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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| #' Helper function for package development | ||
| #' | ||
| #' This is a manual extension of [testthat::snapshot_review()] which works for the \code{.rds} files used in | ||
| #' this package. | ||
| #' | ||
| #' @param path Character | ||
| #' @param ... Additional arguments passed to [waldo::compare()] | ||
| #' Gives the relative path to the test files to review | ||
| #' | ||
| snapshot_review_man <- function(path, ...) { | ||
| changed <- testthat:::snapshot_meta(path) | ||
| these_rds <- (tools::file_ext(changed$name) == "rds") | ||
| if (any(these_rds)) { | ||
| for (i in which(these_rds)) { | ||
| old <- readRDS(changed[i, "cur"]) | ||
| new <- readRDS(changed[i, "new"]) | ||
|
|
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| cat(paste0("Difference for check ", changed[i, "name"], " in test ", changed[i, "test"], "\n")) | ||
| print(waldo::compare(old, new, max_diffs = 50, ...)) | ||
| browser() | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -29,4 +29,4 @@ jobs: | |
| run: lintr::lint_package() | ||
| shell: Rscript {0} | ||
| env: | ||
| LINTR_ERROR_ON_LINT: true | ||
| LINTR_ERROR_ON_LINT: false | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -31,3 +31,6 @@ docs/* | |
| doc | ||
| Meta | ||
| docs | ||
| /doc/ | ||
| /Meta/ | ||
| .idea | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| Package: shapr | ||
| Version: 0.2.3 | ||
| Version: 0.2.3.9000 | ||
| Title: Prediction Explanation with Dependence-Aware Shapley Values | ||
| Description: Complex machine learning models are often hard to interpret. However, in | ||
| many situations it is crucial to understand and explain why a model made a specific | ||
|
|
@@ -12,6 +12,7 @@ Authors@R: c( | |
| person("Nikolai", "Sellereite", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-4671-0337")), | ||
| person("Martin", "Jullum", email = "[email protected]", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-3908-5155")), | ||
| person("Annabelle", "Redelmeier", email = "[email protected]", role = "aut"), | ||
| person("Jon", "Lachmann", email = "[email protected]", role = "aut"), | ||
| person("Anders", "Løland", email = "[email protected]", role = "ctb"), | ||
| person("Jens Christian", "Wahl", email = "[email protected]", role = "ctb"), | ||
| person("Camilla", "Lingjærde", role = "ctb"), | ||
|
|
@@ -32,22 +33,29 @@ Imports: | |
| Rcpp (>= 0.12.15), | ||
| condMVNorm, | ||
| mvnfast, | ||
| Matrix | ||
| Matrix, | ||
| future.apply | ||
| Suggests: | ||
| ranger, | ||
| xgboost, | ||
| mgcv, | ||
| testthat, | ||
| testthat (>= 3.0.0), | ||
| knitr, | ||
| rmarkdown, | ||
| roxygen2, | ||
| MASS, | ||
| ggplot2, | ||
| caret, | ||
| gbm, | ||
| party, | ||
| partykit | ||
| partykit, | ||
| waldo, | ||
| progressr, | ||
| future, | ||
| ggbeeswarm, | ||
| vdiffr, | ||
| forecast | ||
| LinkingTo: | ||
| RcppArmadillo, | ||
| Rcpp | ||
| VignetteBuilder: knitr | ||
| Config/testthat/edition: 3 | ||
| Roxygen: list(markdown = TRUE) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| #' Set up the framework chosen approach | ||
| #' | ||
| #' The different choices of `approach` takes different (optional) parameters, which are forwarded from [explain()]. | ||
| #' | ||
| #' @param ... `approach`-specific arguments. See below. | ||
| #' | ||
| #' @inheritParams default_doc_explain | ||
| #' | ||
| #' @export | ||
| setup_approach <- function(internal, ...) { | ||
| approach <- internal$parameters$approach | ||
|
|
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| this_class <- "" | ||
|
|
||
| if (length(approach) > 1) { | ||
| class(this_class) <- "combined" | ||
| } else { | ||
| class(this_class) <- approach | ||
| } | ||
|
|
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| UseMethod("setup_approach", this_class) | ||
| } | ||
|
|
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| #' @inheritParams default_doc | ||
| #' @export | ||
| setup_approach.combined <- function(internal, ...) { | ||
| org_approach <- internal$parameters$approach | ||
| unique_approaches <- unique(org_approach) | ||
|
|
||
| for (i in unique_approaches) { | ||
| internal$parameters$approach <- i | ||
| internal <- setup_approach(internal, ...) | ||
| } | ||
| internal$parameters$approach <- org_approach | ||
|
|
||
| return(internal) | ||
| } | ||
|
|
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| #' Generate data used for predictions | ||
| #' | ||
| #' @param x Explainer object. See [explain()] for more information. | ||
| #' | ||
| #' @param seed Positive integer. If `NULL` the seed will be inherited from the calling environment. | ||
| #' | ||
| #' @param index_features Positive integer vector. Specifies the indices of combinations to apply to the present method. | ||
| #' `NULL` means all combinations. Only used internally. | ||
| #' | ||
| #' @param ... Currently not used. | ||
| #' | ||
| #' @return A data.table containing simulated data passed to prediction(). | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| prepare_data <- function(internal, ...) { | ||
| this_class <- "" | ||
| class(this_class) <- internal$parameters$approach | ||
| UseMethod("prepare_data", this_class) | ||
| } | ||
|
|
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| #' @keywords internal | ||
| insert_defaults <- function(internal, defaults) { | ||
| par_names <- names(defaults) | ||
|
|
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| overwrite_names <- par_names[!(par_names %in% names(internal$parameters))] | ||
|
|
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| internal$parameters <- append(internal$parameters, defaults[overwrite_names]) | ||
|
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| return(internal) | ||
| } | ||
|
|
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| #' @keywords internal | ||
| get_factor_approaches <- function() { | ||
| c("'independence' (not recommended)", "'ctree'", "'categorical'") | ||
| } |
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