A package to create odds plots after running a GLM
The package can be installed by using the following command : devtools::install_github("StatsGary/OddsPlotty", dependencies=TRUE) directly from GitHub. If Devtools is not loaded on to your machine - then this can be done by using install.packages("devtools") or using the package installation UI in R Studio.
The main way to install is to get the package from CRAN, as follows:
install.packages("OddsPlotty") # if not already installed
To load the package into the library you can achieve this as hereunder:
library(OddsPlotty)
This package allows the user to generate multiple odds ratio plots. These are the outcome of fitting a logistic regression model and will show how the odds work. The vignette explains how to train a model and then use the odds plot package.
The following shows how to take the results of a predictive model trained in CARET and produce the Odds Plots via OddsPlotty:
# Pass in the trained model from CARET and expose the finalModel list element from CARET
plotty <- OddsPlotty::odds_plot(glm_model$finalModel,
title = "Odds Plot with ggthemes economist",
subtitle = "Showing odds of cancer based on various factors",
point_col = "#00f2ff",
error_bar_colour = "black",
point_size = .5,
error_bar_width = .8,
h_line_color = "red")
plot <- plotty$odds_plot #Returns the plot element from the list
plot <- plot + ggthemes::theme_economist() + theme(legend.position = "NULL")
# Add odds ratios to labels by calling the data list element
# The round function is used to return 2 decimal place values
plot + geom_text(label=round(plotty$odds_plot$data$OR, digits=2),
hjust=0.1, vjust=1)
This returns:
To get the tibble from the list, simply use the plotty variable, or whatever you call it, to return the odds ratios and the confidence intervals:
plotty$odds_data
To find out more, please use the Vignette associated with this package for the full and correct usage.
In the coming months I aim to produce all my packages I have been previously squirreling away on to Github, so please look out for those.
Created and owned by Gary Hutson.
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