trqwe
Performance oriented statistical metrics and utility functions in R
Installation
devtools::install_github("traversc/trqwe")(On Windows, install Rtools first.)
A summary of functions
Classification/model metrics and functions
- f1score - f1 classification metric
- fastAUC - Area under the receiver-operator curve
- fastPR - Precision recall curve
- fastROC - Receiver-operator curve
- mccscore - Matthew's correlation coefficient
- posteriorBalance - Adjust classification posterior probability due to unbalanced dataset
- cindex - Concordance index for survival data
- nelson_aelen_surv - Nelson Aelen estimator of cumulative hazard
Statistical tests and functions
- ww_test - k-category Wald-Wolfowitz Runs Tests
- se - Calculate standard error
- matrixFactor - Returns a design matrix from a factor
Misc. mathematical functions
- cosineDist - Calculates the cosine distance between rows in a matrix
- logit - Logit transformation function
- sigmoid - Calculates the sigmoid function
- topn - returns the top "n" values in a vector
Multithreaded functions (*nix only)
- mcreadRDS - Multithreaded readRDS
- mcsaveRDS - Multithreaded saveRDS
- mcsplitapply - Apply loop over matrix subsets
Utility functions
- tablec - Very fast tabulation of vectors writen in C++
- allDups - Like the duplicated function, but returns the first instance as well
- append<- - Append to a vector in-place
- prepend<- - Prepend to a vetor in-place
- chop - chop leading and trailing white space in a string
- head2 - Like head, but limits the number of columns returned
- tail2 - Like tail, but limits the number of columns returned
- mgrepl - Multiple grepl for a list of regular expressions
- %Q% - Infix operator for string concatenation
- TCGA_barcode - Extracts information from TCGA barcodes
Package/environment management
- reload - Reload a package and set the position in the search order
- bioc - Easy installation bioconductor packages
- install - Easy installation of CRAN packages
- timePrompt - Adds a time prompt to the R command prompt
- statsCallback - Automated summary of R objects using callbacks
- varSizes - Returns a data.frame of all R objects and their sizes in memory