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
NIEHS · Apr 26, 2024 · aa730b5 · aa730b5
2 parents 4aa13ad + d596c46
commit aa730b5
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
diff --git a/.github/workflows/sanitizers.yaml b/.github/workflows/sanitizers.yaml
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
diff --git a/.lintr b/.lintr
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PrestoGP
 Type: Package
 Title: Penalized Regression for Spatio-Temporal Outcomes via Gaussian Processes 
-Version: 0.2.0.9030
+Version: 0.2.0.9031
 Authors@R: c(
     person(given = "Eric",
            family = "Bair",
@@ -35,7 +35,6 @@ Imports:
     foreach,
     rlang,
     mvtnorm,
-    spam,
     psych,
     MASS,
     Matrix,

diff --git a/R/PrestoGP_Util_Functions.R b/R/PrestoGP_Util_Functions.R
@@ -131,12 +131,12 @@ transform_iid <- function(data, vecchia.approx, covparms, nuggets) {
   U.y <- U.obj$U[U.obj$latent, ]
 
   # compute transformed data in parts
-  part1.ord <- Matrix::crossprod(U.z, data[U.obj$ord.z, ]) # C.hat^-1
+  part1.ord <- crossprod(U.z, data[U.obj$ord.z, ]) # C.hat^-1
   temp1 <- U.y %*% part1.ord
   revord <- rev(seq_len(nrow(temp1)))
-  temp2 <- spam::solve(V.ord, temp1[revord, ])
-  part2.rev <- spam::solve(Matrix::t(V.ord), temp2)
-  part2.ord <- spam::crossprod(U.y, part2.rev[revord, ])
+  temp2 <- solve(V.ord, temp1[revord, ])
+  part2.rev <- solve(Matrix::t(V.ord), temp2)
+  part2.ord <- crossprod(U.y, part2.rev[revord, ])
   transform.ord <- part1.ord - part2.ord
 
   # return to original ordering
@@ -156,12 +156,12 @@ transform_miid <- function(data, vecchia.approx, params) {
   U.y <- U.obj$U[U.obj$latent, ]
 
   # compute transformed data in parts
-  part1.ord <- Matrix::crossprod(U.z, data[U.obj$ord.z, ]) # C.hat^-1
+  part1.ord <- crossprod(U.z, data[U.obj$ord.z, ]) # C.hat^-1
   temp1 <- U.y %*% part1.ord #
   revord <- rev(seq_len(nrow(temp1)))
-  temp2 <- spam::solve(V.ord, temp1[revord, ])
-  part2.rev <- spam::solve(Matrix::t(V.ord), temp2)
-  part2.ord <- spam::crossprod(U.y, part2.rev[revord, ])
+  temp2 <- solve(V.ord, temp1[revord, ])
+  part2.rev <- solve(Matrix::t(V.ord), temp2)
+  part2.ord <- crossprod(U.y, part2.rev[revord, ])
   transform.ord <- part1.ord - part2.ord
 
   # return to original ordering

diff --git a/R/Visualization.R b/R/Visualization.R
diff --git a/R/utils-tidy-eval.R b/R/utils-tidy-eval.R
diff --git a/man/FullModel-class.Rd b/man/FullModel-class.Rd
diff --git a/man/MultivariateVecchiaModel-class.Rd b/man/MultivariateVecchiaModel-class.Rd
diff --git a/man/PrestoGP-package.Rd b/man/PrestoGP-package.Rd
diff --git a/man/PrestoGPModel-class.Rd b/man/PrestoGPModel-class.Rd
diff --git a/man/VecchiaModel-class.Rd b/man/VecchiaModel-class.Rd
diff --git a/man/create.param.sequence.Rd b/man/create.param.sequence.Rd
diff --git a/man/createUMultivariate.Rd b/man/createUMultivariate.Rd
diff --git a/man/max_min_ordering.Rd b/man/max_min_ordering.Rd
diff --git a/man/prestogp_predict.Rd b/man/prestogp_predict.Rd
diff --git a/man/show-PrestoGPModel-method.Rd b/man/show-PrestoGPModel-method.Rd
diff --git a/man/show_theta-PrestoGPModel-method.Rd b/man/show_theta-PrestoGPModel-method.Rd
diff --git a/man/soil.Rd b/man/soil.Rd
diff --git a/man/tidyeval.Rd b/man/tidyeval.Rd
diff --git a/man/vecchia_Mlikelihood.Rd b/man/vecchia_Mlikelihood.Rd
diff --git a/man/vecchia_Mprediction.Rd b/man/vecchia_Mprediction.Rd
diff --git a/man/vecchia_Mspecify.Rd b/man/vecchia_Mspecify.Rd
diff --git a/man/weather.Rd b/man/weather.Rd
diff --git a/tests/testthat/Umat.rds b/tests/testthat/Umat.rds
diff --git a/tests/testthat/multivariate_sim_spatial3.Rdata b/tests/testthat/multivariate_sim_spatial3.Rdata
diff --git a/tests/testthat/small_sim.Rdata b/tests/testthat/small_sim.Rdata