NEWS.md

In wanchanglin/mt: Metabolomics Data Analysis Toolbox

mt 2.0-1.1:

• pca.outlier: add prefix to ellipse to avoid conflict with package car.

mt 2.0-1.2:

• corrgram.circle and corrgram.ellipse: move 'scales' into argument list.

mt 2.0-1.3:

• cl.auc: adjust auc: if (auc < 0.5) auc <- 1 - auc

mt 2.0-1.4: (14-05-2012)

• accest: Fix bugs and add more output.

mt 2.0-1.5: (16-05-2012)

• cl.roc: change output and fix bugs.

mt 2.0-1.6: (19-05-2012)

• cl.roc: add output of positive level.
• cl.perf: add confusion matrix, Kappa and positive outputs.

mt 2.0-1.7: (21-05-2012)

• plsc: minor changes for returned component pls.out so that R2 can be applied.
• plslda: minor changes for returned component pls.out so that R2 can be applied.

mt 2.0-1.8: (22-05-2012)

• classifier: bugs fix

mt 2.0-1.9: (22-05-2013)

• df.summ: add dots argument and modify an user-defined function.

mt 2.0-1.10: (09-01-2014)

• stats.vec and stats.mat: summarising two groups stats, such as p-values.
• fs.cl.2, perf and perf.aam: internal functions (21-01-2014).

mt 2.0-1.11: (22-01-2014)

• re-write shrink.list
• add proprec.auto as hidden function and tidy up

mt 2.0-1.12: (07-08-2014)

• fix bug in pval.reject: add na.rm = TRUE
• change in .grpplot: remove xlab and ylab inside.

mt 2.0-1.13: (10-06-2015)

• two functions mdsplot and mds_plot_wrap for MDS plotting.

mt 2.0-1.14: (16-07-2015)

• Re-write two functions for ellipse: panel.elli and panel.elli.1
• Provide panel.outl for labelling data points outside ellipse. They can be considered as outliers.

mt 2.0-1.15: (19-11-2015)

• .path.package is defunct so use path.package instead in csv2xls.
• Use pls:::coef.mvr replace coef.mvr since it hides in the new version of 'pls'.

mt 2.0-1.16: (30-11-2015)

• Add log2 fold-change for stats.mat and stats.vec.
• Add adjusted p-values for stats.mat only.
• Provide documents for pca.outlier and pca.outlier.1. The former is lattice version and the later is the basic graphics version.

mt 2.0-1.17: (26-01-2016)

• Remove returned values of "direction" in stats.vec and stats.mat. So the results are numeric, not character.

mt 2.0-1.18: (06-11-2021)

• Replace melt and ddply with base R functions. So no need to load two packages reshape and plyr.
• Move out some un-documented functions.
• Change CHANGELOG as NEWS.md
• Move packages from Depends to Imports in DESCRIPTION
• Spell check on R scripts using RStudio

mt 2.0-1.19: (31-01-2022)

• no changes but test against new version of randomForest 4.7.1 as requested.

mt 2.0-1.20: (12-02-2024)

• No changes but new R version of R complains S3 method in RD file. So change the dot as underscore for: pca_plot_wrap, mds_plot_wrap, lda_plot_wrap, lda_plot_wrap_1 and pls_plot_wrap. (probably '.plot' is the problem)

wanchanglin/mt documentation built on Feb. 15, 2024, 4:05 a.m.