From 6c79863ddc2be267b2b21f267733cbe12c49ce25 Mon Sep 17 00:00:00 2001 From: Shail Choksi Date: Tue, 9 Apr 2024 17:18:44 -0400 Subject: [PATCH] Pull request #43: Fix documentation issue blocking R CMD check and revert execute permission on all files Squashed commit of the following: commit 00171d7caa5c0eb0678401379566a722ba6ca7e7 Merge: cb9236b e0c9039 Author: Shail Choksi 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 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 Date: Tue Apr 9 17:10:53 2024 -0400 chmod changes commit cb9236b8adab059b338ef4d06c5fc1f4e262a6d8 Merge: cae8439 218a18a Author: Eric Bair 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 Date: Mon Apr 8 02:18:24 2024 -0400 Fixed a documentation issue commit cae8439517a38f41ff826018ce1d4719365695c1 Merge: c15c519 6bafe5c Author: Eric Bair 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 Date: Thu Apr 4 00:17:45 2024 -0400 Imputation beta implemented commit 1f4bcc714fbd43bfbe315a61ad03120c8fbc07ae Author: Eric Bair Date: Sun Mar 17 16:36:13 2024 -0400 Updated version number commit c15c519e6a81e7b899090e500cc278c795548ac2 Merge: 350b236 bab8357 Author: sciome-bot 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 Date: Thu Feb 8 14:24:34 2024 -0500 Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP commit bab8357d1f3cdc45ab38110355cc6d106dba8440 Merge: 55c0e8e 5394772 Author: Eric Bair Date: Thu Feb 8 14:19:24 2024 -0500 Pull request #38: Removed vignette, fixed lint issues Merge in STAT/prestogp from eb-dev to master * commit '53947729624b47fa1920ef39bd23d86f6e5cd7b7': Removed vignette, fixed lint issues commit 55c0e8e5ed2e189876c39d9e2337b51020b6505b Merge: 7e330f3 076c0a1 Author: sciome-bot Date: Thu Feb 8 14:18:48 2024 -0500 Merge branch 'main-sciome' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP commit 53947729624b47fa1920ef39bd23d86f6e5cd7b7 Merge: b431df4 7e330f3 Author: Eric Bair Date: Thu Feb 8 14:07:54 2024 -0500 Resolved merge conflict commit b431df45c0f80a54451536033c355b47620f3077 Author: Eric Bair Date: Thu Feb 8 13:56:38 2024 -0500 Removed vignette, fixed lint issues commit 7e330f30a659c579a3f291bc65c7918b9859c619 Merge: 13a6f44 f49d076 Author: sciome-bot Date: Wed Feb 7 23:25:05 2024 -0500 Merge branch 'master' of ssh://sciome-bot/stat/prestogp commit f49d0769a892df5dd711a2f8ebe08a3f9ca7af7b Merge: 439790c 59baf72 Author: Eric Bair Date: Wed Feb 7 23:19:54 2024 -0500 Pull request #35: Eb dev Merge in STAT/prestogp from eb-dev to master * commit '59baf720737abe59a04c98705c950ef1c7b63321': Fixed some documentation issues Removed C++11 compiler flag Added RandomFields data sets to PrestoGP Added knitr to Suggests in DESCRIPTION Documentation, R-cmd-check fixes, binomial regression commit 59baf720737abe59a04c98705c950ef1c7b63321 Author: Eric Bair Date: Tue Feb 6 17:49:48 2024 -0500 Fixed some documentation issues commit d857d8b367e3b46581677c4925ba8617f462c4d5 Author: Eric Bair Date: Thu Feb 1 02:16:44 2024 -0500 Removed C++11 compiler flag commit 662907d9e98a20ad06602c0dfe7e81b6390e3485 Author: Eric Bair Date: Wed Jan 31 15:36:37 2024 -0500 Added RandomFields data sets to PrestoGP commit cf2aadb50ecebd9e2f4401493da6901f10ee993a Author: Eric Bair Date: Wed Jan 31 13:40:24 2024 -0500 Added knitr to Suggests in DESCRIPTION ... and 35 more commits --- .Rbuildignore | 0 .gitignore | 0 DESCRIPTION | 2 +- Makefile | 0 NAMESPACE | 0 R/Log_Likelihood.R | 0 R/PrestoGP-package.R | 0 R/PrestoGP_CreateU_Multivariate.R | 0 R/PrestoGP_Full.R | 0 R/PrestoGP_Model.R | 0 R/PrestoGP_Multivariate_Vecchia.R | 0 R/PrestoGP_Util_Functions.R | 0 R/PrestoGP_Vecchia.R | 0 R/datadocs.R | 0 README.md | 0 data/soil.rda | Bin data/weather.rda | Bin examples/Analysis_NO2.R | 0 examples/Analysis_Simulations.R | 0 examples/Analysis_Simulations_Nugget_Sill_Ratio.R | 0 examples/Analysis_Simulations_Spatial_Range.R | 0 examples/Analysis_Simulations_Temporal_Range.R | 0 examples/Analysis_Simulations_Total_Variance.R | 0 .../Analysis_Simulations_Vecchia_Convergence.R | 0 examples/Multivariate_Example.R | 0 examples/Multivariate_Spatial.R | 0 examples/Multivariate_Spatial_multiple_outcomes.R | 0 examples/Multivariate_multiple_outcomes.R | 0 examples/Simple_Example.R | 0 examples/Simple_Example_Full.R | 0 examples/Simple_Spatial.R | 0 examples/Simple_Spatial_Full.R | 0 man/.Rhistory | 0 man/figures/prestoGP-logo.png | Bin man/prestogp_fit-PrestoGPModel-method.Rd | 13 +++++++++++++ src/Makevars | 0 src/Makevars.win | 0 src/createUMC.cpp | 0 tests/testthat.R | 0 tests/testthat/covlist.rds | Bin tests/testthat/covmat.rds | Bin tests/testthat/sim_multivariate.R | 0 tests/testthat/sim_multivariate_big.R | 0 tests/testthat/sim_multivariate_big.RData | Bin tests/testthat/sim_multivariate_big_pred.R | 0 tests/testthat/sim_multivariate_big_st.R | 0 tests/testthat/sim_multivariate_lik.R | 0 tests/testthat/sim_multivariate_small.R | 0 tests/testthat/sim_multivariate_small_pred.R | 0 tests/testthat/sim_vecchia.R | 0 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mode change 100755 => 100644 tests/testthat/test-PrestoGP_Univariate.R diff --git a/.Rbuildignore b/.Rbuildignore old mode 100755 new mode 100644 diff --git a/.gitignore b/.gitignore old mode 100755 new mode 100644 diff --git a/DESCRIPTION b/DESCRIPTION old mode 100755 new mode 100644 index f8cb765..00d3086 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: PrestoGP Type: Package Title: Penalized Regression for Spatio-Temporal Outcomes via Gaussian Processes -Version: 0.2.0.9028 +Version: 0.2.0.9029 Authors@R: c( person(given = "Eric", family = "Bair", diff --git a/Makefile b/Makefile old mode 100755 new mode 100644 diff --git a/NAMESPACE b/NAMESPACE old mode 100755 new mode 100644 diff --git a/R/Log_Likelihood.R b/R/Log_Likelihood.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP-package.R b/R/PrestoGP-package.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_CreateU_Multivariate.R b/R/PrestoGP_CreateU_Multivariate.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_Full.R b/R/PrestoGP_Full.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_Model.R b/R/PrestoGP_Model.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_Multivariate_Vecchia.R b/R/PrestoGP_Multivariate_Vecchia.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_Util_Functions.R b/R/PrestoGP_Util_Functions.R old mode 100755 new mode 100644 diff --git a/R/PrestoGP_Vecchia.R b/R/PrestoGP_Vecchia.R old mode 100755 new mode 100644 diff --git a/R/datadocs.R b/R/datadocs.R old mode 100755 new mode 100644 diff --git a/README.md b/README.md old mode 100755 new mode 100644 diff --git a/data/soil.rda b/data/soil.rda old mode 100755 new mode 100644 diff --git a/data/weather.rda b/data/weather.rda old mode 100755 new mode 100644 diff --git a/examples/Analysis_NO2.R b/examples/Analysis_NO2.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations.R b/examples/Analysis_Simulations.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations_Nugget_Sill_Ratio.R b/examples/Analysis_Simulations_Nugget_Sill_Ratio.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations_Spatial_Range.R b/examples/Analysis_Simulations_Spatial_Range.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations_Temporal_Range.R b/examples/Analysis_Simulations_Temporal_Range.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations_Total_Variance.R b/examples/Analysis_Simulations_Total_Variance.R old mode 100755 new mode 100644 diff --git a/examples/Analysis_Simulations_Vecchia_Convergence.R b/examples/Analysis_Simulations_Vecchia_Convergence.R old mode 100755 new mode 100644 diff --git a/examples/Multivariate_Example.R b/examples/Multivariate_Example.R old mode 100755 new mode 100644 diff --git a/examples/Multivariate_Spatial.R b/examples/Multivariate_Spatial.R old mode 100755 new mode 100644 diff --git a/examples/Multivariate_Spatial_multiple_outcomes.R b/examples/Multivariate_Spatial_multiple_outcomes.R old mode 100755 new mode 100644 diff --git a/examples/Multivariate_multiple_outcomes.R b/examples/Multivariate_multiple_outcomes.R old mode 100755 new mode 100644 diff --git a/examples/Simple_Example.R b/examples/Simple_Example.R old mode 100755 new mode 100644 diff --git a/examples/Simple_Example_Full.R b/examples/Simple_Example_Full.R old mode 100755 new mode 100644 diff --git a/examples/Simple_Spatial.R b/examples/Simple_Spatial.R old mode 100755 new mode 100644 diff --git a/examples/Simple_Spatial_Full.R b/examples/Simple_Spatial_Full.R old mode 100755 new mode 100644 diff --git a/man/.Rhistory b/man/.Rhistory old mode 100755 new mode 100644 diff --git a/man/figures/prestoGP-logo.png b/man/figures/prestoGP-logo.png old mode 100755 new mode 100644 diff --git a/man/prestogp_fit-PrestoGPModel-method.Rd b/man/prestogp_fit-PrestoGPModel-method.Rd old mode 100755 new mode 100644 index c45e599..bac8613 --- a/man/prestogp_fit-PrestoGPModel-method.Rd +++ b/man/prestogp_fit-PrestoGPModel-method.Rd @@ -16,7 +16,9 @@ beta.hat = NULL, tol = 0.999999, max_iters = 100, + center.y = NULL, impute.y = FALSE, + lod = NULL, verbose = FALSE, optim.method = "Nelder-Mead", optim.control = list(trace = 0, reltol = 0.001, maxit = 5000), @@ -59,6 +61,17 @@ tol*previous_error (optional). Defaults to 0.999999.} \item{max_iters}{Maximum number of iterations for the model fitting procedure. Defaults to 100.} +\item{center.y}{Should the Y's be mean centered before fitting the model? +Defaults to TRUE for gaussian models and FALSE for binomial models.} + +\item{impute.y}{Should missing Y's be imputed? Defaults to FALSE.} + +\item{lod}{Limit of detection value(s). Any Y value less than lod is +assumed to be missing when performing missing data imputation. Should be +numeric for univariate models and a list for multivariate models, where +each element of the list corresponds to an outcome. If not specified, it +is assumed that no limit of detection exists. Ignored if impute.y is FALSE.} + \item{verbose}{If TRUE, additional information about model fit will be printed. Defaults to FALSE.} diff --git a/src/Makevars b/src/Makevars old mode 100755 new mode 100644 diff --git a/src/Makevars.win b/src/Makevars.win old mode 100755 new mode 100644 diff --git a/src/createUMC.cpp b/src/createUMC.cpp old mode 100755 new mode 100644 diff --git a/tests/testthat.R b/tests/testthat.R old mode 100755 new mode 100644 diff --git a/tests/testthat/covlist.rds b/tests/testthat/covlist.rds old mode 100755 new mode 100644 diff --git a/tests/testthat/covmat.rds b/tests/testthat/covmat.rds old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate.R b/tests/testthat/sim_multivariate.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_big.R b/tests/testthat/sim_multivariate_big.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_big.RData b/tests/testthat/sim_multivariate_big.RData old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_big_pred.R b/tests/testthat/sim_multivariate_big_pred.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_big_st.R b/tests/testthat/sim_multivariate_big_st.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_lik.R b/tests/testthat/sim_multivariate_lik.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_small.R b/tests/testthat/sim_multivariate_small.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_multivariate_small_pred.R b/tests/testthat/sim_multivariate_small_pred.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia.R b/tests/testthat/sim_vecchia.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia.RData b/tests/testthat/sim_vecchia.RData old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia_pred.R b/tests/testthat/sim_vecchia_pred.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia_small.R b/tests/testthat/sim_vecchia_small.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia_small_pred.R b/tests/testthat/sim_vecchia_small_pred.R old mode 100755 new mode 100644 diff --git a/tests/testthat/sim_vecchia_st.R b/tests/testthat/sim_vecchia_st.R old mode 100755 new mode 100644 diff --git a/tests/testthat/test-Log_Likelihood.R b/tests/testthat/test-Log_Likelihood.R old mode 100755 new mode 100644 diff --git a/tests/testthat/test-PrestoGP_CreateU_Multivariate.R b/tests/testthat/test-PrestoGP_CreateU_Multivariate.R old mode 100755 new mode 100644 diff --git a/tests/testthat/test-PrestoGP_Model.R b/tests/testthat/test-PrestoGP_Model.R old mode 100755 new mode 100644 diff --git a/tests/testthat/test-PrestoGP_Multivariate_Vecchia_Model.R b/tests/testthat/test-PrestoGP_Multivariate_Vecchia_Model.R old mode 100755 new mode 100644 diff --git a/tests/testthat/test-PrestoGP_Univariate.R b/tests/testthat/test-PrestoGP_Univariate.R old mode 100755 new mode 100644