R package

SHAP for XGBoost in R: SHAPforxgboost

Yang Liu / 2019-07-18

I wrote the R package SHAPforxgboost to cover all the plotting functions illustrated in this post. This post serves as the vignette for the package. Please install from CRAN or Github. install.packages("SHAPforxgboost") # or devtools::install_github("liuyanguu/SHAPforxgboost") Why SHAP values SHAP’s main advantages are local explanation and consistency in global model…

Data Visualization

Shiny in Blogdown

Yang Liu / 2019-02-24

Since Blogdown is for static websites, it cannot run Shiny in rmarkdown directly. According to discussion here and document here. The only way to do it is using iframe and write outside the chunk: <iframe src="https://liuyanguu.shinyapps.io/bcl_app/" width=1000 height=800"></iframe> There is also a built-in function in knitr to do the same thing and write in the chunk. The only…

Machine Learning

Study shrinkage and DART in xgboost modeling using a simple dataset

Yang Liu / 2018-11-15

It is always a good idea to study the packaged algorithm with a simple example. Inspired by my colleague Kodi’s excellent work showing how xgboost handles missing values, I tried a simple 5x2 dataset to show how shrinkage and DART influence the growth of trees in the model. […] set.seed(123) n0 <- 5 X <- data.frame(x1 = runif(n0), x2 = runif(n0)) Y <- c(1, 5, 20, 50, 100) cbind(X,…

Machine Learning

SHAP Visualization in R (first post)

Yang Liu / 2018-10-14

Update 19/07/21: Since my R Package SHAPforxgboost has been released on CRAN, I updated this post using the new functions and illustrate how to use these functions using two datasets. For more information, please refer to: SHAP visualization for XGBoost in R […] This is the example I used in the package SHAPforxgboost # Example use iris suppressPackageStartupMessages({…

Data Visualization

Spatial data in R: Dividing raster layers into equal-area rings

Yang Liu / 2018-07-20

This data visualization example include: * Import .img file as a raster * Turn raster into a data.frame of points (coordinates) and values * Dividing the points into 100 equal-area rings * Calculate Built-up Area/Urban Extent for each ring * Turn dataframe into raster * Plot multiple figures on the same color scale […] […] list.of.packages <- c("raster",…

Data Visualization

How to Draw Heatmap with Colorful Dendrogram

Yang Liu / 2018-07-16

This data visualization example include: * Hierarchical clustering, dendrogram and heat map based on normalized odds ratios * The dendrogram was built separately to give color to dendrogram’s branches/labels based on cluster using dendextend * Heatmap is made by heatmap.2 from gplots using the built dendrogram * The rows are sorted by means from highest to lowest, it can be done in either the…