diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index ad8c5d35..90324f74 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.3.2 -Date: 2025-01-22 13:41:25 UTC -SHA: 81e3e39c3bb82e1b067fee72f6642d5f1cf1d55f +Version: 1.3.3 +Date: 2025-02-22 11:02:29 UTC +SHA: ecca8e4f69f34dc593e13c88236df68b722d9921 diff --git a/DESCRIPTION b/DESCRIPTION index 379b373e..72c228a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CausalQueries Type: Package Title: Make, Update, and Query Binary Causal Models -Version: 1.3.2 +Version: 1.3.3 Authors@R: c(person("Clara", "Bicalho", email = "clarabmcorreia@gmail.com", role = c("ctb")), person("Jasper", "Cooper", email = "jjc2247@columbia.edu", role = c("ctb")), person("Macartan", "Humphreys", email = "macartan@gmail.com", role = c("aut"), @@ -23,7 +23,7 @@ LazyData: true RoxygenNote: 7.3.2 Depends: methods, - R (>= 3.5.0) + R (>= 4.2.0) Imports: dplyr, dirmult (>= 0.1.3-4), diff --git a/NEWS.md b/NEWS.md index 3ac45a9f..074b58a0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# CausalQueries 1.3.3 + +This is a patch release implementing Stan optimization improving run time and +output formatting of the core Stan model. Additionally `type_distribution` has +been renamed to `type_posterior` for clarity. See `grab()` or `inspect()` +documentation for details. + # CausalQueries 1.3.2 This is a patch release updating documentation and removing the deprecated diff --git a/R/prep_stan_data.R b/R/prep_stan_data.R index 4319816a..6de83953 100644 --- a/R/prep_stan_data.R +++ b/R/prep_stan_data.R @@ -18,6 +18,8 @@ prep_stan_data <- function(model, keep_type_distribution = TRUE, censored_types = NULL) { i <- NULL + s <- NULL + # check data is in correct compact form if (!all(c("event", "count") %in% names(data))) { stop("Data should contain columns `event` and `count`") diff --git a/cran-comments.md b/cran-comments.md index 36662ce4..397e24d0 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,8 @@ -This is a patch release updating documentation and removing deprecated classes. +This is a patch release implementing Stan optimization. ## Test environments -* local Ubuntu 22.04.3 LTS install, R 4.4.1 +* local Ubuntu 22.04.5 LTS install, R 4.4.2 * win-builder, R version 4.4.2 * win-builder, R version 4.3.3 * win-builder, R r-devel diff --git a/man/prep_stan_data.Rd b/man/prep_stan_data.Rd index dcec38a4..fe89b5be 100644 --- a/man/prep_stan_data.Rd +++ b/man/prep_stan_data.Rd @@ -29,11 +29,6 @@ Create a list containing the data to be passed to 'stan model <- make_model('X->Y') data <- collapse_data(make_data(model, n = 6), model) CausalQueries:::prep_stan_data(model, data) - -model <- make_model('X->Y') |> - set_confound(list(X = 'Y[X=1]>Y[X=0]')) -data <- collapse_data(make_data(model, n = 6), model) -CausalQueries:::prep_stan_data(model, data) } } diff --git a/src/stanExports_simplexes.h b/src/stanExports_simplexes.h index cf1590ce..8bf03283 100644 --- a/src/stanExports_simplexes.h +++ b/src/stanExports_simplexes.h @@ -29,105 +29,105 @@ using namespace stan::math; stan::math::profile_map profiles__; static constexpr std::array locations_array__ = {" (found before start of program)", - " (in 'string', line 33, column 2 to column 49)", - " (in 'string', line 36, column 2 to column 45)", - " (in 'string', line 37, column 2 to column 43)", - " (in 'string', line 38, column 2 to column 35)", - " (in 'string', line 39, column 2 to column 35)", - " (in 'string', line 40, column 2 to column 40)", - " (in 'string', line 41, column 2 to column 37)", - " (in 'string', line 42, column 2 to column 44)", - " (in 'string', line 43, column 2 to column 38)", - " (in 'string', line 91, column 2 to column 24)", - " (in 'string', line 50, column 6 to column 78)", - " (in 'string', line 51, column 6 to line 53, column 22)", - " (in 'string', line 49, column 11 to line 54, column 5)", - " (in 'string', line 47, column 6 to column 24)", - " (in 'string', line 48, column 6 to column 31)", - " (in 'string', line 46, column 34 to line 49, column 5)", - " (in 'string', line 46, column 4 to line 54, column 5)", - " (in 'string', line 45, column 28 to line 55, column 3)", - " (in 'string', line 45, column 2 to line 55, column 3)", - " (in 'string', line 57, column 2 to column 50)", - " (in 'string', line 60, column 4 to column 71)", - " (in 'string', line 59, column 23 to line 61, column 3)", - " (in 'string', line 59, column 2 to line 61, column 3)", - " (in 'string', line 64, column 4 to column 41)", - " (in 'string', line 63, column 23 to line 65, column 3)", - " (in 'string', line 63, column 2 to line 65, column 3)", - " (in 'string', line 67, column 2 to column 17)", - " (in 'string', line 69, column 2 to column 17)", - " (in 'string', line 71, column 2 to column 35)", - " (in 'string', line 97, column 4 to column 35)", - " (in 'string', line 96, column 9 to line 98, column 3)", - " (in 'string', line 94, column 6 to column 54)", - " (in 'string', line 93, column 25 to line 95, column 5)", - " (in 'string', line 93, column 4 to line 95, column 5)", - " (in 'string', line 92, column 35 to line 96, column 3)", - " (in 'string', line 92, column 2 to line 98, column 3)", - " (in 'string', line 76, column 4 to line 77, column 67)", - " (in 'string', line 78, column 4 to column 51)", - " (in 'string', line 75, column 28 to line 79, column 3)", - " (in 'string', line 75, column 2 to line 79, column 3)", - " (in 'string', line 82, column 4 to line 86, column 6)", - " (in 'string', line 81, column 28 to line 87, column 3)", - " (in 'string', line 81, column 2 to line 87, column 3)", - " (in 'string', line 9, column 2 to column 24)", - " (in 'string', line 10, column 2 to column 23)", - " (in 'string', line 11, column 2 to column 23)", - " (in 'string', line 12, column 2 to column 28)", - " (in 'string', line 13, column 2 to column 23)", - " (in 'string', line 14, column 8 to column 20)", - " (in 'string', line 14, column 2 to column 48)", - " (in 'string', line 15, column 2 to column 22)", - " (in 'string', line 16, column 2 to column 24)", - " (in 'string', line 17, column 2 to column 28)", - " (in 'string', line 18, column 2 to column 47)", - " (in 'string', line 19, column 18 to column 26)", - " (in 'string', line 19, column 2 to column 42)", - " (in 'string', line 20, column 8 to column 20)", - " (in 'string', line 20, column 2 to column 44)", - " (in 'string', line 21, column 8 to column 20)", - " (in 'string', line 21, column 2 to column 42)", - " (in 'string', line 22, column 8 to column 15)", - " (in 'string', line 22, column 2 to column 42)", - " (in 'string', line 23, column 8 to column 15)", - " (in 'string', line 23, column 2 to column 40)", - " (in 'string', line 24, column 8 to column 20)", - " (in 'string', line 24, column 2 to column 51)", - " (in 'string', line 25, column 8 to column 20)", - " (in 'string', line 25, column 2 to column 49)", - " (in 'string', line 26, column 9 to column 17)", - " (in 'string', line 26, column 19 to column 26)", - " (in 'string', line 26, column 2 to column 30)", - " (in 'string', line 27, column 9 to column 17)", - " (in 'string', line 27, column 19 to column 26)", - " (in 'string', line 27, column 2 to column 35)", - " (in 'string', line 28, column 9 to column 16)", - " (in 'string', line 28, column 18 to column 24)", - " (in 'string', line 28, column 2 to column 30)", - " (in 'string', line 29, column 27 to column 35)", - " (in 'string', line 29, column 37 to column 43)", - " (in 'string', line 29, column 2 to column 47)", - " (in 'string', line 30, column 8 to column 16)", - " (in 'string', line 30, column 2 to column 33)", - " (in 'string', line 33, column 18 to column 41)", - " (in 'string', line 36, column 27 to column 35)", - " (in 'string', line 37, column 18 to column 30)", - " (in 'string', line 38, column 9 to column 17)", - " (in 'string', line 38, column 19 to column 26)", - " (in 'string', line 39, column 9 to column 16)", - " (in 'string', line 39, column 18 to column 25)", - " (in 'string', line 40, column 27 to column 34)", - " (in 'string', line 41, column 27 to column 33)", - " (in 'string', line 42, column 27 to column 35)", - " (in 'string', line 43, column 9 to column 21)", - " (in 'string', line 91, column 9 to column 16)", - " (in 'string', line 3, column 15 to column 22)", - " (in 'string', line 3, column 4 to column 26)", - " (in 'string', line 4, column 4 to column 39)", - " (in 'string', line 5, column 4 to column 13)", - " (in 'string', line 2, column 32 to line 6, column 3)"}; + " (in 'simplexes', line 33, column 2 to column 49)", + " (in 'simplexes', line 36, column 2 to column 45)", + " (in 'simplexes', line 37, column 2 to column 43)", + " (in 'simplexes', line 38, column 2 to column 35)", + " (in 'simplexes', line 39, column 2 to column 35)", + " (in 'simplexes', line 40, column 2 to column 40)", + " (in 'simplexes', line 41, column 2 to column 37)", + " (in 'simplexes', line 42, column 2 to column 44)", + " (in 'simplexes', line 43, column 2 to column 38)", + " (in 'simplexes', line 91, column 2 to column 24)", + " (in 'simplexes', line 50, column 6 to column 78)", + " (in 'simplexes', line 51, column 6 to line 53, column 22)", + " (in 'simplexes', line 49, column 11 to line 54, column 5)", + " (in 'simplexes', line 47, column 6 to column 24)", + " (in 'simplexes', line 48, column 6 to column 31)", + " (in 'simplexes', line 46, column 34 to line 49, column 5)", + " (in 'simplexes', line 46, column 4 to line 54, column 5)", + " (in 'simplexes', line 45, column 28 to line 55, column 3)", + " (in 'simplexes', line 45, column 2 to line 55, column 3)", + " (in 'simplexes', line 57, column 2 to column 50)", + " (in 'simplexes', line 60, column 4 to column 71)", + " (in 'simplexes', line 59, column 23 to line 61, column 3)", + " (in 'simplexes', line 59, column 2 to line 61, column 3)", + " (in 'simplexes', line 64, column 4 to column 41)", + " (in 'simplexes', line 63, column 23 to line 65, column 3)", + " (in 'simplexes', line 63, column 2 to line 65, column 3)", + " (in 'simplexes', line 67, column 2 to column 17)", + " (in 'simplexes', line 69, column 2 to column 17)", + " (in 'simplexes', line 71, column 2 to column 35)", + " (in 'simplexes', line 97, column 4 to column 35)", + " (in 'simplexes', line 96, column 9 to line 98, column 3)", + " (in 'simplexes', line 94, column 6 to column 54)", + " (in 'simplexes', line 93, column 25 to line 95, column 5)", + " (in 'simplexes', line 93, column 4 to line 95, column 5)", + " (in 'simplexes', line 92, column 35 to line 96, column 3)", + " (in 'simplexes', line 92, column 2 to line 98, column 3)", + " (in 'simplexes', line 76, column 4 to line 77, column 67)", + " (in 'simplexes', line 78, column 4 to column 51)", + " (in 'simplexes', line 75, column 28 to line 79, column 3)", + " (in 'simplexes', line 75, column 2 to line 79, column 3)", + " (in 'simplexes', line 82, column 4 to line 86, column 6)", + " (in 'simplexes', line 81, column 28 to line 87, column 3)", + " (in 'simplexes', line 81, column 2 to line 87, column 3)", + " (in 'simplexes', line 9, column 2 to column 24)", + " (in 'simplexes', line 10, column 2 to column 23)", + " (in 'simplexes', line 11, column 2 to column 23)", + " (in 'simplexes', line 12, column 2 to column 28)", + " (in 'simplexes', line 13, column 2 to column 23)", + " (in 'simplexes', line 14, column 8 to column 20)", + " (in 'simplexes', line 14, column 2 to column 48)", + " (in 'simplexes', line 15, column 2 to column 22)", + " (in 'simplexes', line 16, column 2 to column 24)", + " (in 'simplexes', line 17, column 2 to column 28)", + " (in 'simplexes', line 18, column 2 to column 47)", + " (in 'simplexes', line 19, column 18 to column 26)", + " (in 'simplexes', line 19, column 2 to column 42)", + " (in 'simplexes', line 20, column 8 to column 20)", + " (in 'simplexes', line 20, column 2 to column 44)", + " (in 'simplexes', line 21, column 8 to column 20)", + " (in 'simplexes', line 21, column 2 to column 42)", + " (in 'simplexes', line 22, column 8 to column 15)", + " (in 'simplexes', line 22, column 2 to column 42)", + " (in 'simplexes', line 23, column 8 to column 15)", + " (in 'simplexes', line 23, column 2 to column 40)", + " (in 'simplexes', line 24, column 8 to column 20)", + " (in 'simplexes', line 24, column 2 to column 51)", + " (in 'simplexes', line 25, column 8 to column 20)", + " (in 'simplexes', line 25, column 2 to column 49)", + " (in 'simplexes', line 26, column 9 to column 17)", + " (in 'simplexes', line 26, column 19 to column 26)", + " (in 'simplexes', line 26, column 2 to column 30)", + " (in 'simplexes', line 27, column 9 to column 17)", + " (in 'simplexes', line 27, column 19 to column 26)", + " (in 'simplexes', line 27, column 2 to column 35)", + " (in 'simplexes', line 28, column 9 to column 16)", + " (in 'simplexes', line 28, column 18 to column 24)", + " (in 'simplexes', line 28, column 2 to column 30)", + " (in 'simplexes', line 29, column 27 to column 35)", + " (in 'simplexes', line 29, column 37 to column 43)", + " (in 'simplexes', line 29, column 2 to column 47)", + " (in 'simplexes', line 30, column 8 to column 16)", + " (in 'simplexes', line 30, column 2 to column 33)", + " (in 'simplexes', line 33, column 18 to column 41)", + " (in 'simplexes', line 36, column 27 to column 35)", + " (in 'simplexes', line 37, column 18 to column 30)", + " (in 'simplexes', line 38, column 9 to column 17)", + " (in 'simplexes', line 38, column 19 to column 26)", + " (in 'simplexes', line 39, column 9 to column 16)", + " (in 'simplexes', line 39, column 18 to column 25)", + " (in 'simplexes', line 40, column 27 to column 34)", + " (in 'simplexes', line 41, column 27 to column 33)", + " (in 'simplexes', line 42, column 27 to column 35)", + " (in 'simplexes', line 43, column 9 to column 21)", + " (in 'simplexes', line 91, column 9 to column 16)", + " (in 'simplexes', line 3, column 15 to column 22)", + " (in 'simplexes', line 3, column 4 to column 26)", + " (in 'simplexes', line 4, column 4 to column 39)", + " (in 'simplexes', line 5, column 4 to column 13)", + " (in 'simplexes', line 2, column 32 to line 6, column 3)"}; template , stan::is_vt_not_complex>* = nullptr>