Prepare the release of version 1.0.0 (#70)

* Fix typos * Update NEWS, bump version * Fix moved link * update cran_comments.md * update cran_comments.md * Add badges in README.md
ModelOriented · Mar 20, 2023 · 76993e0 · 76993e0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: survex
 Title: Explainable Machine Learning in Survival Analysis
-Version: 0.2.2.9000
+Version: 1.0.0
 Authors@R: 
     c(
         person("Mikołaj", "Spytek", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7111-2286")),

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,7 @@
 * *breaking change:* refactored the structure of `model_performance_survival` object - calculated metrics are now in a `$result` list.
 * added new `calculation_method` for `surv_shap()` called `"kernelshap"` that use `kernelshap` package and its implementation of improved Kernel SHAP (set as default) ([#45](https://github.com/ModelOriented/survex/issues/45))
 * rename old method `"kernel"` to `"exact_kernel"`
-* added new import ([`kernelshap`](https://github.com/mayer79/kernelshap) package) 
+* added new import ([`kernelshap`](https://github.com/ModelOriented/kernelshap) package) 
 * fixed invalid color palette order in plot feature importance
 * fixed predict_parts survshap running out of memory with more than 16 variables ([#25](https://github.com/ModelOriented/survex/issues/25))
 * added `max_vars` parameter for predict_parts explanations ([#27](https://github.com/ModelOriented/survex/issues/27))
@@ -26,7 +26,6 @@
 * reduced the default number of time points for evaluation when creating the explainer to 50
 
 
-
 # survex 0.2.2
 
 * improved and unified API documentation ([#2](https://github.com/ModelOriented/survex/issues/2))

diff --git a/R/explain.R b/R/explain.R
@@ -38,7 +38,7 @@
 #' * `residual_function` - function that returns residuals, shall return a single numerical value for each observation.
 #' * `class` - class/classes of a model.
 #' * `label` - label of explainer.
-#' * `model_info` - named list contating basic information about model, like package, version of package and type.
+#' * `model_info` - named list containing basic information about model, like package, version of package and type.
 #' * `times` - a vector of times, that are used for evaluation of survival function and cumulative hazard function by default
 #' * `predict_survival_function` - function that is used for model predictions in the form of survival function
 #' * `predict_cumulative_hazard_function` - function that is used for model predictions in the form of cumulative hazard function

diff --git a/R/plot_model_parts_survival.R b/R/plot_model_parts_survival.R
@@ -11,7 +11,7 @@
 #' @section Plot options:
 #'
 #' * `title` - character, title of the plot
-#' * `subtitle` - character, subtitle of the plot, if `NULL` automaticaly generated as "created for XXX, YYY models", where XXX and YYY are explainer labels
+#' * `subtitle` - character, subtitle of the plot, if `NULL` automatically generated as "created for XXX, YYY models", where XXX and YYY are explainer labels
 #' * `max_vars` - maximum number of variables to be plotted (least important variables are ignored)
 #' * `colors` - character vector containing the colors to be used for plotting variables (containing either hex codes "#FF69B4", or names "blue")
 #' * `rug` - character, one of `"all"`, `"events"`, `"censors"`, `"none"` or `NULL`. Which times to mark on the x axis in `geom_rug()`.

diff --git a/R/plot_surv_feature_importance.R b/R/plot_surv_feature_importance.R
@@ -1,4 +1,4 @@
-#' Plot Permuatational Feature Importance for Survival Models
+#' Plot Permutational Feature Importance for Survival Models
 #'
 #' This function plots feature importance objects created for survival models using the
 #' `model_parts()` function with a time-dependent metric, that is `loss_one_minus_cd_auc()` or

diff --git a/R/predict_profile.R b/R/predict_profile.R
@@ -1,6 +1,6 @@
 #' Instance Level Profile as Ceteris Paribus for Survival Models
 #'
-#' This function calculates Ceteris Paribus Proifles for a specific observation with the possibility to take the time dimension into account.
+#' This function calculates Ceteris Paribus Profiles for a specific observation with the possibility to take the time dimension into account.
 #'
 #' @param explainer an explainer object - model preprocessed by the `explain()` function
 #' @param new_observation a new observation for which the prediction need to be explained

diff --git a/R/surv_feature_importance.R b/R/surv_feature_importance.R
@@ -1,6 +1,6 @@
 #' Helper functions for `model_parts.R`
 #'
-#' This function is used to calculate permutational feature imporance using
+#' This function is used to calculate permutational feature importance using
 #' a time-dependent metric. The result is the change in loss function at each
 #' time point after permuting each selected variable.
 #'

diff --git a/R/utils.R b/R/utils.R
@@ -78,7 +78,7 @@ generate_discrete_color_scale <- function(n, colors = NULL) {
 
 #' Transform Fixed Point Prediction into a Stepfunction
 #'
-#' Some models return the survival funciton or cumulative hazard function prediction at the times of events present in the training data set. This is a convenient utility to allow the prediction to be evaluated at any time.
+#' Some models return the survival function or cumulative hazard function prediction at the times of events present in the training data set. This is a convenient utility to allow the prediction to be evaluated at any time.
 #'
 #' @param predict_function a function making the prediction based on `model` and `newdata` arguments, the `...` parameter is also passed to this function. It has to return either a numeric vector of the same length as `eval_times`, a matrix with this number of columns and the same number of rows as `nrow(newdata)`. It can also return a list, with one of the elements containing such an object.
 #' @param eval_times a numeric vector of times, at which the fixed predictions are made. This can be `NULL`, if `predict_function` returns a list which contains such a vector.

diff --git a/README.md b/README.md
@@ -3,6 +3,9 @@
 [![R-CMD-check](https://github.com/ModelOriented/survex/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ModelOriented/survex/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/ModelOriented/survex/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ModelOriented/survex?branch=main)
 [![CRAN status](https://www.r-pkg.org/badges/version/survex)](https://cran.r-project.org/package=survex)
+[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/survex?color=orange)](https://cranlogs.r-pkg.org/badges/grand-total/survex)
+[![DrWhy-BackBone](https://img.shields.io/badge/DrWhy-BackBone-373589)](http://drwhy.ai/#BackBone)
+
 
 ## Overview 
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,8 +1,4 @@
-## Resubmission 30/11/2022
-
-* wrapped long examples in \donttest{}
-  they no longer exceed 5s
-* fixed NOTE about doi numbers using wrong tags
+## Submission 20/03/2023 v.1.0.0
 
 ## R CMD check results
 

diff --git a/man/explain_survival.Rd b/man/explain_survival.Rd
diff --git a/man/plot.model_parts_survival.Rd b/man/plot.model_parts_survival.Rd
diff --git a/man/plot.surv_feature_importance.Rd b/man/plot.surv_feature_importance.Rd
diff --git a/man/predict_profile.surv_explainer.Rd b/man/predict_profile.surv_explainer.Rd
diff --git a/man/surv_feature_importance.Rd b/man/surv_feature_importance.Rd
diff --git a/man/transform_to_stepfunction.Rd b/man/transform_to_stepfunction.Rd