Changes in version lmdme 1.5.2 ---------------------------------------------------------------- DOCUMENTATION * VignetteIndexEntry, VignetteDepends and \VignetteKeyword added. Changes in version lmdme 1.5.1 ---------------------------------------------------------------- DOCUMENTATION * Vignette was updated to use a modification of Journal of Statistical Software's article. * CITATION file was included. * Minor updates to lmdme and decomposition man pages and Roxygen2 quotes, in order to include the article citation. DEPENDENCY CHANGES * methods and limma packages were moved to import. * NAMESPACE file updated accordingly. Changes in version lmdme 1.5.0 ---------------------------------------------------------------- MINOR CHANGES * Bump y in version x.y.z to odd number in devel Changes in version lmdme 1.4.0 ---------------------------------------------------------------- MINOR CHANGES * bump y of x.y.z version number for BioC 2.13 release Changes in version lmdme 1.3.1 ---------------------------------------------------------------- BUGS FIXED * NA manipulation of lmFit for coefficient is now contemplated Changes in version lmdme 1.3.0 ---------------------------------------------------------------- MINOR CHANGES * Bump y in version x.y.z to odd number in devel Changes in version lmdme 1.2.0 ---------------------------------------------------------------- MINOR CHANGES * bump y of x.y.z version number for BioC 2.12 release Changes in version lmdme 1.1.5 ---------------------------------------------------------------- DOCUMENTATION * Vignette was updated to cope with Journal of Statistical Software article. * Minor updates to the man pages. Changes in version lmdme 1.1.4 ---------------------------------------------------------------- MINOR CHANGES * Enhance `biplot` function now accepts single character for `xlabs` and `ylabs`. In addition `which` parameter was also included for `plsr`decomposition (Thanks to Editor and two reviewers of Journal of Statistical Software). Changes in version lmdme 1.1.3 ---------------------------------------------------------------- MAYOR CHANGES * `lmDME` on class/files/.Rd names changed to `lmdme` in order to match package name (Thanks to Editor and two reviewers of Journal of Statistical Software). Changes in version lmdme 1.1.2 ---------------------------------------------------------------- MINOR CHANGES * Getters functions for lmDME class now have drop=TRUE parameter, in order to avoid using [[1]] when only one term/component is returned (Thanks to Elmer Fernandez). DOCUMENTATION * Missing usage functions helps for F.p.values, p.values, etc. were added. Changes in version lmdme 1.1.1 ---------------------------------------------------------------- MINOR CHANGES * R code, documentation, examples, etc. were modify to cope with Journal of Statistical Software style rules: i) 2 character spaces for indentation. ii) lines with at most 80 characters. iii) avoid typo errors. * URL field in Description file was updated. DEPENDENCY CHANGES * stemHypoxia data package was moved back to Depends in order to avoid if(required){ #on example code } (Thanks to Editor of Journal of Statistical Software). Changes in version lmdme 1.0.0 ---------------------------------------------------------------- DEPENDENCY CHANGES * stemHypoxia data package was moved to Suggests and in examples included the appropriate if(required){ #example code } (Thanks to Valerie Obenchain). Changes in version lmdme 0.99.1 ---------------------------------------------------------------- MINOR CHANGES * Getters now accept a character vector in `term` parameter, in order to specify one than one term if required. In addition, `design` and `model` were added, and `pvalues` like `Fvalues` were changed to match slot names. (Thanks to Valerie Obenchain) * `lmdme` now works with NA presence in data matrix. This bug is related to lmFit intercept coefficient behavior, which breaks the data structure using drop (to numeric instead of keeping a matrix with one column) only if NA are present. * `lmdme` is now the only constructor. Method `initialize` was erased due to different reasons as described in https://stat.ethz.ch/pipermail/bioc­devel/2012­August/003554.html * `decomposition` example sections using `subset` parameter for simplicity (not all the data has to be decomposed in the example). * Enhance of `biplot` and `screeplot` functions with `term` and `mfcol` to simplify the graphic output specification. DOCUMENTATION * `NEWS` file was added.