Merge branch 'develop'

svkucheryavski · Jan 3, 2019 · 3aaae88 · 3aaae88
2 parents 1a44ae6 + a129cef
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,17 @@
 Package: mdatools
 Title: Multivariate Data Analysis for Chemometrics
-Version: 0.9.2
-Date: 2018-11-09
+Version: 0.9.3
+Date: 2019-01-03
 Author: Sergey Kucheryavskiy
 Maintainer: Sergey Kucheryavskiy <[email protected]>
 Description: Package implements projection based methods for preprocessing,
     exploring and analysis of multivariate data used in chemometrics.
+Encoding: UTF-8
 License: MIT + file LICENSE
 Imports:
     methods,
     graphics,
     grDevices,
     stats
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Suggests: testthat
diff --git a/NAMESPACE b/NAMESPACE
@@ -130,6 +130,8 @@ S3method(summary,simca)
 S3method(summary,simcam)
 S3method(summary,simcamres)
 S3method(summary,simcares)
+export(classres)
+export(crossval)
 export(erfinv)
 export(getCalibrationData)
 export(getConfusionMatrix)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+v.0.9.3
+=======
+* fixed a bug leading to wrong results in multiclass PLS-DA if class labels in reference class variable (factor) were not in alphabetical order
+
 v.0.9.2
 =======
 * improvements to `ipls()` method plus fixed a bug preventing breaking the selection loop (#56)

diff --git a/R/classres.R b/R/classres.R
@@ -208,7 +208,7 @@ getConfusionMatrix.classres = function(obj, ncomp = NULL, ...) {
    # get class names and numbers
    classes = dimnames(obj$c.pred)[[3]]
    nclasses = length(classes)
-   ref.classes = unique(obj$c.ref)
+   ref.classes = levels(as.factor(obj$c.ref))
    ref.nclasses = length(ref.classes)
 
    # compute the confusion matrix

diff --git a/R/pca.R b/R/pca.R
@@ -222,12 +222,14 @@ getCalibrationData.pca = function(obj, ...) {
 #' PCA model (object of class \code{pca})
 #' @param ncomp
 #' number of components to select
+#' @param ...
+#' other parameters if any
 #' 
 #' @return
 #' the same model with selected number of components
 #' 
 #' @export
-selectCompNum.pca = function(model, ncomp) {
+selectCompNum.pca = function(model, ncomp, ...) {
    if (ncomp < 1 || ncomp > model$ncomp)
       stop('Wrong number of selected components!')
 

diff --git a/R/pls.R b/R/pls.R
@@ -801,6 +801,8 @@ pls.crossval = function(model, x, y, cv, center, scale, method, jack.knife = T)
 #' @param selcrit
 #' criterion for selecting optimal number of components (\code{'min'} for 
 #' first local minimum of RMSECV and \code{'wold'} for Wold's rule.)
+#' @param ...
+#' other parameters if any
 #' 
 #' @return
 #' the same model with selected number of components
@@ -813,7 +815,7 @@ pls.crossval = function(model, x, y, cv, center, scale, method, jack.knife = T)
 #' See examples in help for \code{\link{pls}} function.
 #' 
 #' @export
-selectCompNum.pls = function(model, ncomp = NULL, selcrit = model$ncomp.selcrit) {
+selectCompNum.pls = function(model, ncomp = NULL, selcrit = model$ncomp.selcrit, ...) {
    if (!is.null(ncomp)) {
       # user defined number of components
       if (ncomp > model$ncomp || ncomp < 0)

diff --git a/R/plsda.R b/R/plsda.R
@@ -217,8 +217,9 @@ plsda.cal = function(x, c, ncomp, center, scale, cv, method, light, alpha, coeff
    } else {
       c = checkReferenceValues.classmodel(m, c, x)
       y = mda.df2mat(as.factor(c), full = TRUE)
-      classnames = unique(c)
+      classnames = levels(as.factor(c))
    }
+
    y[y == 0] = -1      
    colnames(y) = classnames
    rownames(y) = rownames(x)

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ For more details and examples read a [Bookdown tutorial](http://svkucheryavski.g
 What is new
 -----------
 
-New minor release (0.9.2) is available both from GitHub and CRAN (from 9.11.2018).
+New minor release (0.9.3) is available both from GitHub and CRAN (from 3.01.2019).
 
 The latest major release (0.9.0) brings a set of new features, including methods for computing of critical limits for PCA/SIMCA residuals, adjuested residuals plot, and randomized algorithms for fast PCA decomposition of dataset with large number of rows. The text of tutorial has been amended correspondingly and now also includes a new chapter with detailed explanation of calculation of the critical limits. 
 
@@ -20,10 +20,10 @@ A full list of changes is available [here](NEWS.md)
 How to install
 --------------
 
-The package is available from CRAN by usual installing procedure. However due to restrictions in CRAN politics regarding number of submissions (one in 3-4 month) only major releases will be published  there (with 2-3 weeks delay after GitHub release as more thorought testing is needed). To get the latest release plase use [GitHub sources](https://github.com/svkucheryavski/mdatools). You can [download](https://github.com/svkucheryavski/mdatools/releases) a zip-file with source package and install it using the `install.packages` command, e.g. if the downloaded file is `mdatools_0.9.2.tar.gz` and it is located in a current working directory, just run the following:
+The package is available from CRAN by usual installing procedure. However due to restrictions in CRAN politics regarding number of submissions (one in 3-4 month) only major releases will be published  there (with 2-3 weeks delay after GitHub release as more thorought testing is needed). To get the latest release plase use [GitHub sources](https://github.com/svkucheryavski/mdatools). You can [download](https://github.com/svkucheryavski/mdatools/releases) a zip-file with source package and install it using the `install.packages` command, e.g. if the downloaded file is `mdatools_0.9.3.tar.gz` and it is located in a current working directory, just run the following:
 
 ```
-install.packages('mdatools_0.9.2.tar.gz')
+install.packages('mdatools_0.9.3.tar.gz')
 ```
 
 If you have `devtools` package installed, the following command will install the latest release from the master branch of GitHub repository (do not forget to load the `devtools` package first):

diff --git a/man/getRegcoeffs.pls.Rd b/man/getRegcoeffs.pls.Rd
diff --git a/man/ipls.Rd b/man/ipls.Rd
diff --git a/man/ldecomp.getDistances.Rd b/man/ldecomp.getDistances.Rd
diff --git a/man/mdaplot.Rd b/man/mdaplot.Rd
diff --git a/man/mdaplot.getAxesLim.Rd b/man/mdaplot.getAxesLim.Rd
diff --git a/man/mdaplot.plotAxes.Rd b/man/mdaplot.plotAxes.Rd
diff --git a/man/mdaplot.showLines.Rd b/man/mdaplot.showLines.Rd
diff --git a/man/mdaplot.showRegressionLine.Rd b/man/mdaplot.showRegressionLine.Rd
diff --git a/man/mdaplotg.Rd b/man/mdaplotg.Rd
diff --git a/man/pca.Rd b/man/pca.Rd
diff --git a/man/pca.cal.Rd b/man/pca.cal.Rd
diff --git a/man/pca.mvreplace.Rd b/man/pca.mvreplace.Rd
diff --git a/man/plot.randtest.Rd b/man/plot.randtest.Rd
diff --git a/man/plot.regcoeffs.Rd b/man/plot.regcoeffs.Rd
diff --git a/man/plotCooman.simcamres.Rd b/man/plotCooman.simcamres.Rd
diff --git a/man/plotCumVariance.ldecomp.Rd b/man/plotCumVariance.ldecomp.Rd
diff --git a/man/plotModelDistance.simcam.Rd b/man/plotModelDistance.simcam.Rd
diff --git a/man/plotPerformance.classmodel.Rd b/man/plotPerformance.classmodel.Rd
diff --git a/man/plotPredictions.plsres.Rd b/man/plotPredictions.plsres.Rd
diff --git a/man/plotPredictions.regres.Rd b/man/plotPredictions.regres.Rd
diff --git a/man/plotRMSE.ipls.Rd b/man/plotRMSE.ipls.Rd