkedFit
s: MPois and GMM (with and without a custompiFun
), DS and GDS, PCount, GPC, and PCO, and Occu.It does not work for
unmarkedFit
s without asimulate
method (e.g., OccuPEN) or withfitted
orresiduals
methods (e.g., OccuFP).I've changed the DESCRIPTION and NAMESPACE files to reflect the
parallel
package dependency.I also updated parboot.Rd file to reflect the new arguments related to parallel computation.