Merge branch '12.1_noFusedPCA'

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -8,54 +8,22 @@ on:
 
 name: R-CMD-check
 
-jobs:
+jobs: 
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache: FALSE
-          extra-packages: any::rcmdcheck, glmgen=?ignore
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
-        env:
-          _R_CHECK_FORCE_SUGGESTS_: false
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.11.2
-Date: 2022-07-06 06:00:41 UTC
-SHA: 4ceb750658f87bcb34eff8ed1e264fdd9bbdbed4
+Version: 0.12.1
+Date: 2023-01-25 15:43:00 UTC
+SHA: f47ea59f215f7df7e60d29676018efdb5d282e67

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: fMRIscrub
 Type: Package
 Title: Scrubbing and Other Data Cleaning Routines for fMRI
-Version: 0.11.2
+Version: 0.12.1
 Authors@R: c(
     person(given = "Amanda",
            family = "Mejia",
@@ -30,14 +30,15 @@ Description: Data-driven fMRI denoising with projection scrubbing (Pham et al
     (2012) <doi:10.1016/j.neuroimage.2011.10.018>), aCompCor (anatomical 
     Components Correction) (Muschelli et al (2014)
     <doi:10.1016/j.neuroimage.2014.03.028>), detrending, and nuisance
-    regression. Projection scrubbing and DVARS are also applicable to other
+    regression. Projection scrubbing is also applicable to other
     outlier detection tasks involving high-dimensional data.
 Depends: R (>= 3.5.0)
 License: GPL-3
 Encoding: UTF-8
 Imports:
     MASS,
     e1071,
+    fMRItools (>= 0.2.2),
     pesel,
     robustbase,
     stats,
@@ -51,13 +52,12 @@ Suggests:
     rmarkdown,
     RNifti,
     ggplot2,
-    gsignal,
     fastICA,
     oro.nifti,
     testthat (>= 3.0.0),
     covr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 URL: https://github.com/mandymejia/fMRIscrub
 BugReports: https://github.com/mandymejia/fMRIscrub/issues
 LazyData: true

NAMESPACE

@@ -12,39 +12,29 @@ S3method(print,summary.scrub_projection)
 S3method(summary,scrub_DVARS)
 S3method(summary,scrub_FD)
 S3method(summary,scrub_projection)
-export(CompCor)
-export(CompCor_HCP)
 export(DVARS)
 export(FD)
 export(artifact_images)
-export(bandstop_filter)
-export(carpetplot)
-export(carpetplot_stack)
-export(dct_bases)
-export(dct_convert)
-export(detrend)
-export(erode_vol)
-export(fsl_bptf)
 export(high_kurtosis)
 export(leverage)
-export(nuisance_regression)
-export(pct_sig)
 export(pscrub)
 export(rob_stabilize)
 export(scrub)
 export(scrub_xifti)
-export(unmask_vol)
 importFrom(MASS,mvrnorm)
 importFrom(e1071,kurtosis)
-importFrom(grDevices,dev.off)
-importFrom(grDevices,gray.colors)
-importFrom(grDevices,pdf)
-importFrom(grDevices,png)
+importFrom(fMRItools,as.matrix_ifti)
+importFrom(fMRItools,dct_bases)
+importFrom(fMRItools,hat_matrix)
+importFrom(fMRItools,is_constant)
+importFrom(fMRItools,is_integer)
+importFrom(fMRItools,nuisance_regression)
+importFrom(fMRItools,scale_med)
+importFrom(fMRItools,validate_design_mat)
 importFrom(pesel,pesel)
 importFrom(robustbase,rowMedians)
 importFrom(stats,mad)
 importFrom(stats,median)
-importFrom(stats,mvfft)
 importFrom(stats,pchisq)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)

NEWS.md

@@ -1,17 +1,8 @@
-# 0.11.1
+# 0.12.1
 
-* Remove `fusedPCA`
-* Remove unused dependencies
-
-# 0.10.0
-
-* General package cleanup
-
-# 0.9.0
-
-* Add detrending
-* Add grayplot
-* Switch to `fastICA`
+* Use `fMRItools` where possible and remove duplicated functions from here.
+* Remove AppVeyor
+* Remove fusedPCA (glmgen is not on CRAN, and C++ has some problems)
 
 # 0.8.0