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| 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) | ||
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| 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 | ||
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| 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 | ||
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| 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 | ||
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| 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 | ||
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| 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 | ||
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| 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 | ||
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| v. 0.5.3 | ||
| ======== | ||
| * fixed several small bugs | ||
| * improvemed documentation for basic methods | ||
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| v. 0.5.2 | ||
| ======== | ||
| * fixed bug for computing classification performance for numeric class names | ||
| * improvements to SIMCA implementation | ||
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| v. 0.5.1 | ||
| ======== | ||
| * added more details to documentation | ||
| * bug fixes for variable selection methods | ||
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| 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 | ||
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| 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 | ||
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| v. 0.3.2 | ||
| ======== | ||
| * Enhancements in group bar plot | ||
| * Fixed bugs with wrong labels of bar plot with negative values | ||
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| v. 0.3.1 | ||
| ======== | ||
| * Corrected errors and typos in README.md and small bg fixes | ||
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| 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. | ||
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