From 89ff4282451de4e166203c27cd8141674a4b2040 Mon Sep 17 00:00:00 2001 From: Deyu Ming Date: Mon, 16 Dec 2024 11:11:05 +0000 Subject: [PATCH] Doc updates --- 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/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 +- 33 files changed, 33 insertions(+), 33 deletions(-) diff --git a/man/alm.Rd b/man/alm.Rd index fc3fd2e..7cc16b7 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 72298f4..02ed8a1 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \keyword{internal} diff --git a/man/continue.Rd b/man/continue.Rd index 19ef3e5..a4602bb 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/deserialize.Rd b/man/deserialize.Rd index 1d1d596..03b7c35 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ See the \emph{Note} section in \code{\link[=serialize]{serialize()}}. diff --git a/man/design.Rd b/man/design.Rd index e8de129..4cbd3a0 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/dgp.Rd b/man/dgp.Rd index 77d05cb..c886949 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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/draw.Rd b/man/draw.Rd index 66950d2..f48b209 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/get_thread_num.Rd b/man/get_thread_num.Rd index 6e786fe..b10a81d 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } diff --git a/man/gp.Rd b/man/gp.Rd index 0919908..7ccc037 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 615275c..2366313 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/lgp.Rd b/man/lgp.Rd index 2092906..1cbb0f2 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/mice.Rd b/man/mice.Rd index a20ecdc..4dd84eb 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 ec404e9..ea450aa 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } diff --git a/man/pack.Rd b/man/pack.Rd index 7b5c0f3..27c0767 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/plot.Rd b/man/plot.Rd index 4ec333e..428640c 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/predict.Rd b/man/predict.Rd index 29290df..98e6801 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/prune.Rd b/man/prune.Rd index 8cb0503..f9bfd98 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/read.Rd b/man/read.Rd index 103dd48..d7678a6 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/serialize.Rd b/man/serialize.Rd index 9d1c6b6..b73d4f0 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 5d270d1..0c4a0f6 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/set_imp.Rd b/man/set_imp.Rd index 1245807..555aca2 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/set_linked_idx.Rd b/man/set_linked_idx.Rd index acb5461..996657f 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 2c0330d..05d92b3 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/set_thread_num.Rd b/man/set_thread_num.Rd index 005cd5a..526a55c 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } diff --git a/man/set_vecchia.Rd b/man/set_vecchia.Rd index 2dee8f2..8e26f78 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 c326c7f..4f780de 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/trace_plot.Rd b/man/trace_plot.Rd index 7b30f14..d3b6f0b 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/unpack.Rd b/man/unpack.Rd index 9bd1d8e..400a058 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \examples{ \dontrun{ diff --git a/man/update.Rd b/man/update.Rd index 019b11d..38b4451 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/validate.Rd b/man/validate.Rd index 9f07d31..4d08e13 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/vigf.Rd b/man/vigf.Rd index c82b3e0..b80137f 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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 63bb2ad..ac189a0 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \note{ \itemize{ diff --git a/man/write.Rd b/man/write.Rd index b45a26a..016c974 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/}. +See further examples and tutorials at \url{https://mingdeyu.github.io/dgpsi-R/dev/}. } \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}