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