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Show/accessor methods need to be updated (or created) #48
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@ericbair-sciome Accessing beta and theta parameters is pretty important - beta especially. One may want to even see the last iteration betas as a function of the penalty, so you can make plots like this BTW: Are the objects S4 or S3? |
These are S4 objects. Currently, one can access the betas by referencing the slots directly: PrestoGP_object@beta or PrestoGP_object@covparams, but that's not very user friendly. That's especially true for the Matern parameters, since it is just a long vector, and it's not immediately obvious which elements are sigma, scale, smoothness, etc. So I will add some methods to make that easier. And the final glmnet object is stored in the PrestoGP class, so it would easy to add a method to create that type of plot as well. We can do all of this without creating new methods, to be clear, so it's not a show stopper in terms of analyzing your data. But I wanted to put it on my to do list. |
Squashed commit of the following: commit aa730b5eb427e9b7770834084d6ebf0486d6af91 Merge: 4aa13ad d596c46 Author: Eric Bair <eric.bair@sciome.com> Date: Fri Apr 26 14:26:42 2024 -0400 Pull request #48: Eb dev Merge in STAT/prestogp from eb-dev to master * commit 'd596c46f0d84704329b02cdf39f419e1ee9f626b': Fixed file permissions Removed the spam dependency to fix an R CMD check issue Observation-level lod, imputation tests, updated README commit d596c46f0d84704329b02cdf39f419e1ee9f626b Author: Eric Bair <eric.bair@sciome.com> Date: Fri Apr 26 14:05:23 2024 -0400 Fixed file permissions commit 654390898843a67f3b0b6b8160688bee1a8049be Merge: 86bdd92 4aa13ad Author: Eric Bair <eric.bair@sciome.com> Date: Thu Apr 25 18:19:08 2024 -0400 Fixed a merge conflict commit 86bdd92b511c482f5677644a8616d12593ca52b1 Author: Eric Bair <eric.bair@sciome.com> Date: Thu Apr 25 18:11:04 2024 -0400 Removed the spam dependency to fix an R CMD check issue commit 4aa13ad28f920ddad21f1fef99900173f12f4827 Author: sciome-bot <software.tools@sciome.com> Date: Wed Apr 24 20:16:19 2024 -0400 Remove dependency on sysreqs to fix sanitizer action. commit 7fad5a6b6d3f6e8a73565e359601c2f8a4dd43a7 Merge: 3f3c9e3 df836b7 Author: sciome-bot <software.tools@sciome.com> Date: Wed Apr 24 20:12:09 2024 -0400 Merge branch 'main-sciome' of sciome-bot-git:NIEHS/PrestoGP commit 3f3c9e3ca731faf18111e29d8245609b2b45e391 Author: Eric Bair <eric.bair@sciome.com> Date: Wed Apr 24 17:17:41 2024 -0400 Observation-level lod, imputation tests, updated README Squashed commit of the following: commit 9dfcef34dd108dad30ec5cb72a66308073f5d1a2 Merge: 33b0560 68671e6 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Apr 23 16:41:15 2024 -0400 Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into eb-dev Conflicts: README.md commit 33b0560503970cbd4410e2750a157561cc2a2994 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Apr 23 03:05:12 2024 -0400 Observation-level lod, imputation tests, updated README commit 9dfcef34dd108dad30ec5cb72a66308073f5d1a2 Merge: 33b0560 68671e6 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Apr 23 16:41:15 2024 -0400 Merge branch 'master' of http://192.168.167.103:7990/bitbucket/scm/stat/prestogp into eb-dev Conflicts: README.md commit 33b0560503970cbd4410e2750a157561cc2a2994 Author: Eric Bair <eric.bair@sciome.com> Date: Tue Apr 23 03:05:12 2024 -0400 Observation-level lod, imputation tests, updated README commit 68671e6eadf74fca86937c3363ba2f6f606fa39c Merge: 00171d7 7fe8997 Author: sciome-bot <software.tools@sciome.com> Date: Wed Apr 10 09:51:12 2024 -0400 Merge branch 'main-sciome' of sciome-bot-git:NIEHS/PrestoGP commit 00171d7caa5c0eb0678401379566a722ba6ca7e7 Merge: cb9236b e0c9039 Author: Shail Choksi <shail.choksi@sciome.com> Date: Tue Apr 9 17:17:39 2024 -0400 Pull request #44: Revert execute permissions on all files Merge in STAT/prestogp from shail-dev-2 to master * commit 'e0c90391f290dd2f6ebe62f6a69db8ec006c1872': chmod changes Implement imputation beta commit e0c90391f290dd2f6ebe62f6a69db8ec006c1872 Merge: b8f91fd 05e7dfb Author: sciome-bot <software.tools@sciome.com> Date: Tue Apr 9 17:16:29 2024 -0400 Merge branch 'to-git' of ssh://sciome-bot/stat/prestogp into shail-dev-2 commit b8f91fdaa970f2eff4608cd71fdf8d7a6e79588f Author: sciome-bot <software.tools@sciome.com> Date: Tue Apr 9 17:10:53 2024 -0400 chmod changes commit cb9236b8adab059b338ef4d06c5fc1f4e262a6d8 Merge: cae8439 218a18a Author: Eric Bair <eric.bair@sciome.com> Date: Tue Apr 9 17:03:10 2024 -0400 Pull request #42: Fixed a documentation issue Merge in STAT/prestogp from eb-dev to master * commit '218a18a6cd2891c7c4975e408f7308243c11abbf': Fixed a documentation issue commit 218a18a6cd2891c7c4975e408f7308243c11abbf Author: Eric Bair <eric.bair@sciome.com> Date: Mon Apr 8 02:18:24 2024 -0400 Fixed a documentation issue commit cae8439517a38f41ff826018ce1d4719365695c1 Merge: c15c519 6bafe5c Author: Eric Bair <eric.bair@sciome.com> Date: Fri Apr 5 16:38:34 2024 -0400 Pull request #40: Imputation beta Merge in STAT/prestogp from eb-dev to master * commit '6bafe5cf9d5574074bdcb0288e4b48efb87a8840': Imputation beta implemented Updated version number commit 6bafe5cf9d5574074bdcb0288e4b48efb87a8840 Author: Eric Bair <eric.bair@sciome.com> Date: Thu Apr 4 00:17:45 2024 -0400 Imputation beta implemented commit 1f4bcc714fbd43bfbe315a61ad03120c8fbc07ae Author: Eric Bair <eric.bair@sciome.com> Date: Sun Mar 17 16:36:13 2024 -0400 Updated version number commit c15c519e6a81e7b899090e500cc278c795548ac2 Merge: 350b236 bab8357 Author: sciome-bot <software.tools@sciome.com> Date: Thu Feb 8 14:25:12 2024 -0500 Merge branch 'master' of ssh://sciome-bot/stat/prestogp commit 350b236ba0b77dfc5056e9e53b00f05cbb1cc4d0 Merge: 55c0e8e 95fef8c Author: sciome-bot <software.tools@sciome.com> Date: Thu Feb 8 14:24:34 2024 -0500 Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP ... and 43 more commits
At the moment, there is no way to show or access the regression coefficients or Matern covariance parameters for a PrestoGP model other than examining the "beta" and "covparams" slots directly. (Some "show" methods exist, but they have not been updated since I started working on this project.) That is confusing and not user friendly. Aside from "show" methods, I thought it would be useful to create some accessor methods such as "prestogp_get_beta", "prestogp_get_sigma", "prestogp_get_smoothness", etc. to allow users to easily extract any parameters of interest after fitting a model.
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