Package: dgpsi 2.4.0-9000

dgpsi: Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations

Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process, and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and Ming & Williamson (2023) <arxiv:2306.01212>. To get started with the package, see <https://mingdeyu.github.io/dgpsi-R/>.

Authors:Deyu Ming [aut, cre, cph], Daniel Williamson [aut]

dgpsi_2.4.0-9000.tar.gz
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dgpsi.pdf |dgpsi.html✨
dgpsi/json (API)
NEWS

# Install 'dgpsi' in R:

install.packages('dgpsi', repos = c('https://mingdeyu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mingdeyu/dgpsi-r/issues

On CRAN:

deep-gaussian-processes emulation gaussian-processes surrogate-models

32 exports 1.65 score 81 dependencies 53 scripts 224 downloads

Last updated 3 months agofrom:1988310d7c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 02 2024
R-4.5-win	OK	Sep 02 2024
R-4.5-linux	OK	Sep 02 2024
R-4.4-win	OK	Sep 02 2024
R-4.4-mac	OK	Sep 02 2024
R-4.3-win	OK	Sep 02 2024
R-4.3-mac	OK	Sep 02 2024

Exports:alm combine continue design dgp draw get_thread_num gp Hetero init_py kernel lgp mice NegBin nllik pack pei Poisson prune read set_imp set_linked_idx set_seed set_thread_num set_vecchia trace_plot unpack update validate vigf window write

Dependencies:askpass benchmarkme benchmarkmeData bitops class classInt clhs cli cluster codetools colorspace cpp11 curl DBI doParallel dplyr e1071 fansi farver foreach generics ggforce ggplot2 glue gtable here httr isoband iterators jsonlite KernSmooth labeling lattice lhs lifecycle magrittr MASS Matrix mgcv mime munsell nlme openssl patchwork pillar pkgconfig plyr png polyclip proxy R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML reshape2 reticulate rlang rprojroot s2 scales sf sp stringi stringr sys systemfonts terra tibble tidyselect tweenr units utf8 uuid vctrs viridisLite withr wk

A Quick Guide to dgpsi

Rendered fromdgpsi.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-01-15
Started: 2022-08-16

DGP Emulation with the Heteroskedastic Gaussian Likelihood

Rendered frommotorcycle.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-11-14
Started: 2022-08-23

Large-scale DGP Emulation

Rendered fromlarge_scale_emulation.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-06-07
Started: 2024-06-07

Linked (D)GP Emulation

Rendered fromlinked_DGP.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-11-14
Started: 2022-08-13

Sequential Design I

Rendered fromseq_design.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-01-15
Started: 2022-11-14

Sequential Design II

Rendered fromseq_design_2.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-06-07
Started: 2022-11-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Locate the next design point for a (D)GP emulator or a bundle of (D)GP emulators using ALM	alm alm.bundle alm.dgp alm.gp
Combine layers	combine
Continue the training of a DGP emulator	continue
Sequential design of a (D)GP emulator or a bundle of (D)GP emulators	design design.bundle design.dgp design.gp
Deep Gaussian process emulator construction	dgp
Validation plots of a sequential design	draw draw.bundle draw.dgp draw.gp
Get the number of threads	get_thread_num
Gaussian process emulator construction	gp
Initialize a heteroskedastic Gaussian likelihood node	Hetero
'python' environment initialization	init_py
Initialize a Gaussian process node	kernel
Linked (D)GP emulator construction	lgp
Locate the next design point for a (D)GP emulator or a bundle of (D)GP emulators using MICE	mice mice.bundle mice.dgp mice.gp
Initialize a negative Binomial likelihood node	NegBin
Calculate negative predicted log-likelihood	nllik
Pack GP and DGP emulators into a bundle	pack
Locate the next design point for a (D)GP emulator or a bundle of (D)GP emulators using PEI	pei pei.bundle pei.dgp pei.gp
Validation plots of a constructed GP, DGP, or linked (D)GP emulator	plot plot.dgp plot.gp plot.lgp
Initialize a Poisson likelihood node	Poisson
Predictions from GP, DGP, or linked (D)GP emulators	predict predict.dgp predict.gp predict.lgp
Static pruning of a DGP emulator	prune
Load the stored emulator	read
Reset number of imputations for a DGP emulator	set_imp
Set linked indices	set_linked_idx
Random seed generator	set_seed
Set the number of threads	set_thread_num
Add or remove the Vecchia approximation	set_vecchia
Summary of a constructed GP, DGP, or linked (D)GP emulator	summary summary.dgp summary.gp summary.lgp
Plot of DGP model parameter traces	trace_plot
Unpack a bundle of (D)GP emulators	unpack
Update a GP or DGP emulator	update update.dgp update.gp
Validate a constructed GP, DGP, or linked (D)GP emulator	validate validate.dgp validate.gp validate.lgp
Locate the next design point for a (D)GP emulator or a bundle of (D)GP emulators using VIGF	vigf vigf.bundle vigf.dgp vigf.gp
Trim the sequences of model parameters of a DGP emulator	window
Save the constructed emulator	write