Changes in version 1.5.7 ============= o Improved description in the tutorial (BioMM() function returns the prediction scores instead of metrics) o Updated BioMMstage2pred() and BioMM() functions to get prediction scores instead of performance metrics o Updated getMetrics() to cope with the 'probability' predicted score as well. Changes in version 1.5.4 ============= o Improved description in the tutorial Changes in version 1.5.2 ============= o updated R functions for reporting results and plotting. o added another omics data (gene expression) and KEGG pathway. o updated tutorial by demonstrating BioMM with another omics data (gene expression) and KEGG pathway annotation. Changes in version 1.1.10 ============= o updated tutorial: added circular plot Changes in version 1.1.9 ============= o updated tutorial: updated description for two parallel computing; cirPlot4pathway() example added; seeds added o updated plotRankedFeature(). Changes in version 1.1.8 ============= o updated tutorial: fixed typo 'param1' to 'param2' o added a new function cirPlot4pathway() Changes in version 1.1.7 ============= o updated tutorial Changes in version 1.1.6 ============= o improved plotVarExplained() and plotRankedFeature() o renamed R functions for getDataAfterFS, BioMMreconData, BioMMstage1pca o updated installation approaches (including R 3.5 from Github) o updated tutorial to adapt the usage of the parallel package installed from Github Changes in version 1.1.5 ============= o updated BioMM(); 'dataMode' added. o fixed roc() in getMetrics() Changes in version 1.1.4 ============= o removed the examples with omcis2chrlist() o updated the omics2pathlist() Changes in version 1.1.3 ============= o added required package pROC for getMetrics() o updated NAMESPACE and Rd file. Changes in version 1.1.2 ============= o added the library pROC in the tutorial. Changes in version 1.1.1 ============= o updated functions getMetrics(), plotVarExplained() and plotRankedFeature(); to focus on pathway based result report. o updated BioMMtutorial.Rmd Changes in version 1.1.0 ============= o removed gene and chromosome based stratification methods. o updated feature selection method based on filtering getDataAfterFS(). o updated BioMM() function to focus on pathway based machine learning. o updated BioMMtutorial.Rmd Changes in version 0.99.13 ============= o updated the format of NEWS o updated BioMMtutorial.Rmd o updated data4demo.R o replaced the generation of stage-2 data by BioMMreconData() with preprocessed 'stage2dataA' to reduce runtime o increased repeatA1 to 50 for BioMM() example to avoid any NAs. o created stage2dataA.rds Changes in version 0.99.12 ============= o updated the format of NEWS Changes in version 0.99.11 ============= o updated DESCRIPTION file Changes in version 0.99.10 ============= o minor bug fixed in getDataAfterFS() o updated installation method ============= Changes in version 0.99.9 o removed uncessary print statements o removed 'return' calls for some functions o removed unnecessary 'which' statements o replaced the usage of MulticoreParam() o updated tutorial with smaller examples and models with less computation ============= Changes in version 0.99.8 o updated author, maintainer section in DESCRIPTION o updated parallel computing cores used in the vignettes ============= Changes in version 0.99.7 o updated parallel evaluation environments o updated installation method in README.md o more cores (non-windows) for parallel computing used in the vignettes to reduce runtime ============= Changes in version 0.99.6 o updated plotRankedFeature() and getMetrics() o increased core number for parallel computing o removed Duplicated descriptions in *.Rd files ============= Changes in version 0.99.5 o reformatted code by using formatR o bplapply() instead of mclapply o message() instead of print() for end-user messages o improved usage of which() o use seq_along() instead of seq_len(length()) o updated installation method o renamed R source files ============= Changes in version 0.99.4 o updated example in BioMMreconData() ============= Changes in version 0.99.3 o updated example in BioMM() ============= Changes in version 0.99.2 o updated R version dependency (from 3.5.2 to 3.6) o Removed the file LICENSE ============= Changes in version 0.99.1 o updated R version dependency (from 3.5.0 to 3.5.2) ============= Changes in version 0.99.0 o Removed the file "BioMM.Rproj"