diff --git a/NEWS.md b/NEWS.md new file mode 100755 index 0000000..300271f --- /dev/null +++ b/NEWS.md @@ -0,0 +1,118 @@ +v.0.8.0 +======= +* tutorial has been moved from GitBook to Bookdown and fully rewritten +* GitHub repo for the package has the tutorial as a static html site in `docs` folder +* the `mdaplot()` and `mdaplotg()` were rewritten completely and now are more easy to use (check tutorial) +* new color scheme 'jet' with jet colors +* new plot type (`'d'`) for density scatter plot +* support for `xlas` and `ylas` in plots to rotate axis ticks +* support for several data attributes to give extra functionality for plots (including manual x-values for line plots) +* rows and columns can be now hidden/excluded via attributes +* factor columns of data frames are now converted to dummy variables automatically when model is created/applied +* scores and loadings plots show % of explained variance in axis labels +* biplot is now available for PCA models (`plotBiplot()`) +* scores plot for PCA model can be now also shown with color grouping (`cgroup`) if no there is no test set +* cross-validation in PCA and PLS has been improved to make it faster +* added a posibility to exclude selected rows and columns from calculations +* added support for images (check tutorial) + +v.0.7.2 +======= +* corrected a typo in title of selectivity ratio plot +* `prep.autoscale()` now do not scale columns with coefficient of variation below given threshold + +v.0.7.1 +======= +* fixed an issue lead to plot.new() error in some cases +* documentation was regenerated with new version of Roxygen +* file People.RData was renamed to people.RData +* NIPALS method for PCA has been added +* code optimization to speed calculations up + +v.0.7.0 +======= +* interval PLS variable selection (iPLS) is implemented +* normalization was added to preprocessing methods (`prep.norm`) +* method `getRegcoeffs` was added to PLS model +* automatic selection of optimal components in PLS (Wold's criterion and first local min) +* parameter `cgroup` for plots now can work with factors correctly (including ones with text levels) +* all documentation was converted to roxygen2 format +* NAMESPACE file is generated by roxygen2 +* fixed several small bugs and typos + +v.0.6.2 +======== +* Q2 residuals renamed to Q (Squared residual distance) +* All plots have parameters `lab.col` and `lab.cex` for changing color and font size for data point labels + +v.0.6.1 +======== +* fixed a bug led to incorrect calculation of specificity +* jack-knife confidence intervals now also calculated for PLS-DA models +* confidence intervals for regression coefficients are shown by default if calculated + +v.0.6.0 +======== +* randomization test for PLS has been added, see `?randtest` +* systematic and repeated random cross-validation are available, see `?crossval` +* fixed bug with labels on bar plot with confidence intervals +* fixed bug in PLS when using maximum number of components lead to NA values in weights + +v. 0.5.3 +======== +* fixed several small bugs +* improvemed documentation for basic methods + +v. 0.5.2 +======== +* fixed bug for computing classification performance for numeric class names +* improvements to SIMCA implementation + +v. 0.5.1 +======== +* added more details to documentation +* bug fixes for variable selection methods + +v. 0.5.0 +======== +* all documentation has been rewritten using `roxygen2` package +* added extra preprocessing methods +* added VIP scores calculation and plot for PLS and PLS-DA models +* addec Selectivity ratio calculation and plot for PLS and PLS-DA models +* added calculation of confidence intervals for PLS regression coefficient using jack-knife +* bug fixes and small improvements +* the first release available in CRAN + +v. 0.4.0 +======== +* New `classres` class for representation and visualisation of classification results +* in PCA model, limits for T2 and Q2 now are calculated for all available components +* in PCA results, limits for T2 and Q2 calculated for a model are kept and shown on residuals plot +* added parameters `xticklabels` and `yticklabels` to `mdaplot` and `mdaplotg` functions +* New `simca` and `simcares` classes for one-class SIMCA model and results +* New `simcam` and `simcamres` classes for multiclass SIMCA model and results +* New `plsda`and `plsdares`classes for PLS-DA model and results +* bug fixes and improvements + +v. 0.3.2 +======== +* Enhancements in group bar plot +* Fixed bugs with wrong labels of bar plot with negative values + +v. 0.3.1 +======== +* Corrected errors and typos in README.md and small bg fixes + +v. 0.3.0 +======== +* PLS and all related methods were rewritten from the scratch to make them faster, more efficient +and also to follow the same code conventions as previously rewritten PCA. Here are main changes +you need to do in your code if you used mdatools PLS before: `selectNumComp(model, ncomp)` instead +of `pls.selectncomp(model, ncomp)`, `test.x` ad `test.y` instead of `Xt` and `yt`, finally separate logical +arguments `center` and `scale` are used instead of previously used `autoscale`. By default `scale = F` and `center = T`. +* PLS and all related methods are now well documented (see `?pls`) +* plotting tools for all classes and methods were rewritten completely. Now all plotting methods +use either `mdaplot` or `mdaplotg` functions, which extend basic functionality of R plots. For example, +they allow to make color groups and colorbar legend, calculate limits automatically depending on +elements on a plot, make automatic legend and many other things. +