{"id":25441384,"url":"https://github.com/bertcarnell/tornado","last_synced_at":"2025-11-01T12:30:37.420Z","repository":{"id":56934257,"uuid":"171073931","full_name":"bertcarnell/tornado","owner":"bertcarnell","description":"tornado plots for model sensitivity 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\"tornado\"\noutput: \n  md_document:\n    variant: gfm\n  \n---\n\n\u003c!-- DO NOT EDIT:  README.md is created from README.Rmd --\u003e\n\n\u003cdiv\u003e\n  \u003ctable\u003e\n    \u003ctr\u003e\n      \u003ctd\u003e\n        \u003cimg align=\"left\" width=\"200\" height=\"200\" src=\"man/figures/logo.png\"/\u003e\n      \u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/table\u003e\n\u003c/div\u003e\n\u003cfooter\u003e\u0026copy; Copyright 2024 Robert Carnell\u003c/footer\u003e\n\n\n```{r setup, echo=FALSE, include=FALSE}\nrequire(knitr)\nrequire(survival)\nrequire(caret)\nrequire(randomForest)\nrequire(tornado)\nknitr::opts_chunk$set(fig.path = \"man/figures/\")\n```\n\n```{r badges, echo=FALSE, results=\"asis\"}\ncat(paste0(\"|\u003csub\u003e\", \n           paste0(\n             c(\"Actions\", \"Code Coverage\", \"Website\", \"Downloads\", \"CRAN\"), \n             collapse=\"\u003c/sub\u003e|\u003csub\u003e\"), \n           \"\u003c/sub\u003e|\\n\"))\ncat(paste0(\"|\", paste0(rep(\":---:\", 5), collapse=\"|\"), \"|\\n\"))\ncat(paste0(\"|\", \n           paste0(c(\"[![R-CMD-CHECK](https://github.com/bertcarnell/tornado/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/bertcarnell/tornado/actions/workflows/r-cmd-check.yml)\",\n                    \"[![Coverage status](https://codecov.io/gh/bertcarnell/tornado/branch/master/graph/badge.svg)](https://codecov.io/github/bertcarnell/tornado?branch=master)\",\n                    \"[![](https://img.shields.io/badge/pkgdown-tornado-blue.svg)](https://bertcarnell.github.io/tornado/)\",\n                    \"[![](https://cranlogs.r-pkg.org/badges/tornado)](https://cran.r-project.org/package=tornado)\",\n                    \"[![CRAN status](https://www.r-pkg.org/badges/version/tornado)](https://cran.r-project.org/package=tornado)\"),\n                  collapse=\"|\"), \n           \"|\"))\n```\n\n# tornado\n\n`tornado` plots for model sensitivity analysis.\n\n[website](https://bertcarnell.github.io/tornado/)\n\n## Installation\n\nYou can also install the development version of `tornado` from github with:\n\n```{r install2, echo=TRUE, eval=FALSE}\nif (!require(devtools)) install.packages(\"devtools\")\ndevtools::install_github(\"bertcarnell/tornado\")\n```\n\n## Quick Start - Torndao Plots\n\n### Linear Models\n\n```{r random, echo=TRUE}\nlm1 \u003c- lm(mpg ~ cyl*wt*hp, data = mtcars)\ntorn1 \u003c- tornado(lm1, type = \"PercentChange\", alpha = 0.10)\nplot(torn1, xlabel = \"MPG\", geom_bar_control = list(width = 0.5))\n```\n\n### Generalized Linear Models\n\nPlots can also be created for the range of the input data\n\n```{r glm_section, echo=TRUE}\nglm2 \u003c- glm(vs ~ wt + disp + cyl, data = mtcars, family = binomial(link = \"logit\"))\ntorn2 \u003c- tornado(glm2, type = \"ranges\", alpha = 0.10)\nplot(torn2, xlabel = \"Probability of Straight Engine\", geom_bar_control = list(width = 0.5))\n```\n\nPlots can include factors and percentiles of the data as well.\n\n```{r glm_factor_section, echo=TRUE}\nmydata \u003c- mtcars\nmydata$am \u003c- factor(mtcars$am)\nmydata$vs \u003c- factor(mtcars$vs)\nglm2 \u003c- glm(mpg ~ wt + cyl + am + vs, data = mydata, family = gaussian)\ntorn2 \u003c- tornado(glm2, type = \"percentiles\", alpha = 0.10)\nplot(torn2, xlabel = \"MPG\", \n     geom_bar_control = list(width = 0.5),\n     sensitivity_colors = c(\"#E41A1C\", \"#377EB8\"),\n     geom_point_control = list(fill = \"red\", col = \"red\", size = 3))\n```\n\n### Censored Data\n\nAccelerated Failure Model\n\n```{r censored_section, echo=TRUE}\nsurvreg3 \u003c- survival::survreg(survival::Surv(futime, fustat) ~ ecog.ps + rx + age + resid.ds, \n                              survival::ovarian, dist = 'weibull', scale = 1)\ntorn3 \u003c- tornado(survreg3, modeldata = survival::ovarian, type = \"PercentChange\", alpha = 0.10)\nplot(torn3, xlabel = \"Survival Time\", geom_bar_control = list(width = 0.5))\n```\n\nCox Proportional Hazard Model with 2 Standard Deviation bars\n\n```{r censored_coxph_setion, echo=TRUE}\ncoxph4 \u003c- survival::coxph(survival::Surv(stop, event) ~ rx + size + number,\n                          survival::bladder)\ntorn4 \u003c- tornado(coxph4, modeldata = survival::bladder, type = \"StdDev\",\n                 alpha = 2)\nplot(torn4, xlabel = \"Risk\", geom_bar_control = list(width = 0.5))\n```\n\n### Machine Learning Models from caret::train\n\nThe `plot` method can also return a ggplot object\n\n```{r train_section, echo = TRUE}\nmydat \u003c- mtcars\nmydat$am \u003c- factor(mydat$am, labels = c(\"A\", \"M\"))\nmydat$vs \u003c- factor(mydat$vs, labels = c(\"V\", \"S\"))\nmydat$cyl \u003c- factor(mydat$cyl)\nmydat$gear \u003c- factor(mydat$gear)\nmydat$carb \u003c- factor(mydat$carb)\n\ngtest \u003c- caret::train(x = subset(mydat, select = -vs), y = mydat$vs, method = \"rf\")\ntorn \u003c- tornado(gtest, type = \"percentiles\", alpha = 0.10, class_number = 1)\ng \u003c- plot(torn, plot = FALSE, xlabel = \"Probability of Class V-shaped Engine\", geom_bar_control = list(width = 0.5))\ng \u003c- g + ggtitle(\"Classifier caret::train randomforest, 90-110% of the mean in each variable\")\nplot(g)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbertcarnell%2Ftornado","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbertcarnell%2Ftornado","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbertcarnell%2Ftornado/lists"}