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jgabryjgabry
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Merge branch 'master' into pr/932
2 parents 513d09e + 4a865bb commit 6b47912

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Lines changed: 394 additions & 96 deletions

‎.github/workflows/R-CMD-check-wsl.yaml‎

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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.7.2
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with:
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r-version: 'release'
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rtools-version: '42'
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- uses: r-lib/actions/setup-pandoc@v2.7.2
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |
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install.packages("curl")
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shell: Rscript {0}
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- uses: Vampire/setup-wsl@v2
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- uses: Vampire/setup-wsl@v3
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with:
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distribution: Ubuntu-22.04
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use-cache: 'false'

‎.github/workflows/R-CMD-check.yaml‎

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- {os: ubuntu-20.04, r: 'devel', rtools: ''}
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- {os: ubuntu-20.04, r: 'release', rtools: ''}
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- {os: ubuntu-20.04, r: 'oldrel', rtools: ''}
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- {os: ubuntu-20.04, r: '3.6', rtools: ''}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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sudo apt-get install -y libcurl4-openssl-dev || true
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sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
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- uses: r-lib/actions/setup-r@v2.7.2
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- uses: r-lib/actions/setup-r@v2.8.7
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with:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools }}
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- uses: r-lib/actions/setup-pandoc@v2.7.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

‎.github/workflows/Test-coverage.yaml‎

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if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'"
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.7.2
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- uses: r-lib/actions/setup-pandoc@v2.7.2
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Install Ubuntu dependencies
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run: |
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2.7.2
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with:
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r-version: 'release'
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rtools-version: '42'
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- uses: r-lib/actions/setup-r@v2.8.7
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- uses: r-lib/actions/setup-pandoc@v2.7.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

‎.github/workflows/cmdstan-tarball-check.yaml‎

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sudo apt-get install -y libcurl4-openssl-dev || true
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sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
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- uses: r-lib/actions/setup-r@v2.7.2
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- uses: r-lib/actions/setup-r@v2.8.7
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with:
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r-version: ${{ matrix.config.r }}
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rtools-version: ${{ matrix.config.rtools }}
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- uses: r-lib/actions/setup-pandoc@v2.7.2
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- uses: r-lib/actions/setup-pandoc@v2.8.7
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- name: Query dependencies
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run: |

‎DESCRIPTION‎

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@@ -3,12 +3,13 @@ Title: R Interface to 'CmdStan'
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Version: 0.7.1
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Date: 2024-01-09
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Authors@R:
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c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
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email = "jsg2201@columbia.edu"),
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c(person(given = "Jonah", family = "Gabry", role = "aut",
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email = "jsg2201@columbia.edu"),
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person(given = "Rok", family = "Češnovar", role = "aut",
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email = "rok.cesnovar@fri.uni-lj.si"),
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person(given = "Andrew", family = "Johnson", role = "aut",
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comment = c(ORCID = "0000-0001-7000-8065")),
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email = "rok.cesnovar@fri.uni-lj.si"),
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person(given = "Andrew", family = "Johnson", role = c("aut", "cre"),
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email = "andrew.johnson@arjohnsonau.com",
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comment = c(ORCID = "0000-0001-7000-8065")),
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person(given = "Ben", family = "Bales", role = "ctb"),
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person(given = "Mitzi", family = "Morris", role = "ctb"),
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person(given = "Mikhail", family = "Popov", role = "ctb"),
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Roxygen: list(markdown = TRUE, r6 = FALSE)
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SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan)
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Depends:
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R (>= 3.5.0)
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R (>= 4.0.0)
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Imports:
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checkmate,
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data.table,

‎NAMESPACE‎

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S3method(as_draws,CmdStanMLE)
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S3method(as_draws,CmdStanPathfinder)
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S3method(as_draws,CmdStanVB)
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export(as.CmdStanDiagnose)
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export(as.CmdStanGQ)
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export(as.CmdStanLaplace)
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export(as.CmdStanMCMC)
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export(as.CmdStanMLE)
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export(as.CmdStanPathfinder)
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export(as.CmdStanVB)
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export(as_cmdstan_fit)
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export(as_draws)
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export(as_mcmc.list)

‎R/args.R‎

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fileext = ".json"
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)
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for (i in seq_along(inv_metric_paths)) {
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if (length(inv_metric[[i]]) == 1 && metric == "diag_e") {
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inv_metric[[i]] <- array(inv_metric[[i]], dim = c(1))
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}
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write_stan_json(list(inv_metric = inv_metric[[i]]), inv_metric_paths[i])
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}
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‎R/cmdstanr-package.R‎

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#' [_Getting started with CmdStanR_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html)
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#' demonstrates the basic functionality of the package.
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#'
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#' For a list of global [options][base::options()] see
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#' [cmdstanr_global_options].
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#'
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#' @template seealso-docs
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#' @inherit cmdstan_model examples
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#' @import R6

‎R/fit.R‎

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out <- private$inv_metric_
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if (matrix && !is.matrix(out[[1]])) {
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# convert each vector to a diagonal matrix
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out <- lapply(out, diag)
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out <- lapply(out, function(x) diag(x, nrow = length(x)))
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} else if (length(out[[1]]) == 1) {
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# convert each scalar to an array with dimension 1
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out <- lapply(out, array, dim = c(1))
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}
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out
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}

‎R/generics.R‎

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#' Coercion methods for CmdStan objects
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#'
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#' These are generic functions intended to primarily be used by developers of
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#' packages that interface with on CmdStanR. Developers can define methods on
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#' top of these generics to coerce objects into CmdStanR's fitted model objects.
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#'
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#' @param object to be coerced
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#' @param ... additional arguments
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#'
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#' @name cmdstan_coercion
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NULL
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanMCMC <- function(object, ...) {
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UseMethod("as.CmdStanMCMC")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanMLE <- function(object, ...) {
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UseMethod("as.CmdStanMLE")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanLaplace <- function(object, ...) {
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UseMethod("as.CmdStanLaplace")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanVB <- function(object, ...) {
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UseMethod("as.CmdStanVB")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanPathfinder <- function(object, ...) {
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UseMethod("as.CmdStanPathfinder")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanGQ <- function(object, ...) {
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UseMethod("as.CmdStanGQ")
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}
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#' @rdname cmdstan_coercion
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#' @export
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as.CmdStanDiagnose <- function(object, ...) {
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UseMethod("as.CmdStanDiagnose")
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}

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