Merge branch 'develop'

.github/workflows/test-package.yml

@@ -0,0 +1,82 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+      - develop
+  pull_request:
+    branches:
+      - main
+      - master
+      - develop
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -6,6 +6,7 @@
 .DS_Store
 .lintr
 .vscode/*
+LICENSE
 
 tests/plots/*.pdf
 tests/plots/*.txt

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mdatools
 Title: Multivariate Data Analysis for Chemometrics
-Version: 0.11.2
-Date: 2020-10-22
-Author: Sergey Kucheryavskiy
+Version: 0.11.3
+Date: 2021-01-21
+Author: Sergey Kucheryavskiy (<https://orcid.org/0000-0002-3145-7244>)
 Maintainer: Sergey Kucheryavskiy <[email protected]>
 Description: Projection based methods for preprocessing,
     exploring and analysis of multivariate data used in chemometrics.

LICENSE.md

@@ -0,0 +1,20 @@
+Copyright (c) 2016-2021 Sergey Kucheryavskiy
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

NAMESPACE

@@ -172,6 +172,7 @@ export(ddmoments.param)
 export(ddrobust.param)
 export(ellipse)
 export(employ)
+export(eye)
 export(fprintf)
 export(getCalibrationData)
 export(getConfusionMatrix)
@@ -233,6 +234,7 @@ export(pca)
 export(pca.mvreplace)
 export(pca.run)
 export(pcares)
+export(pcv)
 export(pinv)
 export(plotBars)
 export(plotBiplot)
@@ -297,6 +299,7 @@ export(prep.alsbasecorr)
 export(prep.autoscale)
 export(prep.msc)
 export(prep.norm)
+export(prep.ref2km)
 export(prep.savgol)
 export(prep.snv)
 export(prepCalData)

NEWS.md

@@ -1,3 +1,19 @@
+v.0.11.3
+========
+
+* added [Procrustes Cross-Validation method](https://doi.org/10.1021/acs.analchem.0c02175), `pcv()` (it is also available as a [separate project](https://github.com/svkucheryavski/pcv)).
+
+* added Kubelka-Munk transformation for diffuse reflectance spectra (`prep.ref2km()`).
+
+* fixed bug [#94](https://github.com/svkucheryavski/mdatools/issues/94) which caused wrong limits in PCA distance plot when outliers are present but excluded.
+
+* fixed bug [#95](https://github.com/svkucheryavski/mdatools/issues/95) which lead to issues when PLS regression methods (e.g. `plotRMSE()`) are used for PLS-DA model object.
+
+* added additional check that parameter `cgroup` for plotting functions is provided as a vector or as a factor to avoid confusion.
+
+* added link to [YouTube channel](https://www.youtube.com/channel/UCox0H4utfMq4FIu2kymuyTA) with Chemometric course based on *mdatools* package.
+
+
 v.0.11.2
 ========
 

R/ldecomp.R

@@ -964,6 +964,8 @@ ldecomp.getLimitsCoordinates <- function(Qlim, T2lim, ncomp, norm, log,
 #' logical, show or not legend on the plot (if more than one result object)
 #' @param legend.position
 #' if legend must be shown, where it should be
+#' @param show.excluded
+#' logical, show or hide rows marked as excluded (attribute `exclrows`).
 #' @param ...
 #' other plot parameters (see \code{mdaplotg} for details)
 #'
@@ -988,12 +990,18 @@ ldecomp.getLimitsCoordinates <- function(Qlim, T2lim, ncomp, norm, log,
 ldecomp.plotResiduals <- function(res, Qlim, T2lim, ncomp, log = FALSE, norm = FALSE,
    cgroup = NULL, xlim = NULL, ylim = NULL, show.limits = c(TRUE, TRUE),
    lim.col = c("darkgray", "darkgray"), lim.lwd = c(1, 1), lim.lty = c(2, 3),
-   show.legend = TRUE, legend.position = "topright", ...) {
+   show.legend = TRUE, legend.position = "topright", show.excluded = FALSE, ...) {
 
-   getPlotLim <- function(lim, pd, ld, dim, show.limits) {
+   # return column with values either with or without excluded outliers
+   getValues <- function(x, dim) {
+      return(if (show.excluded) x[, dim] else mda.purgeRows(x)[, dim])
+   }
+
+   # compute limits fo axis depending on values and position of critical limits
+   getPlotLim <- function(lim, pd, ld, dim) {
       if (!is.null(lim) || all(!show.limits)) return(lim)
-      limits <- if (show.limits[[2]]) ld$outliers else ld$extremes
-      return(c(0, max(sapply(pd, function(x) max(x[, dim])), limits[, dim])) * 1.05)
+      limits <- if (show.limits[[2]]) max(ld$outliers[, dim]) else max(ld$extremes[, dim])
+      return( c(0, max(sapply(pd, function(x) { max(c(getValues(x, dim), limits)) * 1.05}))) )
    }
 
    # check that show.limits is logical
@@ -1015,15 +1023,16 @@ ldecomp.plotResiduals <- function(res, Qlim, T2lim, ncomp, log = FALSE, norm = F
 
    # get coordinates for critical limits
    lim_data <- ldecomp.getLimitsCoordinates(Qlim, T2lim, ncomp = ncomp, norm = norm, log = log)
-   xlim <- getPlotLim(xlim, plot_data, lim_data, 1, show.limits)
-   ylim <- getPlotLim(ylim, plot_data, lim_data, 2, show.limits)
+   xlim <- getPlotLim(xlim, plot_data, lim_data, 1)
+   ylim <- getPlotLim(ylim, plot_data, lim_data, 2)
 
    # make plot
    if (length(plot_data) == 1) {
-      mdaplot(plot_data[[1]], type = "p", xlim = xlim, ylim = ylim, cgroup = cgroup, ...)
+      mdaplot(plot_data[[1]], type = "p", xlim = xlim, ylim = ylim, cgroup = cgroup,
+         show.excluded = show.excluded, ...)
    } else {
       mdaplotg(plot_data, type = "p", xlim = xlim, ylim = ylim, show.legend = show.legend,
-         legend.position = legend.position, ...)
+         show.excluded = show.excluded, legend.position = legend.position, ...)
    }
 
    # show critical limits

R/mdaplot.R

@@ -273,6 +273,10 @@ mdaplot.getColors <- function(ngroups = NULL, cgroup = NULL, colmap = "default",
       return(mdaplot.prepareColors(palette, ngroups, opacity))
    }
 
+   if (!is.null(dim(cgroup))) {
+      stop("Parameter 'cgroup' should be a vector of values or a factor.")
+   }
+
    # if cgroup is factor return vector with corresponding values
    if (is.factor(cgroup)) {
       ngroups <- length(attr(cgroup, "levels"))