From e214c25969aadc3c1528eeac8b92070a23b040a1 Mon Sep 17 00:00:00 2001 From: Deyu Ming Date: Sat, 14 Dec 2024 20:33:19 +0000 Subject: [PATCH] update to v2.5.0 update to v2.5.0 --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- R/initi_py.R | 12 ++++++------ README.md | 9 +++++---- man/alm.Rd | 2 +- man/combine.Rd | 2 +- man/continue.Rd | 2 +- man/deserialize.Rd | 2 +- man/design.Rd | 2 +- man/dgp.Rd | 2 +- man/dgpsi-package.Rd | 2 +- man/draw.Rd | 2 +- man/get_thread_num.Rd | 2 +- man/gp.Rd | 2 +- man/init_py.Rd | 2 +- man/lgp.Rd | 2 +- man/mice.Rd | 2 +- man/nllik.Rd | 2 +- man/pack.Rd | 2 +- man/plot.Rd | 2 +- man/predict.Rd | 2 +- man/prune.Rd | 2 +- man/read.Rd | 2 +- man/serialize.Rd | 2 +- man/set_id.Rd | 2 +- man/set_imp.Rd | 2 +- man/set_linked_idx.Rd | 2 +- man/set_seed.Rd | 2 +- man/set_thread_num.Rd | 2 +- man/set_vecchia.Rd | 2 +- man/summary.Rd | 2 +- man/trace_plot.Rd | 2 +- man/unpack.Rd | 2 +- man/update.Rd | 2 +- man/validate.Rd | 2 +- man/vigf.Rd | 2 +- man/window.Rd | 2 +- man/write.Rd | 2 +- 38 files changed, 48 insertions(+), 47 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c61c77b..5080cb0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: dgpsi Type: Package Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process Emulations -Version: 2.4.0-9000 +Version: 2.5.0 Authors@R: c( person('Deyu', 'Ming', role = c('aut', 'cre', 'cph'), email = 'deyu.ming.16@ucl.ac.uk'), @@ -13,7 +13,7 @@ Description: Interface to the 'python' package 'dgpsi' for Gaussian process, dee and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI). The implementations follow Ming & Guillas (2021) and Ming, Williamson, & Guillas (2023) and - Ming & Williamson (2023) . To get started with the package, + Ming & Williamson (2023) . To get started with the package, see . License: MIT + file LICENSE URL: https://github.com/mingdeyu/dgpsi-R, https://mingdeyu.github.io/dgpsi-R/ diff --git a/NEWS.md b/NEWS.md index 170f1da..eaec235 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# dgpsi 2.4.0-9000 (development version) +# dgpsi 2.5.0 - Training times for DGP emulators are now approximately 30%-40% faster. - The computation of (D)GP predictions and Leave-One-Out (LOO) evaluations is now 6-7 times faster. - The `nb_parallel` argument has been removed from relevant functions, as multi-threading is now integrated by default. diff --git a/R/initi_py.R b/R/initi_py.R index 302032d..b36da23 100644 --- a/R/initi_py.R +++ b/R/initi_py.R @@ -43,13 +43,13 @@ init_py <- function(py_ver = NULL, dgpsi_ver = NULL, reinstall = FALSE, uninstal if ( is.null(py_ver) ) py_ver <- '3.9.13' if ( is.null(dgpsi_ver) ) { ##For devel version - dgpsi_ver <- c('cython>=0.29.30', 'dill>=0.3.2, <=0.3.5.1', 'jupyter>=1.0.0', 'matplotlib-base>=3.2.1', 'numba >=0.51.2', - 'numpy >=1.18.2', 'pathos ==0.2.9', 'multiprocess ==0.70.13', 'psutil >=5.8.0', 'pybind11 >=2.10.0', 'pythran >=0.11.0', - 'scikit-build >=0.15.0', 'scikit-learn >=0.22.0', 'scipy >=1.4.1', 'tqdm >=4.50.2', 'tabulate >=0.8.7', 'faiss-cpu >=1.7.4') - env_name <- 'dgp_si_R_2_4_0_9000' + #dgpsi_ver <- c('cython>=0.29.30', 'dill>=0.3.2, <=0.3.5.1', 'jupyter>=1.0.0', 'matplotlib-base>=3.2.1', 'numba >=0.51.2', + # 'numpy >=1.18.2', 'pathos ==0.2.9', 'multiprocess ==0.70.13', 'psutil >=5.8.0', 'pybind11 >=2.10.0', 'pythran >=0.11.0', + # 'scikit-build >=0.15.0', 'scikit-learn >=0.22.0', 'scipy >=1.4.1', 'tqdm >=4.50.2', 'tabulate >=0.8.7', 'faiss-cpu >=1.7.4') + #env_name <- 'dgp_si_R_2_4_0_9000' ##For release version - #dgpsi_ver <- 'dgpsi==2.4.0' - #env_name <- 'dgp_si_R_2_4_0' + dgpsi_ver <- 'dgpsi==2.5.0' + env_name <- 'dgp_si_R_2_5_0' } else { env_name <- paste('dgp_si_R_', gsub(".", "_", dgpsi_ver,fixed=TRUE), sep = "") dgpsi_ver <- paste('dgpsi==', dgpsi_ver, sep = "") diff --git a/README.md b/README.md index 7e3d89b..3b17670 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Download](https://cranlogs.r-pkg.org/badges/grand-total/dgpsi?color=brightgreen)](https://CRAN.R-project.org/package=dgpsi) [![R-CMD-check](https://github.com/mingdeyu/dgpsi_R/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mingdeyu/dgpsi-R/actions/workflows/R-CMD-check.yaml) [![DOC](https://img.shields.io/badge/DOC-release-brightgreen)](https://mingdeyu.github.io/dgpsi-R/) -[![python](https://img.shields.io/badge/Python-dgpsi%20v2.4.0-informational)](https://github.com/mingdeyu/DGP) +[![python](https://img.shields.io/badge/Python-dgpsi%20v2.5.0-informational)](https://github.com/mingdeyu/DGP) The R package `dgpsi` provides R interface to Python package [`dgpsi`](https://github.com/mingdeyu/DGP) for deep and linked Gaussian process emulations using stochastic imputation (SI). @@ -29,8 +29,9 @@ The R package `dgpsi` provides R interface to Python package [`dgpsi`](https://g * Multi-core predictions and validations for GP, DGP, and Linked (D)GP emulators. * Sequential designs for (D)GP emulators and bundles of (D)GP emulators. * Automatic pruning of DGP emulators, both statically and dynamically. -* [![Feature Badge](https://img.shields.io/badge/New-In%20Dev%20Version-orange)](https://mingdeyu.github.io/dgpsi-R/dev/) [Large-scale GP, DGP, and Linked (D)GP emulations](https://mingdeyu.github.io/dgpsi-R/dev/articles/large_scale_emulation.html). -* [![Feature Badge](https://img.shields.io/badge/New-In%20Dev%20Version-orange)](https://mingdeyu.github.io/dgpsi-R/dev/) [Scalable DGP classification using Stochastic Imputation](https://mingdeyu.github.io/dgpsi-R/dev/articles/classification.html). +* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Large-scale GP, DGP, and Linked (D)GP emulations](https://mingdeyu.github.io/dgpsi-R/articles/large_scale_emulation.html). +* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Scalable DGP classification using Stochastic Imputation](https://mingdeyu.github.io/dgpsi-R/articles/classification.html). +* [![Feature Badge](https://img.shields.io/badge/New-In%20v2.5.0-orange)](https://mingdeyu.github.io/dgpsi-R/) [Bayesian optimization](https://mingdeyu.github.io/dgpsi-R/articles/bayes_opt.html). ## Getting started * Check [A Quick Guide to dgpsi](https://mingdeyu.github.io/dgpsi-R/articles/dgpsi.html) to get started with the package. @@ -55,7 +56,7 @@ After the installation, run library(dgpsi) ``` -to load the package. To install or activate the required Python environment automatically, simply run a function from the package. That's it, the package is now ready to use! +to load the package. To install or activate the required Python environment automatically, you can either run `dgpsi::init_py()` explicitly or simply call any function from the package. That's it - the package is ready to use! > **Note** > After loading `dgpsi`, the package may take some time to compile and initiate the underlying Python environment the first diff --git a/man/alm.Rd b/man/alm.Rd index 7cc16b7..fc3fd2e 100644 --- a/man/alm.Rd +++ b/man/alm.Rd @@ -136,7 +136,7 @@ This function searches from a candidate set to locate the next design point(s) t or a bundle of (D)GP emulators using the Active Learning MacKay (ALM) criterion (see the reference below). } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ The first column of the matrix supplied to the first argument of \code{aggregate} must correspond to the first output dimension of the DGP emulator diff --git a/man/combine.Rd b/man/combine.Rd index 02ed8a1..72298f4 100644 --- a/man/combine.Rd +++ b/man/combine.Rd @@ -22,6 +22,6 @@ please use the updated \code{\link[=lgp]{lgp()}} function, which provides a simp approach to building (D)GP emulators. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \keyword{internal} diff --git a/man/continue.Rd b/man/continue.Rd index a4602bb..19ef3e5 100644 --- a/man/continue.Rd +++ b/man/continue.Rd @@ -46,7 +46,7 @@ An updated \code{object}. This function implements additional training iterations for a DGP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/deserialize.Rd b/man/deserialize.Rd index 03b7c35..1d1d596 100644 --- a/man/deserialize.Rd +++ b/man/deserialize.Rd @@ -18,7 +18,7 @@ The S3 class of a GP emulator, a DGP emulator, a linked (D)GP emulator, or a bun This function restores the serialized emulator created by \code{\link[=serialize]{serialize()}}. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ See the \emph{Note} section in \code{\link[=serialize]{serialize()}}. diff --git a/man/design.Rd b/man/design.Rd index 4cbd3a0..e8de129 100644 --- a/man/design.Rd +++ b/man/design.Rd @@ -368,7 +368,7 @@ a bundle of (D)GP emulators, supporting an array of popular methods as well as u It can also be used as a wrapper for Bayesian optimization methods. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/dgp.Rd b/man/dgp.Rd index c886949..77d05cb 100644 --- a/man/dgp.Rd +++ b/man/dgp.Rd @@ -272,7 +272,7 @@ The returned \code{dgp} object can be used by This function builds and trains a DGP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ Any R vector detected in \code{X} and \code{Y} will be treated as a column vector and automatically converted into a single-column diff --git a/man/dgpsi-package.Rd b/man/dgpsi-package.Rd index 89d6887..86ed172 100644 --- a/man/dgpsi-package.Rd +++ b/man/dgpsi-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -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) \href{https://arxiv.org/abs/2306.01212}{arXiv:2306.01212}. To get started with the package, see \url{https://mingdeyu.github.io/dgpsi-R/}. +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) \doi{10.48550/arXiv.2306.01212}. To get started with the package, see \url{https://mingdeyu.github.io/dgpsi-R/}. } \seealso{ Useful links: diff --git a/man/draw.Rd b/man/draw.Rd index f48b209..66950d2 100644 --- a/man/draw.Rd +++ b/man/draw.Rd @@ -48,7 +48,7 @@ A \code{patchwork} object. This function draws diagnostic and validation plots for a sequential design of a (D)GP emulator or a bundle of (D)GP emulators. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/get_thread_num.Rd b/man/get_thread_num.Rd index b10a81d..6e786fe 100644 --- a/man/get_thread_num.Rd +++ b/man/get_thread_num.Rd @@ -16,5 +16,5 @@ This function gets the number of threads used for parallel computations involved in the package. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } diff --git a/man/gp.Rd b/man/gp.Rd index 7ccc037..0919908 100644 --- a/man/gp.Rd +++ b/man/gp.Rd @@ -166,7 +166,7 @@ The returned \code{gp} object can be used by This function builds and trains a GP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ Any R vector detected in \code{X} and \code{Y} will be treated as a column vector and automatically converted into a single-column diff --git a/man/init_py.Rd b/man/init_py.Rd index 2366313..615275c 100644 --- a/man/init_py.Rd +++ b/man/init_py.Rd @@ -41,7 +41,7 @@ No return value, called to install required 'python' environment. This function initializes the 'python' environment for the package. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/lgp.Rd b/man/lgp.Rd index 1cbb0f2..2092906 100644 --- a/man/lgp.Rd +++ b/man/lgp.Rd @@ -105,7 +105,7 @@ The returned \code{lgp} object can be used by This function constructs a linked (D)GP emulator for a model chain or network. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/mice.Rd b/man/mice.Rd index 4dd84eb..a20ecdc 100644 --- a/man/mice.Rd +++ b/man/mice.Rd @@ -141,7 +141,7 @@ This function searches from a candidate set to locate the next design point(s) t or a bundle of (D)GP emulators using the Mutual Information for Computer Experiments (MICE), see the reference below. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ The first column of the matrix supplied to the first argument of \code{aggregate} must correspond to the first output dimension of the DGP emulator diff --git a/man/nllik.Rd b/man/nllik.Rd index ea450aa..ec404e9 100644 --- a/man/nllik.Rd +++ b/man/nllik.Rd @@ -24,5 +24,5 @@ This function computes the predictive negative log-likelihood from a DGP emulator with a likelihood layer. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } diff --git a/man/pack.Rd b/man/pack.Rd index 928fa09..f24f253 100644 --- a/man/pack.Rd +++ b/man/pack.Rd @@ -28,7 +28,7 @@ This function packs GP emulators and DGP emulators into a \code{bundle} class fo sequential designs if each emulator emulates one output dimension of the underlying simulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/plot.Rd b/man/plot.Rd index 428640c..4ec333e 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -143,7 +143,7 @@ A \code{patchwork} object. This function draws validation plots of a GP, DGP, or linked (D)GP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/predict.Rd b/man/predict.Rd index 98e6801..29290df 100644 --- a/man/predict.Rd +++ b/man/predict.Rd @@ -198,7 +198,7 @@ The \code{results} slot will also include: This function implements prediction from GP, DGP, or linked (D)GP emulators. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/prune.Rd b/man/prune.Rd index f9bfd98..8cb0503 100644 --- a/man/prune.Rd +++ b/man/prune.Rd @@ -24,7 +24,7 @@ An updated \code{object} that could be an instance of \code{gp}, \code{dgp}, or This function implements static pruning for a DGP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/read.Rd b/man/read.Rd index d7678a6..103dd48 100644 --- a/man/read.Rd +++ b/man/read.Rd @@ -16,7 +16,7 @@ The S3 class of a GP emulator, a DGP emulator, a linked (D)GP emulator, or a bun This function loads the \code{.pkl} file that stores the emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/serialize.Rd b/man/serialize.Rd index b73d4f0..9d1c6b6 100644 --- a/man/serialize.Rd +++ b/man/serialize.Rd @@ -21,7 +21,7 @@ A serialized version of \code{object}. This function serializes the constructed emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ Since the constructed emulators are 'python' objects, they cannot be directly exported to other R processes for parallel diff --git a/man/set_id.Rd b/man/set_id.Rd index 0c4a0f6..5d270d1 100644 --- a/man/set_id.Rd +++ b/man/set_id.Rd @@ -22,7 +22,7 @@ The updated \code{object}, with the assigned ID stored in its \code{id} slot. This function assigns a unique identifier to an emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/set_imp.Rd b/man/set_imp.Rd index 555aca2..1245807 100644 --- a/man/set_imp.Rd +++ b/man/set_imp.Rd @@ -18,7 +18,7 @@ An updated \code{object} with the information of \code{B} incorporated. This function resets the number of imputations for prediction from a DGP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/set_linked_idx.Rd b/man/set_linked_idx.Rd index 996657f..acb5461 100644 --- a/man/set_linked_idx.Rd +++ b/man/set_linked_idx.Rd @@ -22,7 +22,7 @@ This function is deprecated and will be removed in the next release. The updated for (D)GP emulators. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ This function is useful when different models are emulated by different teams. Each team can create their (D)GP emulator diff --git a/man/set_seed.Rd b/man/set_seed.Rd index 05d92b3..2c0330d 100644 --- a/man/set_seed.Rd +++ b/man/set_seed.Rd @@ -17,7 +17,7 @@ This function initializes a random number generator that sets the random seed in to ensure reproducible results from the package. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/set_thread_num.Rd b/man/set_thread_num.Rd index 526a55c..005cd5a 100644 --- a/man/set_thread_num.Rd +++ b/man/set_thread_num.Rd @@ -20,5 +20,5 @@ This function sets the number of threads for parallel computations involved in the package. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } diff --git a/man/set_vecchia.Rd b/man/set_vecchia.Rd index 8e26f78..2dee8f2 100644 --- a/man/set_vecchia.Rd +++ b/man/set_vecchia.Rd @@ -46,7 +46,7 @@ This function adds or removes the Vecchia approximation from a GP, DGP or linked constructed by \code{\link[=gp]{gp()}}, \code{\link[=dgp]{dgp()}} or \code{\link[=lgp]{lgp()}}. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ This function is useful for quickly switching between Vecchia and non-Vecchia approximations for an existing emulator diff --git a/man/summary.Rd b/man/summary.Rd index 4f780de..c326c7f 100644 --- a/man/summary.Rd +++ b/man/summary.Rd @@ -46,7 +46,7 @@ This function provides a summary of key information for a GP, DGP, or linked (D) by generating either a table or an interactive plot of the emulator’s structure. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/trace_plot.Rd b/man/trace_plot.Rd index d3b6f0b..7b30f14 100644 --- a/man/trace_plot.Rd +++ b/man/trace_plot.Rd @@ -22,7 +22,7 @@ This function draws trace plots for the hyperparameters of a chosen GP node in a DGP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/unpack.Rd b/man/unpack.Rd index 400a058..9bd1d8e 100644 --- a/man/unpack.Rd +++ b/man/unpack.Rd @@ -18,7 +18,7 @@ This function unpacks a bundle of (D)GP emulators safely so that any further man will not impact those in the bundle. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \examples{ \dontrun{ diff --git a/man/update.Rd b/man/update.Rd index 38b4451..019b11d 100644 --- a/man/update.Rd +++ b/man/update.Rd @@ -73,7 +73,7 @@ An updated \code{object}. This function updates the training input and output of a GP or DGP emulator with an option to refit the emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/validate.Rd b/man/validate.Rd index 4d08e13..9f07d31 100644 --- a/man/validate.Rd +++ b/man/validate.Rd @@ -206,7 +206,7 @@ emulator. This function calculates Leave-One-Out (LOO) cross validation or Out-Of-Sample (OOS) validation statistics for a constructed GP, DGP, or linked (D)GP emulator. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/vigf.Rd b/man/vigf.Rd index b80137f..c82b3e0 100644 --- a/man/vigf.Rd +++ b/man/vigf.Rd @@ -137,7 +137,7 @@ This function searches from a candidate set to locate the next design point(s) t or a bundle of (D)GP emulators using the Variance of Improvement for Global Fit (VIGF). For VIGF on GP emulators, see the reference below. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ The first column of the matrix supplied to the first argument of \code{aggregate} must correspond to the first output dimension of the DGP emulator diff --git a/man/window.Rd b/man/window.Rd index ac189a0..63bb2ad 100644 --- a/man/window.Rd +++ b/man/window.Rd @@ -25,7 +25,7 @@ This function trims the sequence of hyperparameter estimates within a DGP emulat generated during training. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ \itemize{ diff --git a/man/write.Rd b/man/write.Rd index 016c974..b45a26a 100644 --- a/man/write.Rd +++ b/man/write.Rd @@ -22,7 +22,7 @@ No return value. \code{object} will be saved to a local \code{.pkl} file specifi This function saves the constructed emulator to a \code{.pkl} file. } \details{ -See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/}. } \note{ Since emulators built from the package are 'python' objects, \code{\link[=save]{save()}} from R will not work as it would for R objects. If \code{object}