jasenfinch/metabolyseR-v0.14.9.zip
jasenfinch-metabolyseR-80181f5
.Rbuildignore
111 Bytes
.github
.gitignore
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workflows
R-CMD-check.yaml
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.gitignore
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DESCRIPTION
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NAMESPACE
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NEWS.md
6.9 kB
R
QC.R
5.7 kB
aggregate.R
4.1 kB
allClasses.R
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analysis-accessors.R
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analysisData.R
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correction.R
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correlations.R
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impute.R
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info.R
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join.R
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keep.R
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mds.R
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metabolyse.R
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metabolyseR.R
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modelling-accessors.R
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modelling.R
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modellingPlots.R
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nlda.R
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occupancy.R
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parameters.R
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plotExplanatoryHeatmap.R
17.3 kB
plotFeature.R
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plotLDA.R
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plotOccupancy.R
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plotPCA.R
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plotRSD.R
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plotSupervisedRF.R
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plotTIC.R
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plotUnsupervisedRF.R
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plotting.R
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pre-treatment.R
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randomForest.R
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reexports.R
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remove.R
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roc.R
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rsd.R
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show-method.R
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split.R
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transform.R
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univariate.R
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README.Rmd
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README.md
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_pkgdown.yml
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codecov.yml
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docs
404.html
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articles
01_quick_start.html
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01_quick_start_files
figure-html
feature_plot-1.png
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pca-1.png
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rf_heatmap-1.png
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supervised_RF-1.png
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header-attrs-2.10
header-attrs.js
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02_introduction.html
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02_introduction_files
header-attrs-2.10
header-attrs.js
507 Bytes
03_pre_treatment.html
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03_pre_treatment_files
figure-html
QC_occupancy_rsd-1.png
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QC_rsd_plot-1.png
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TICnorm_RF-1.png
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corrected-TIC plot-1.png
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day_TICs-1.png
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day_mean_pca-1.png
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impute_all_lda-1.png
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imputed_class_lda-1.png
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lda-1.png
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log10_RF-1.png
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pca-1.png
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plot_filtered_occupancy-1.png
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plot_occupancy-1.png
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supervised-rf-1.png
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transform_RF-1.png
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header-attrs-2.10
header-attrs.js
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04_modelling.html
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04_modelling_files
figure-html
anova-feature-1.png
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binary-heatmap-1.png
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binary-mds-1.png
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binary-metrics-1.png
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classification-comparison-mds-roc-1.png
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explanatory-heatmap-1.png
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linear-regression-feature-1.png
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multinomial-mds-1.png
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multinomial-multiple-mds-1.png
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multinomial-roc-1.png
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outlier-detect-1.png
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regression-feature-1.png
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regression-importance-plot-1.png
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regression-mds-1.png
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t-test-heatmap-1.png
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unsupervised-feature-1.png
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unsupervised-rf-1.png
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header-attrs-2.10
header-attrs.js
507 Bytes
index.html
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introduction.html
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introduction_files
header-attrs-2.10
header-attrs.js
507 Bytes
header-attrs-2.7
header-attrs.js
507 Bytes
metabolyseR.html
87.7 kB
metabolyseR_files
header-attrs-2.11
header-attrs.js
507 Bytes
modelling.html
109.0 kB
modelling_files
figure-html
anova-feature-1.png
48.5 kB
binary-heatmap-1.png
207.0 kB
binary-mds-1.png
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binary-metrics-1.png
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classification-comparison-mds-roc-1.png
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explanatory-heatmap-1.png
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linear-regression-feature-1.png
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multinomial-mds-1.png
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multinomial-multiple-mds-1.png
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multinomial-roc-1.png
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outlier-detect-1.png
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regression-feature-1.png
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regression-importance-plot-1.png
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regression-mds-1.png
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t-test-heatmap-1.png
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unsupervised-feature-1.png
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unsupervised-rf-1.png
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header-attrs-2.10
header-attrs.js
507 Bytes
header-attrs-2.11
header-attrs.js
507 Bytes
header-attrs-2.7
header-attrs.js
507 Bytes
pre_treatment.html
67.4 kB
pre_treatment_files
figure-html
QC_occupancy_rsd-1.png
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QC_rsd_plot-1.png
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TICnorm_RF-1.png
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corrected-TIC plot-1.png
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day_TICs-1.png
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day_mean_pca-1.png
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impute_all_lda-1.png
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imputed_class_lda-1.png
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lda-1.png
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log10_RF-1.png
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pca-1.png
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plot_filtered_occupancy-1.png
71.5 kB
plot_occupancy-1.png
76.0 kB
supervised-rf-1.png
118.4 kB
transform_RF-1.png
128.1 kB
header-attrs-2.10
header-attrs.js
507 Bytes
header-attrs-2.11
header-attrs.js
507 Bytes
header-attrs-2.7
header-attrs.js
507 Bytes
quick_start.html
20.9 kB
quick_start_files
figure-html
feature_plot-1.png
49.8 kB
pca-1.png
170.1 kB
rf_heatmap-1.png
133.4 kB
supervised_RF-1.png
126.3 kB
header-attrs-2.10
header-attrs.js
507 Bytes
header-attrs-2.11
header-attrs.js
507 Bytes
header-attrs-2.7
header-attrs.js
507 Bytes
authors.html
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bootstrap-toc.css
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bootstrap-toc.js
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docsearch.css
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docsearch.js
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index.html
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link.svg
810 Bytes
news
index.html
17.4 kB
pkgdown.css
7.3 kB
pkgdown.js
3.2 kB
pkgdown.yml
347 Bytes
reference
Analysis-class.html
6.3 kB
AnalysisData-class.html
6.0 kB
AnalysisParameters-class.html
6.1 kB
QC-1.png
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QC-2.png
72.6 kB
QC.html
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QCimpute.html
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QCoccupancy.html
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QCremove.html
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QCrsdFilter.html
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RandomForest-class.html
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Rplot001.png
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Rplot002.png
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Rplot003.png
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Rplot004.png
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Rplot005.png
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Rplot006.png
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Rplot007.png
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Rplot008.png
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Rplot009.png
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Rplot010.png
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Rplot011.png
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Rplot012.png
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Univariate-class.html
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aggregate-1.png
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aggregate-2.png
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aggregate-3.png
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aggregate-4.png
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aggregate.html
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aggregateMean.html
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aggregateMedian.html
6.8 kB
aggregateSum.html
6.8 kB
analysis-accessors.html
26.6 kB
analysisData.html
7.8 kB
analysisElements.html
6.4 kB
analysisParameters.html
10.8 kB
analysisResults.html
6.8 kB
anova.html
13.0 kB
binaryComparisons.html
6.9 kB
bind.html
8.5 kB
bindAnalysesRows.html
6.7 kB
changeParameter.html
10.7 kB
cls.html
21.1 kB
clsAdd.html
7.4 kB
clsArrange.html
7.8 kB
clsAvailable.html
7.1 kB
clsExtract.html
7.4 kB
clsRemove.html
7.2 kB
clsRename.html
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clsReplace.html
7.6 kB
correction-1.png
72.6 kB
correction-2.png
72.0 kB
correction.html
10.9 kB
correctionCenter.html
6.4 kB
correlations.html
12.0 kB
correlationsParameters.html
7.7 kB
dat.html
7.8 kB
explanatoryFeatures.html
8.0 kB
exportParameters.html
7.2 kB
features.html
7.0 kB
figures
README-feature_plot-1.png
18.6 kB
README-pca-1.png
71.9 kB
README-rf_heatmap-1.png
73.0 kB
README-supervised_RF-1.png
54.8 kB
importance.html
7.1 kB
importanceMetrics.html
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impute-1.png
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impute-2.png
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impute-3.png
153.7 kB
impute.html
12.6 kB
imputeAll.html
7.4 kB
imputeClass.html
7.3 kB
index.html
18.3 kB
io-parameters.html
11.1 kB
keep.html
13.1 kB
keepClasses.html
7.2 kB
keepFeatures.html
7.0 kB
keepSamples.html
7.2 kB
linearRegression.html
11.4 kB
mds.html
12.8 kB
metabolyse.html
18.6 kB
metrics.html
6.7 kB
modelling-accessors.html
26.5 kB
modelling-parameters.html
8.6 kB
modellingMethods.html
6.0 kB
modellingParameters.html
7.1 kB
nFeatures.html
6.9 kB
nSamples.html
6.9 kB
occupancy.html
10.1 kB
occupancyFilter-1.png
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occupancyFilter-2.png
149.2 kB
occupancyFilter.html
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occupancyMaximum.html
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occupancyMinimum.html
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parameters.html
16.5 kB
parseParameters.html
7.8 kB
plotExplanatoryHeatmap-1.png
75.6 kB
plotExplanatoryHeatmap-2.png
43.1 kB
plotExplanatoryHeatmap.html
12.4 kB
plotFeature-1.png
51.3 kB
plotFeature-2.png
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plotFeature.html
9.3 kB
plotImportance-1.png
45.2 kB
plotImportance.html
10.2 kB
plotLDA-1.png
175.0 kB
plotLDA.html
11.6 kB
plotMDS-1.png
150.2 kB
plotMDS.html
10.9 kB
plotMetrics-1.png
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plotMetrics.html
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plotOccupancy-1.png
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plotOccupancy.html
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plotPCA-1.png
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plotPCA.html
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plotROC-1.png
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plotROC.html
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plotRSD-1.png
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plotRSD.html
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plotSupervisedRF-1.png
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plotSupervisedRF.html
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plotTIC-1.png
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plotTIC-2.png
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plotTIC.html
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plotUnsupervisedRF-1.png
187.8 kB
plotUnsupervisedRF.html
11.3 kB
pre-treatment-parameters.html
10.6 kB
preTreated.html
7.0 kB
preTreatmentElements.html
6.0 kB
preTreatmentMethods.html
6.4 kB
preTreatmentParameters.html
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randomForest-1.png
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randomForest.html
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raw.html
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reAnalyse.html
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reexports.html
6.1 kB
remove.html
13.2 kB
removeClasses.html
7.2 kB
removeFeatures.html
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removeSamples.html
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response.html
6.6 kB
roc.html
11.7 kB
rsd.html
10.1 kB
show-Analysis-method.html
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show-AnalysisData-method.html
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show-AnalysisParameters-method.html
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show-RandomForest-method.html
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show-Univariate-method.html
6.4 kB
sinfo.html
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split.html
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transform-1.png
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transform-10.png
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transform-11.png
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transform-12.png
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transform-2.png
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transform-3.png
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transform-4.png
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transform-5.png
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transform-6.png
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transform-7.png
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transform-8.png
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transform-9.png
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transform.html
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transformArcSine.html
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transformAuto.html
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transformCenter.html
6.6 kB
transformLevel.html
6.6 kB
transformLn.html
6.8 kB
transformLog10.html
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transformPareto.html
6.6 kB
transformRange.html
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transformSQRT.html
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transformTICnorm.html
6.6 kB
transformVast.html
6.6 kB
ttest.html
13.6 kB
type.html
6.5 kB
sitemap.xml
13.3 kB
inst
defaultParameters.yaml
743 Bytes
exampleParameters.yaml
249 Bytes
man
Analysis-class.Rd
680 Bytes
AnalysisData-class.Rd
390 Bytes
AnalysisParameters-class.Rd
518 Bytes
QC.Rd
3.7 kB
RandomForest-class.Rd
786 Bytes
Univariate-class.Rd
426 Bytes
aggregate.Rd
2.1 kB
analysis-accessors.Rd
4.0 kB
analysisData.Rd
518 Bytes
analysisElements.Rd
356 Bytes
analysisParameters.Rd
630 Bytes
anova.Rd
939 Bytes
bind.Rd
644 Bytes
changeParameter.Rd
1.0 kB
cls.Rd
3.8 kB
correction.Rd
1.6 kB
correlations.Rd
1.3 kB
correlationsParameters.Rd
531 Bytes
figures
README-feature_plot-1.png
18.6 kB
README-pca-1.png
71.9 kB
README-rf_heatmap-1.png
73.0 kB
README-supervised_RF-1.png
54.8 kB
impute.Rd
2.2 kB
io-parameters.Rd
1.1 kB
keep.Rd
1.6 kB
linearRegression.Rd
964 Bytes
mds.Rd
1.1 kB
metabolyse.Rd
2.4 kB
modelling-accessors.Rd
4.1 kB
modelling-parameters.Rd
717 Bytes
occupancy.Rd
723 Bytes
occupancyFilter.Rd
2.5 kB
parameters.Rd
1.4 kB
plotExplanatoryHeatmap.Rd
2.6 kB
plotFeature.Rd
1.2 kB
plotImportance.Rd
1.3 kB
plotLDA.Rd
2.2 kB
plotMDS.Rd
1.7 kB
plotMetrics.Rd
842 Bytes
plotOccupancy.Rd
886 Bytes
plotPCA.Rd
2.2 kB
plotROC.Rd
989 Bytes
plotRSD.Rd
860 Bytes
plotSupervisedRF.Rd
2.2 kB
plotTIC.Rd
1.0 kB
plotUnsupervisedRF.Rd
2.1 kB
pre-treatment-parameters.Rd
1.0 kB
randomForest.Rd
1.8 kB
reexports.Rd
461 Bytes
remove.Rd
1.7 kB
roc.Rd
762 Bytes
rsd.Rd
704 Bytes
split.Rd
728 Bytes
transform.Rd
4.5 kB
ttest.Rd
1.0 kB
metabolyseR.Rproj
343 Bytes
tests
testthat
test-QCMethods.R
888 Bytes
test-aggregateMethods.R
856 Bytes
test-analysisData.R
4.4 kB
test-analysisParameters.R
222 Bytes
test-changeParameter.R
300 Bytes
test-correctionMethods.R
1.2 kB
test-correlations.R
860 Bytes
test-imputeMethods.R
1.2 kB
test-info.R
2.8 kB
test-mds.R
386 Bytes
test-metabolyse.R
969 Bytes
test-modellingPlots.R
3.5 kB
test-occupancyMethods.R
886 Bytes
test-parameters.R
4.9 kB
test-plotExplanatoryHeatmap.R
2.6 kB
test-plotFeature.R
1.7 kB
test-plotLDA.R
1.9 kB
test-plotOccupancy.R
484 Bytes
test-plotPCA.R
750 Bytes
test-plotRSD.R
608 Bytes
test-plotSupervisedRF.R
1.3 kB
test-plotTIC.R
348 Bytes
test-plotUnsupervisedRF.R
784 Bytes
test-randomForest.R
2.3 kB
test-reAnalyse.R
824 Bytes
test-removeMethods.R
1.7 kB
test-roc.R
110 Bytes
test-show.R
856 Bytes
test-split.R
196 Bytes
test-transformMethods.R
1.2 kB
test-univariate.R
697 Bytes
testthat.R
86 Bytes
vignettes
.gitignore
34 Bytes
metabolyseR.Rmd
16.4 kB
modelling.Rmd
25.2 kB
pre_treatment.Rmd
20.5 kB
quick_start.Rmd
4.4 kB