From 55546c0b0465430f704d5603d1f6f0cd8be10261 Mon Sep 17 00:00:00 2001 From: Gavin Rhys Lloyd Date: Fri, 2 Feb 2024 10:50:50 +0000 Subject: [PATCH] rebuild documentation - due to changes in struct (removal of unicode) --- .github/workflows/pkgdown.yaml | 48 ------------------------- man/ANOVA.Rd | 2 +- man/AUC.Rd | 2 +- man/DFA.Rd | 2 +- man/DatasetExperiment_boxplot.Rd | 2 +- man/DatasetExperiment_dist.Rd | 2 +- man/DatasetExperiment_factor_boxplot.Rd | 2 +- man/DatasetExperiment_heatmap.Rd | 2 +- man/HCA.Rd | 2 +- man/HSD.Rd | 2 +- man/HSDEM.Rd | 2 +- man/OPLSDA.Rd | 2 +- man/OPLSR.Rd | 2 +- man/PCA.Rd | 2 +- man/PLSDA.Rd | 2 +- man/PLSR.Rd | 2 +- man/SVM.Rd | 2 +- man/autoscale.Rd | 2 +- man/balanced_accuracy.Rd | 2 +- man/blank_filter.Rd | 2 +- man/blank_filter_hist.Rd | 2 +- man/bootstrap.Rd | 2 +- man/classical_lsq.Rd | 2 +- man/compare_dist.Rd | 2 +- man/confounders_clsq.Rd | 2 +- man/confounders_lsq_barchart.Rd | 2 +- man/confounders_lsq_boxplot.Rd | 2 +- man/constant_sum_norm.Rd | 2 +- man/corr_coef.Rd | 2 +- man/dfa_scores_plot.Rd | 2 +- man/dratio_filter.Rd | 2 +- man/equal_split.Rd | 2 +- man/feature_boxplot.Rd | 2 +- man/feature_profile.Rd | 2 +- man/feature_profile_array.Rd | 2 +- man/filter_by_name.Rd | 2 +- man/filter_na_count.Rd | 2 +- man/filter_smeta.Rd | 2 +- man/fisher_exact.Rd | 2 +- man/fold_change.Rd | 2 +- man/fold_change_int.Rd | 2 +- man/fold_change_plot.Rd | 2 +- man/forward_selection_by_rank.Rd | 2 +- man/fs_line.Rd | 2 +- man/glog_opt_plot.Rd | 2 +- man/glog_transform.Rd | 2 +- man/grid_search_1d.Rd | 2 +- man/gs_line.Rd | 2 +- man/hca_dendrogram.Rd | 2 +- man/kfold_xval.Rd | 2 +- man/kfoldxcv_grid.Rd | 2 +- man/kfoldxcv_metric.Rd | 2 +- man/knn_impute.Rd | 2 +- man/kw_p_hist.Rd | 2 +- man/kw_rank_sum.Rd | 2 +- man/linear_model.Rd | 2 +- man/log_transform.Rd | 2 +- man/mean_centre.Rd | 2 +- man/mean_of_medians.Rd | 2 +- man/mixed_effect.Rd | 2 +- man/mv_boxplot.Rd | 2 +- man/mv_feature_filter.Rd | 2 +- man/mv_feature_filter_hist.Rd | 2 +- man/mv_histogram.Rd | 2 +- man/mv_sample_filter.Rd | 2 +- man/mv_sample_filter_hist.Rd | 2 +- man/nroot_transform.Rd | 2 +- man/pairs_filter.Rd | 2 +- man/pareto_scale.Rd | 2 +- man/pca_biplot.Rd | 2 +- man/pca_correlation_plot.Rd | 2 +- man/pca_dstat_plot.Rd | 2 +- man/pca_loadings_plot.Rd | 2 +- man/pca_scores_plot.Rd | 2 +- man/pca_scree_plot.Rd | 2 +- man/permutation_test.Rd | 2 +- man/permute_sample_order.Rd | 2 +- man/pls_regcoeff_plot.Rd | 2 +- man/pls_scores_plot.Rd | 2 +- man/pls_vip_plot.Rd | 2 +- man/plsda_feature_importance_plot.Rd | 2 +- man/plsda_predicted_plot.Rd | 2 +- man/plsda_roc_plot.Rd | 2 +- man/plsr_cook_dist.Rd | 2 +- man/plsr_prediction_plot.Rd | 2 +- man/plsr_qq_plot.Rd | 2 +- man/plsr_residual_hist.Rd | 2 +- man/pqn_norm.Rd | 2 +- man/pqn_norm_hist.Rd | 2 +- man/prop_na.Rd | 2 +- man/r_squared.Rd | 2 +- man/resample.Rd | 2 +- man/rsd_filter.Rd | 2 +- man/rsd_filter_hist.Rd | 2 +- man/sb_corr.Rd | 2 +- man/scatter_chart.Rd | 2 +- man/split_data.Rd | 2 +- man/stratified_split.Rd | 2 +- man/svm_plot_2d.Rd | 2 +- man/tSNE.Rd | 2 +- man/tSNE_scatter.Rd | 2 +- man/tic_chart.Rd | 2 +- man/ttest.Rd | 2 +- man/vec_norm.Rd | 2 +- man/wilcox_p_hist.Rd | 2 +- man/wilcox_test.Rd | 2 +- 106 files changed, 105 insertions(+), 153 deletions(-) delete mode 100644 .github/workflows/pkgdown.yaml diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml deleted file mode 100644 index 174e23d..0000000 --- a/.github/workflows/pkgdown.yaml +++ /dev/null @@ -1,48 +0,0 @@ -# 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: - branches: [devel] - pull_request: - branches: [devel] - release: - types: [published] - workflow_dispatch: - -name: pkgdown - -jobs: - pkgdown: - runs-on: ubuntu-latest - # Only restrict concurrency for non-PR jobs - concurrency: - group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - permissions: - contents: write - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-pandoc@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::pkgdown, local::. - needs: website - - - name: Build site - run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) - shell: Rscript {0} - - - name: Deploy to GitHub pages 🚀 - if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 - with: - clean: false - branch: gh-pages - folder: docs diff --git a/man/ANOVA.Rd b/man/ANOVA.Rd index 4142b53..dbe7812 100644 --- a/man/ANOVA.Rd +++ b/man/ANOVA.Rd @@ -34,7 +34,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{ANOVA} object inherits the following \code{struct} classes: \cr\cr -\code{ANOVA()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[ANOVA]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/AUC.Rd b/man/AUC.Rd index b3e0e8c..52f578f 100644 --- a/man/AUC.Rd +++ b/man/AUC.Rd @@ -20,7 +20,7 @@ The area under the ROC curve of a classifier is estimated using the trapezoid me \section{Inheritance}{ A \code{AUC} object inherits the following \code{struct} classes: \cr\cr -\code{AUC()} ⭢ \code{metric()} ⭢ \code{struct_class()} +\verb{[AUC]} >> \verb{[metric]} >> \verb{[struct_class]} } \examples{ diff --git a/man/DFA.Rd b/man/DFA.Rd index 282fa15..a2a38a4 100644 --- a/man/DFA.Rd +++ b/man/DFA.Rd @@ -28,7 +28,7 @@ Discriminant Factor Analysis (DFA) is a supervised classification method. Using \section{Inheritance}{ A \code{DFA} object inherits the following \code{struct} classes: \cr\cr -\code{DFA()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[DFA]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/DatasetExperiment_boxplot.Rd b/man/DatasetExperiment_boxplot.Rd index e366bef..fb56996 100644 --- a/man/DatasetExperiment_boxplot.Rd +++ b/man/DatasetExperiment_boxplot.Rd @@ -37,7 +37,7 @@ A boxplot to visualise the distribution of values within a subset of features. \section{Inheritance}{ A \code{DatasetExperiment_boxplot} object inherits the following \code{struct} classes: \cr\cr -\code{DatasetExperiment_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[DatasetExperiment_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/DatasetExperiment_dist.Rd b/man/DatasetExperiment_dist.Rd index a7b9116..7b3b5cd 100644 --- a/man/DatasetExperiment_dist.Rd +++ b/man/DatasetExperiment_dist.Rd @@ -25,7 +25,7 @@ A histogram to visualise the distribution of values within features. \section{Inheritance}{ A \code{DatasetExperiment_dist} object inherits the following \code{struct} classes: \cr\cr -\code{DatasetExperiment_dist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[DatasetExperiment_dist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/DatasetExperiment_factor_boxplot.Rd b/man/DatasetExperiment_factor_boxplot.Rd index 663f2f6..cadbf20 100644 --- a/man/DatasetExperiment_factor_boxplot.Rd +++ b/man/DatasetExperiment_factor_boxplot.Rd @@ -25,7 +25,7 @@ Boxplot for a feature to visualise the distribution of values within each group \section{Inheritance}{ A \code{DatasetExperiment_factor_boxplot} object inherits the following \code{struct} classes: \cr\cr -\code{DatasetExperiment_factor_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[DatasetExperiment_factor_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/DatasetExperiment_heatmap.Rd b/man/DatasetExperiment_heatmap.Rd index 5cb8e2b..d30cf27 100644 --- a/man/DatasetExperiment_heatmap.Rd +++ b/man/DatasetExperiment_heatmap.Rd @@ -26,7 +26,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{DatasetExperiment_heatmap} object inherits the following \code{struct} classes: \cr\cr -\code{DatasetExperiment_heatmap()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[DatasetExperiment_heatmap]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/HCA.Rd b/man/HCA.Rd index 7033bd2..34efc08 100644 --- a/man/HCA.Rd +++ b/man/HCA.Rd @@ -40,7 +40,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{HCA} object inherits the following \code{struct} classes: \cr\cr -\code{HCA()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[HCA]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/HSD.Rd b/man/HSD.Rd index d3bd20f..6e99b7b 100644 --- a/man/HSD.Rd +++ b/man/HSD.Rd @@ -36,7 +36,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{HSD} object inherits the following \code{struct} classes: \cr\cr -\code{HSD()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[HSD]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/HSDEM.Rd b/man/HSDEM.Rd index f7c9b25..2fd8255 100644 --- a/man/HSDEM.Rd +++ b/man/HSDEM.Rd @@ -31,7 +31,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{HSDEM} object inherits the following \code{struct} classes: \cr\cr -\code{HSDEM()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[HSDEM]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/OPLSDA.Rd b/man/OPLSDA.Rd index 4426f0c..afbeed9 100644 --- a/man/OPLSDA.Rd +++ b/man/OPLSDA.Rd @@ -28,7 +28,7 @@ contains information orthogonal to the input vector, and the other is non-orthog \section{Inheritance}{ A \code{OPLSDA} object inherits the following \code{struct} classes: \cr\cr -\code{OPLSDA()} ⭢ \code{OPLSR()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[OPLSDA]} >> \verb{[OPLSR]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/OPLSR.Rd b/man/OPLSR.Rd index fac822c..2e08a68 100644 --- a/man/OPLSR.Rd +++ b/man/OPLSR.Rd @@ -28,7 +28,7 @@ contains information orthogonal to the input vector, and the other is non-orthog \section{Inheritance}{ A \code{OPLSR} object inherits the following \code{struct} classes: \cr\cr -\code{OPLSR()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[OPLSR]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/PCA.Rd b/man/PCA.Rd index dc2af19..c050af6 100644 --- a/man/PCA.Rd +++ b/man/PCA.Rd @@ -28,7 +28,7 @@ PCA is a multivariate data reduction technique. It summarises the data in a smal \section{Inheritance}{ A \code{PCA} object inherits the following \code{struct} classes: \cr\cr -\code{PCA()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[PCA]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/PLSDA.Rd b/man/PLSDA.Rd index 12f5def..8ffe4da 100644 --- a/man/PLSDA.Rd +++ b/man/PLSDA.Rd @@ -42,7 +42,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{PLSDA} object inherits the following \code{struct} classes: \cr\cr -\code{PLSDA()} ⭢ \code{PLSR()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[PLSDA]} >> \verb{[PLSR]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/PLSR.Rd b/man/PLSR.Rd index d33f469..6e67869 100644 --- a/man/PLSR.Rd +++ b/man/PLSR.Rd @@ -37,7 +37,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{PLSR} object inherits the following \code{struct} classes: \cr\cr -\code{PLSR()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[PLSR]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/SVM.Rd b/man/SVM.Rd index ea9a0ab..2571801 100644 --- a/man/SVM.Rd +++ b/man/SVM.Rd @@ -54,7 +54,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{SVM} object inherits the following \code{struct} classes: \cr\cr -\code{SVM()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[SVM]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/autoscale.Rd b/man/autoscale.Rd index ef6758a..682ec19 100644 --- a/man/autoscale.Rd +++ b/man/autoscale.Rd @@ -27,7 +27,7 @@ Each variable/feature is mean centred and scaled by the standard deviation. The \section{Inheritance}{ A \code{autoscale} object inherits the following \code{struct} classes: \cr\cr -\code{autoscale()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[autoscale]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/balanced_accuracy.Rd b/man/balanced_accuracy.Rd index 01f676c..fddfb15 100644 --- a/man/balanced_accuracy.Rd +++ b/man/balanced_accuracy.Rd @@ -20,7 +20,7 @@ Balanced Accuracy is the average proportion of correctly classified samples acro \section{Inheritance}{ A \code{balanced_accuracy} object inherits the following \code{struct} classes: \cr\cr -\code{balanced_accuracy()} ⭢ \code{metric()} ⭢ \code{struct_class()} +\verb{[balanced_accuracy]} >> \verb{[metric]} >> \verb{[struct_class]} } \examples{ diff --git a/man/blank_filter.Rd b/man/blank_filter.Rd index 6f241e3..9aaa2cd 100644 --- a/man/blank_filter.Rd +++ b/man/blank_filter.Rd @@ -42,7 +42,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{blank_filter} object inherits the following \code{struct} classes: \cr\cr -\code{blank_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[blank_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/blank_filter_hist.Rd b/man/blank_filter_hist.Rd index 4232128..9aa4d88 100644 --- a/man/blank_filter_hist.Rd +++ b/man/blank_filter_hist.Rd @@ -21,7 +21,7 @@ A histogram of the calculated fold changes for the blank filter (median samples \section{Inheritance}{ A \code{blank_filter_hist} object inherits the following \code{struct} classes: \cr\cr -\code{blank_filter_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[blank_filter_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/bootstrap.Rd b/man/bootstrap.Rd index 6fb8dc9..2938518 100644 --- a/man/bootstrap.Rd +++ b/man/bootstrap.Rd @@ -27,7 +27,7 @@ In bootstrap resampling a subset of samples is selected at random with replaceme \section{Inheritance}{ A \code{bootstrap} object inherits the following \code{struct} classes: \cr\cr -\code{bootstrap()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[bootstrap]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/classical_lsq.Rd b/man/classical_lsq.Rd index 2155289..b670c56 100644 --- a/man/classical_lsq.Rd +++ b/man/classical_lsq.Rd @@ -33,7 +33,7 @@ In univariate classical least squares regression a line is fitted between each f \section{Inheritance}{ A \code{classical_lsq} object inherits the following \code{struct} classes: \cr\cr -\code{classical_lsq()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[classical_lsq]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/compare_dist.Rd b/man/compare_dist.Rd index 3821280..48d7ed9 100644 --- a/man/compare_dist.Rd +++ b/man/compare_dist.Rd @@ -23,7 +23,7 @@ Histograms and boxplots computed across samples and features are used to visuall \section{Inheritance}{ A \code{compare_dist} object inherits the following \code{struct} classes: \cr\cr -\code{compare_dist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[compare_dist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/confounders_clsq.Rd b/man/confounders_clsq.Rd index 4fa71d8..9609859 100644 --- a/man/confounders_clsq.Rd +++ b/man/confounders_clsq.Rd @@ -42,7 +42,7 @@ Univariate least squares regression models are used to compare models with and w \section{Inheritance}{ A \code{confounders_clsq} object inherits the following \code{struct} classes: \cr\cr -\code{confounders_clsq()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[confounders_clsq]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/confounders_lsq_barchart.Rd b/man/confounders_lsq_barchart.Rd index 4bbae81..ec4a70e 100644 --- a/man/confounders_lsq_barchart.Rd +++ b/man/confounders_lsq_barchart.Rd @@ -25,7 +25,7 @@ A barchart of the relative change (delta) in regression coefficient when potenti \section{Inheritance}{ A \code{confounders_lsq_barchart} object inherits the following \code{struct} classes: \cr\cr -\code{confounders_lsq_barchart()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[confounders_lsq_barchart]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/confounders_lsq_boxplot.Rd b/man/confounders_lsq_boxplot.Rd index e2ba63c..888fb8f 100644 --- a/man/confounders_lsq_boxplot.Rd +++ b/man/confounders_lsq_boxplot.Rd @@ -23,7 +23,7 @@ A boxplot of the relative change (delta) in regression coefficient when potentia \section{Inheritance}{ A \code{confounders_lsq_boxplot} object inherits the following \code{struct} classes: \cr\cr -\code{confounders_lsq_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[confounders_lsq_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/constant_sum_norm.Rd b/man/constant_sum_norm.Rd index 22e1208..e0d4512 100644 --- a/man/constant_sum_norm.Rd +++ b/man/constant_sum_norm.Rd @@ -24,7 +24,7 @@ Each sample is normalised such that the total signal is equal to one (or a scali \section{Inheritance}{ A \code{constant_sum_norm} object inherits the following \code{struct} classes: \cr\cr -\code{constant_sum_norm()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[constant_sum_norm]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/corr_coef.Rd b/man/corr_coef.Rd index 881565b..b91f175 100644 --- a/man/corr_coef.Rd +++ b/man/corr_coef.Rd @@ -34,7 +34,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{corr_coef} object inherits the following \code{struct} classes: \cr\cr -\code{corr_coef()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[corr_coef]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/dfa_scores_plot.Rd b/man/dfa_scores_plot.Rd index 8fd3d49..267517b 100644 --- a/man/dfa_scores_plot.Rd +++ b/man/dfa_scores_plot.Rd @@ -47,7 +47,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{dfa_scores_plot} object inherits the following \code{struct} classes: \cr\cr -\code{dfa_scores_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[dfa_scores_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/dratio_filter.Rd b/man/dratio_filter.Rd index 12e3be3..5528ef5 100644 --- a/man/dratio_filter.Rd +++ b/man/dratio_filter.Rd @@ -40,7 +40,7 @@ The dispersion ratio (d-ratio) compares the standard deviation (or non-parametri \section{Inheritance}{ A \code{dratio_filter} object inherits the following \code{struct} classes: \cr\cr -\code{dratio_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[dratio_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/equal_split.Rd b/man/equal_split.Rd index bad1797..5933593 100644 --- a/man/equal_split.Rd +++ b/man/equal_split.Rd @@ -26,7 +26,7 @@ Samples are randomly chosen from each level such that the training set has equal \section{Inheritance}{ A \code{equal_split} object inherits the following \code{struct} classes: \cr\cr -\code{equal_split()} ⭢ \code{split_data()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[equal_split]} >> \verb{[split_data]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/feature_boxplot.Rd b/man/feature_boxplot.Rd index 1128a44..e08af99 100644 --- a/man/feature_boxplot.Rd +++ b/man/feature_boxplot.Rd @@ -44,7 +44,7 @@ A boxplot to visualise the distribution of values within a feature. \section{Inheritance}{ A \code{feature_boxplot} object inherits the following \code{struct} classes: \cr\cr -\code{feature_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[feature_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/feature_profile.Rd b/man/feature_profile.Rd index 7170952..10aa99d 100644 --- a/man/feature_profile.Rd +++ b/man/feature_profile.Rd @@ -41,7 +41,7 @@ A plot visualising the change in intensity of a feature with a continuous variab \section{Inheritance}{ A \code{feature_profile} object inherits the following \code{struct} classes: \cr\cr -\code{feature_profile()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[feature_profile]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/feature_profile_array.Rd b/man/feature_profile_array.Rd index 829607d..3ad8d43 100644 --- a/man/feature_profile_array.Rd +++ b/man/feature_profile_array.Rd @@ -44,7 +44,7 @@ A plot visualising the change in intensity of a feature with a continuous variab \section{Inheritance}{ A \code{feature_profile_array} object inherits the following \code{struct} classes: \cr\cr -\code{feature_profile_array()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[feature_profile_array]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/filter_by_name.Rd b/man/filter_by_name.Rd index 89cee84..9ffb21c 100644 --- a/man/filter_by_name.Rd +++ b/man/filter_by_name.Rd @@ -27,7 +27,7 @@ Filter samples/variables by row/column name, index or logicals. \section{Inheritance}{ A \code{filter_by_name} object inherits the following \code{struct} classes: \cr\cr -\code{filter_by_name()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[filter_by_name]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/filter_na_count.Rd b/man/filter_na_count.Rd index ee05254..f7ee99b 100644 --- a/man/filter_na_count.Rd +++ b/man/filter_na_count.Rd @@ -28,7 +28,7 @@ The number of measured values is counted for each feature, and any feature with \section{Inheritance}{ A \code{filter_na_count} object inherits the following \code{struct} classes: \cr\cr -\code{filter_na_count()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[filter_na_count]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/filter_smeta.Rd b/man/filter_smeta.Rd index 3db08bf..afe6883 100644 --- a/man/filter_smeta.Rd +++ b/man/filter_smeta.Rd @@ -27,7 +27,7 @@ The data is filtered by so that the named levels of a factor are included/exclud \section{Inheritance}{ A \code{filter_smeta} object inherits the following \code{struct} classes: \cr\cr -\code{filter_smeta()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[filter_smeta]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/fisher_exact.Rd b/man/fisher_exact.Rd index 28ce7da..fdacb98 100644 --- a/man/fisher_exact.Rd +++ b/man/fisher_exact.Rd @@ -30,7 +30,7 @@ A fisher exact test is used to analyse contingency tables by comparing the numbe \section{Inheritance}{ A \code{fisher_exact} object inherits the following \code{struct} classes: \cr\cr -\code{fisher_exact()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[fisher_exact]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/fold_change.Rd b/man/fold_change.Rd index a6eb626..3ecb4d5 100644 --- a/man/fold_change.Rd +++ b/man/fold_change.Rd @@ -47,7 +47,7 @@ Fold change is the relative change in mean (or non-parametric equivalent) intens \section{Inheritance}{ A \code{fold_change} object inherits the following \code{struct} classes: \cr\cr -\code{fold_change()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[fold_change]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/fold_change_int.Rd b/man/fold_change_int.Rd index 6329b7a..0f8c78c 100644 --- a/man/fold_change_int.Rd +++ b/man/fold_change_int.Rd @@ -41,7 +41,7 @@ For more than one factor the fold change calculation is extended to include all \section{Inheritance}{ A \code{fold_change_int} object inherits the following \code{struct} classes: \cr\cr -\code{fold_change_int()} ⭢ \code{fold_change()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[fold_change_int]} >> \verb{[fold_change]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/fold_change_plot.Rd b/man/fold_change_plot.Rd index f8f68c2..91e1b5a 100644 --- a/man/fold_change_plot.Rd +++ b/man/fold_change_plot.Rd @@ -26,7 +26,7 @@ A plot of fold changes calculated for a chosen subset of features. A predefined \section{Inheritance}{ A \code{fold_change_plot} object inherits the following \code{struct} classes: \cr\cr -\code{fold_change_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[fold_change_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/forward_selection_by_rank.Rd b/man/forward_selection_by_rank.Rd index 11eb43d..668d74c 100644 --- a/man/forward_selection_by_rank.Rd +++ b/man/forward_selection_by_rank.Rd @@ -42,7 +42,7 @@ A model is trained and performance metric computed by including increasing numbe \section{Inheritance}{ A \code{forward_selection_by_rank} object inherits the following \code{struct} classes: \cr\cr -\code{forward_selection_by_rank()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[forward_selection_by_rank]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/fs_line.Rd b/man/fs_line.Rd index 5cb5595..eac5716 100644 --- a/man/fs_line.Rd +++ b/man/fs_line.Rd @@ -21,7 +21,7 @@ A line plot for forward selection. The computed model performance metric is plot \section{Inheritance}{ A \code{fs_line} object inherits the following \code{struct} classes: \cr\cr -\code{fs_line()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[fs_line]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/glog_opt_plot.Rd b/man/glog_opt_plot.Rd index ea23562..0e7feaf 100644 --- a/man/glog_opt_plot.Rd +++ b/man/glog_opt_plot.Rd @@ -26,7 +26,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{glog_opt_plot} object inherits the following \code{struct} classes: \cr\cr -\code{glog_opt_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[glog_opt_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/glog_transform.Rd b/man/glog_transform.Rd index a98c173..82bb644 100644 --- a/man/glog_transform.Rd +++ b/man/glog_transform.Rd @@ -31,7 +31,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{glog_transform} object inherits the following \code{struct} classes: \cr\cr -\code{glog_transform()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[glog_transform]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/grid_search_1d.Rd b/man/grid_search_1d.Rd index 0a47c94..70719f1 100644 --- a/man/grid_search_1d.Rd +++ b/man/grid_search_1d.Rd @@ -40,7 +40,7 @@ A one dimensional grid search calculates a performance metric for a model at eve \section{Inheritance}{ A \code{grid_search_1d} object inherits the following \code{struct} classes: \cr\cr -\code{grid_search_1d()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[grid_search_1d]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/gs_line.Rd b/man/gs_line.Rd index e6160b8..f5fb792 100644 --- a/man/gs_line.Rd +++ b/man/gs_line.Rd @@ -21,7 +21,7 @@ A plot of the calculated performance metric against the model input parameter va \section{Inheritance}{ A \code{gs_line} object inherits the following \code{struct} classes: \cr\cr -\code{gs_line()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[gs_line]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/hca_dendrogram.Rd b/man/hca_dendrogram.Rd index 6e0e629..8b3ea28 100644 --- a/man/hca_dendrogram.Rd +++ b/man/hca_dendrogram.Rd @@ -24,7 +24,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{hca_dendrogram} object inherits the following \code{struct} classes: \cr\cr -\code{hca_dendrogram()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[hca_dendrogram]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/kfold_xval.Rd b/man/kfold_xval.Rd index 47be915..cb82238 100644 --- a/man/kfold_xval.Rd +++ b/man/kfold_xval.Rd @@ -33,7 +33,7 @@ k-fold cross-validation is an iterative approach applied to validate models. The \section{Inheritance}{ A \code{kfold_xval} object inherits the following \code{struct} classes: \cr\cr -\code{kfold_xval()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[kfold_xval]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/kfoldxcv_grid.Rd b/man/kfoldxcv_grid.Rd index c68977a..c18b81c 100644 --- a/man/kfoldxcv_grid.Rd +++ b/man/kfoldxcv_grid.Rd @@ -25,7 +25,7 @@ A graphic for visualising the true class and the predicted class of samples in a \section{Inheritance}{ A \code{kfoldxcv_grid} object inherits the following \code{struct} classes: \cr\cr -\code{kfoldxcv_grid()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[kfoldxcv_grid]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/kfoldxcv_metric.Rd b/man/kfoldxcv_metric.Rd index e449ab0..6dacd2a 100644 --- a/man/kfoldxcv_metric.Rd +++ b/man/kfoldxcv_metric.Rd @@ -21,7 +21,7 @@ A boxplot of the performance metric computed for each fold of a k-fold cross-val \section{Inheritance}{ A \code{kfoldxcv_metric} object inherits the following \code{struct} classes: \cr\cr -\code{kfoldxcv_metric()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[kfoldxcv_metric]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/knn_impute.Rd b/man/knn_impute.Rd index 7cb8d49..e4ba220 100644 --- a/man/knn_impute.Rd +++ b/man/knn_impute.Rd @@ -38,7 +38,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{knn_impute} object inherits the following \code{struct} classes: \cr\cr -\code{knn_impute()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[knn_impute]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/kw_p_hist.Rd b/man/kw_p_hist.Rd index 904a655..7bb7955 100644 --- a/man/kw_p_hist.Rd +++ b/man/kw_p_hist.Rd @@ -21,7 +21,7 @@ A histogram of the p-values computed by the kruskal-wallis method \section{Inheritance}{ A \code{kw_p_hist} object inherits the following \code{struct} classes: \cr\cr -\code{kw_p_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[kw_p_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/kw_rank_sum.Rd b/man/kw_rank_sum.Rd index b8fab49..253691e 100644 --- a/man/kw_rank_sum.Rd +++ b/man/kw_rank_sum.Rd @@ -31,7 +31,7 @@ The Kruskal-Wallis test is a univariate hypothesis testing method that allows mu \section{Inheritance}{ A \code{kw_rank_sum} object inherits the following \code{struct} classes: \cr\cr -\code{kw_rank_sum()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[kw_rank_sum]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/linear_model.Rd b/man/linear_model.Rd index 74669e5..c023a4a 100644 --- a/man/linear_model.Rd +++ b/man/linear_model.Rd @@ -36,7 +36,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{linear_model} object inherits the following \code{struct} classes: \cr\cr -\code{linear_model()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[linear_model]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/log_transform.Rd b/man/log_transform.Rd index 35218a8..3ce5b19 100644 --- a/man/log_transform.Rd +++ b/man/log_transform.Rd @@ -25,7 +25,7 @@ A logarithmic transform is applied to all values in the data matrix. \section{Inheritance}{ A \code{log_transform} object inherits the following \code{struct} classes: \cr\cr -\code{log_transform()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[log_transform]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mean_centre.Rd b/man/mean_centre.Rd index 3994fcf..d9bb321 100644 --- a/man/mean_centre.Rd +++ b/man/mean_centre.Rd @@ -25,7 +25,7 @@ The mean sample is subtracted from all samples in the data matrix. The features \section{Inheritance}{ A \code{mean_centre} object inherits the following \code{struct} classes: \cr\cr -\code{mean_centre()} ⭢ \code{preprocess()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[mean_centre]} >> \verb{[preprocess]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mean_of_medians.Rd b/man/mean_of_medians.Rd index 50171b2..b2a3564 100644 --- a/man/mean_of_medians.Rd +++ b/man/mean_of_medians.Rd @@ -23,7 +23,7 @@ The data matrix is normalised by the mean of the median of each factor level. \section{Inheritance}{ A \code{mean_of_medians} object inherits the following \code{struct} classes: \cr\cr -\code{mean_of_medians()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[mean_of_medians]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mixed_effect.Rd b/man/mixed_effect.Rd index 7f2c1c1..6b61ed0 100644 --- a/man/mixed_effect.Rd +++ b/man/mixed_effect.Rd @@ -34,7 +34,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{mixed_effect} object inherits the following \code{struct} classes: \cr\cr -\code{mixed_effect()} ⭢ \code{ANOVA()} ⭢ \code{model()} ⭢ \code{stato()} ⭢ \code{struct_class()} +\verb{[mixed_effect]} >> \verb{[ANOVA]} >> \verb{[model]} >> \verb{[stato]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_boxplot.Rd b/man/mv_boxplot.Rd index 4a13be0..9e5edb1 100644 --- a/man/mv_boxplot.Rd +++ b/man/mv_boxplot.Rd @@ -35,7 +35,7 @@ Boxplots of the number of missing values per sample/feature. \section{Inheritance}{ A \code{mv_boxplot} object inherits the following \code{struct} classes: \cr\cr -\code{mv_boxplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[mv_boxplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_feature_filter.Rd b/man/mv_feature_filter.Rd index bf42bb2..eaa3951 100644 --- a/man/mv_feature_filter.Rd +++ b/man/mv_feature_filter.Rd @@ -39,7 +39,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{mv_feature_filter} object inherits the following \code{struct} classes: \cr\cr -\code{mv_feature_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[mv_feature_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_feature_filter_hist.Rd b/man/mv_feature_filter_hist.Rd index 85b20bd..190395a 100644 --- a/man/mv_feature_filter_hist.Rd +++ b/man/mv_feature_filter_hist.Rd @@ -21,7 +21,7 @@ A histogram of the proportion of missing values per feature. \section{Inheritance}{ A \code{mv_feature_filter_hist} object inherits the following \code{struct} classes: \cr\cr -\code{mv_feature_filter_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[mv_feature_filter_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_histogram.Rd b/man/mv_histogram.Rd index d0ac36d..2cc4e7b 100644 --- a/man/mv_histogram.Rd +++ b/man/mv_histogram.Rd @@ -27,7 +27,7 @@ A histogram of the numbers of missing values per sample/feature \section{Inheritance}{ A \code{mv_histogram} object inherits the following \code{struct} classes: \cr\cr -\code{mv_histogram()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[mv_histogram]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_sample_filter.Rd b/man/mv_sample_filter.Rd index 35fe4f4..572cfa0 100644 --- a/man/mv_sample_filter.Rd +++ b/man/mv_sample_filter.Rd @@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{mv_sample_filter} object inherits the following \code{struct} classes: \cr\cr -\code{mv_sample_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[mv_sample_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/mv_sample_filter_hist.Rd b/man/mv_sample_filter_hist.Rd index 64103b3..97a2b45 100644 --- a/man/mv_sample_filter_hist.Rd +++ b/man/mv_sample_filter_hist.Rd @@ -21,7 +21,7 @@ A histogram of the the proportion of missing values per sample \section{Inheritance}{ A \code{mv_sample_filter_hist} object inherits the following \code{struct} classes: \cr\cr -\code{mv_sample_filter_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[mv_sample_filter_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/nroot_transform.Rd b/man/nroot_transform.Rd index 375edd9..d0c4ea5 100644 --- a/man/nroot_transform.Rd +++ b/man/nroot_transform.Rd @@ -23,7 +23,7 @@ All values in the data matrix are transformed by raising them to the power of 1/ \section{Inheritance}{ A \code{nroot_transform} object inherits the following \code{struct} classes: \cr\cr -\code{nroot_transform()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[nroot_transform]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pairs_filter.Rd b/man/pairs_filter.Rd index 885060c..61bf08e 100644 --- a/man/pairs_filter.Rd +++ b/man/pairs_filter.Rd @@ -28,7 +28,7 @@ This filter is used for study designs with paired sampling to ensure that measu \section{Inheritance}{ A \code{pairs_filter} object inherits the following \code{struct} classes: \cr\cr -\code{pairs_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[pairs_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pareto_scale.Rd b/man/pareto_scale.Rd index 6fcc0cd..082d60e 100644 --- a/man/pareto_scale.Rd +++ b/man/pareto_scale.Rd @@ -23,7 +23,7 @@ The mean sample is subtracted from all samples and then scaled by the square roo \section{Inheritance}{ A \code{pareto_scale} object inherits the following \code{struct} classes: \cr\cr -\code{pareto_scale()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[pareto_scale]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_biplot.Rd b/man/pca_biplot.Rd index ac2c9f3..40ec0f8 100644 --- a/man/pca_biplot.Rd +++ b/man/pca_biplot.Rd @@ -41,7 +41,7 @@ A scatter plot of the selected principal component scores overlaid with the corr \section{Inheritance}{ A \code{pca_biplot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_biplot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_biplot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_correlation_plot.Rd b/man/pca_correlation_plot.Rd index 1f3768d..2a6efea 100644 --- a/man/pca_correlation_plot.Rd +++ b/man/pca_correlation_plot.Rd @@ -23,7 +23,7 @@ A plot of the correlation between the variables/features and the selected princi \section{Inheritance}{ A \code{pca_correlation_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_correlation_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_correlation_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_dstat_plot.Rd b/man/pca_dstat_plot.Rd index 8ad856e..275dd81 100644 --- a/man/pca_dstat_plot.Rd +++ b/man/pca_dstat_plot.Rd @@ -25,7 +25,7 @@ A bar chart of the d-statistics for samples in the input PCA model. Samples abov \section{Inheritance}{ A \code{pca_dstat_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_dstat_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_dstat_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_loadings_plot.Rd b/man/pca_loadings_plot.Rd index a21b7b3..1636491 100644 --- a/man/pca_loadings_plot.Rd +++ b/man/pca_loadings_plot.Rd @@ -32,7 +32,7 @@ A barchart (one component) or scatter plot (two components) of the selected prin \section{Inheritance}{ A \code{pca_loadings_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_loadings_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_loadings_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_scores_plot.Rd b/man/pca_scores_plot.Rd index 64cdbee..25aacc8 100644 --- a/man/pca_scores_plot.Rd +++ b/man/pca_scores_plot.Rd @@ -56,7 +56,7 @@ Plots a 2d scatter plot of the selected components \section{Inheritance}{ A \code{pca_scores_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_scores_plot()} ⭢ \code{scatter_chart()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_scores_plot]} >> \verb{[scatter_chart]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pca_scree_plot.Rd b/man/pca_scree_plot.Rd index 6b1555a..6eae468 100644 --- a/man/pca_scree_plot.Rd +++ b/man/pca_scree_plot.Rd @@ -25,7 +25,7 @@ A plot of the percent variance and cumulative percent variance for the component \section{Inheritance}{ A \code{pca_scree_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pca_scree_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pca_scree_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/permutation_test.Rd b/man/permutation_test.Rd index ffd86d2..0b6b799 100644 --- a/man/permutation_test.Rd +++ b/man/permutation_test.Rd @@ -27,7 +27,7 @@ A permutation test generates a "null" model by randomising the response (for reg \section{Inheritance}{ A \code{permutation_test} object inherits the following \code{struct} classes: \cr\cr -\code{permutation_test()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[permutation_test]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/permute_sample_order.Rd b/man/permute_sample_order.Rd index b0d48b7..f2aea80 100644 --- a/man/permute_sample_order.Rd +++ b/man/permute_sample_order.Rd @@ -25,7 +25,7 @@ The order of samples in the data matrix is randomly permuted. The relationship b \section{Inheritance}{ A \code{permute_sample_order} object inherits the following \code{struct} classes: \cr\cr -\code{permute_sample_order()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[permute_sample_order]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pls_regcoeff_plot.Rd b/man/pls_regcoeff_plot.Rd index 973ca9a..941db1b 100644 --- a/man/pls_regcoeff_plot.Rd +++ b/man/pls_regcoeff_plot.Rd @@ -30,7 +30,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{pls_regcoeff_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pls_regcoeff_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pls_regcoeff_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pls_scores_plot.Rd b/man/pls_scores_plot.Rd index 99c22a1..bbb9a38 100644 --- a/man/pls_scores_plot.Rd +++ b/man/pls_scores_plot.Rd @@ -73,7 +73,7 @@ A scatter plot of the selected PLSDA scores. \section{Inheritance}{ A \code{pls_scores_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pls_scores_plot()} ⭢ \code{scatter_chart()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pls_scores_plot]} >> \verb{[scatter_chart]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pls_vip_plot.Rd b/man/pls_vip_plot.Rd index 5a4e7d4..4052301 100644 --- a/man/pls_vip_plot.Rd +++ b/man/pls_vip_plot.Rd @@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{pls_vip_plot} object inherits the following \code{struct} classes: \cr\cr -\code{pls_vip_plot()} ⭢ \code{chart()} ⭢ \code{stato()} ⭢ \code{struct_class()} +\verb{[pls_vip_plot]} >> \verb{[chart]} >> \verb{[stato]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsda_feature_importance_plot.Rd b/man/plsda_feature_importance_plot.Rd index 2b53782..e0d7322 100644 --- a/man/plsda_feature_importance_plot.Rd +++ b/man/plsda_feature_importance_plot.Rd @@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{plsda_feature_importance_plot} object inherits the following \code{struct} classes: \cr\cr -\code{plsda_feature_importance_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsda_feature_importance_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsda_predicted_plot.Rd b/man/plsda_predicted_plot.Rd index c8d58ce..836a9ff 100644 --- a/man/plsda_predicted_plot.Rd +++ b/man/plsda_predicted_plot.Rd @@ -30,7 +30,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{plsda_predicted_plot} object inherits the following \code{struct} classes: \cr\cr -\code{plsda_predicted_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsda_predicted_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsda_roc_plot.Rd b/man/plsda_roc_plot.Rd index dba9ad2..d9761d1 100644 --- a/man/plsda_roc_plot.Rd +++ b/man/plsda_roc_plot.Rd @@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{plsda_roc_plot} object inherits the following \code{struct} classes: \cr\cr -\code{plsda_roc_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsda_roc_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsr_cook_dist.Rd b/man/plsr_cook_dist.Rd index 16b9d7c..01a2ada 100644 --- a/man/plsr_cook_dist.Rd +++ b/man/plsr_cook_dist.Rd @@ -23,7 +23,7 @@ A barchart of Cook's distance for each sample used to train a PLSR model. Cook's \section{Inheritance}{ A \code{plsr_cook_dist} object inherits the following \code{struct} classes: \cr\cr -\code{plsr_cook_dist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsr_cook_dist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsr_prediction_plot.Rd b/man/plsr_prediction_plot.Rd index 0c3adbc..eec2a7e 100644 --- a/man/plsr_prediction_plot.Rd +++ b/man/plsr_prediction_plot.Rd @@ -23,7 +23,7 @@ A scatter plot of the true response values against the predicted values for a PL \section{Inheritance}{ A \code{plsr_prediction_plot} object inherits the following \code{struct} classes: \cr\cr -\code{plsr_prediction_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsr_prediction_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsr_qq_plot.Rd b/man/plsr_qq_plot.Rd index 596b102..9ac98af 100644 --- a/man/plsr_qq_plot.Rd +++ b/man/plsr_qq_plot.Rd @@ -23,7 +23,7 @@ A plot of the quantiles of the residuals from a PLSR model against the quantiles \section{Inheritance}{ A \code{plsr_qq_plot} object inherits the following \code{struct} classes: \cr\cr -\code{plsr_qq_plot()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsr_qq_plot]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/plsr_residual_hist.Rd b/man/plsr_residual_hist.Rd index e1e0359..5a77777 100644 --- a/man/plsr_residual_hist.Rd +++ b/man/plsr_residual_hist.Rd @@ -23,7 +23,7 @@ A histogram of the residuals for a PLSR model. \section{Inheritance}{ A \code{plsr_residual_hist} object inherits the following \code{struct} classes: \cr\cr -\code{plsr_residual_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[plsr_residual_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pqn_norm.Rd b/man/pqn_norm.Rd index 6e7f6ed..1c34c0e 100644 --- a/man/pqn_norm.Rd +++ b/man/pqn_norm.Rd @@ -45,7 +45,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{pqn_norm} object inherits the following \code{struct} classes: \cr\cr -\code{pqn_norm()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[pqn_norm]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/pqn_norm_hist.Rd b/man/pqn_norm_hist.Rd index d9b7b43..7848731 100644 --- a/man/pqn_norm_hist.Rd +++ b/man/pqn_norm_hist.Rd @@ -21,7 +21,7 @@ A histogram of the PQN coefficients for all features \section{Inheritance}{ A \code{pqn_norm_hist} object inherits the following \code{struct} classes: \cr\cr -\code{pqn_norm_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[pqn_norm_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/prop_na.Rd b/man/prop_na.Rd index 873b5da..e7eebbf 100644 --- a/man/prop_na.Rd +++ b/man/prop_na.Rd @@ -31,7 +31,7 @@ A Fisher's exact test is used to compare the number of missing values in each gr \section{Inheritance}{ A \code{prop_na} object inherits the following \code{struct} classes: \cr\cr -\code{prop_na()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[prop_na]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/r_squared.Rd b/man/r_squared.Rd index 8795d27..4ae83da 100644 --- a/man/r_squared.Rd +++ b/man/r_squared.Rd @@ -20,7 +20,7 @@ R-squared is a metric used to assess the goodness of fit for regression models. \section{Inheritance}{ A \code{r_squared} object inherits the following \code{struct} classes: \cr\cr -\code{r_squared()} ⭢ \code{metric()} ⭢ \code{struct_class()} +\verb{[r_squared]} >> \verb{[metric]} >> \verb{[struct_class]} } \examples{ diff --git a/man/resample.Rd b/man/resample.Rd index 744af35..767090a 100644 --- a/man/resample.Rd +++ b/man/resample.Rd @@ -43,7 +43,7 @@ New training sets are generated from the original data by selecting samples at r \section{Inheritance}{ A \code{resample} object inherits the following \code{struct} classes: \cr\cr -\code{resample()} ⭢ \code{resampler()} ⭢ \code{iterator()} ⭢ \code{struct_class()} +\verb{[resample]} >> \verb{[resampler]} >> \verb{[iterator]} >> \verb{[struct_class]} } \examples{ diff --git a/man/rsd_filter.Rd b/man/rsd_filter.Rd index 49033ee..bec580e 100644 --- a/man/rsd_filter.Rd +++ b/man/rsd_filter.Rd @@ -32,7 +32,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{rsd_filter} object inherits the following \code{struct} classes: \cr\cr -\code{rsd_filter()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[rsd_filter]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/rsd_filter_hist.Rd b/man/rsd_filter_hist.Rd index 4529f7b..878b844 100644 --- a/man/rsd_filter_hist.Rd +++ b/man/rsd_filter_hist.Rd @@ -21,7 +21,7 @@ A histogram of the calculated RSD values. \section{Inheritance}{ A \code{rsd_filter_hist} object inherits the following \code{struct} classes: \cr\cr -\code{rsd_filter_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[rsd_filter_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/sb_corr.Rd b/man/sb_corr.Rd index 1e62ef0..70bc5f8 100644 --- a/man/sb_corr.Rd +++ b/man/sb_corr.Rd @@ -54,7 +54,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{sb_corr} object inherits the following \code{struct} classes: \cr\cr -\code{sb_corr()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[sb_corr]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/scatter_chart.Rd b/man/scatter_chart.Rd index bf5f309..2615bd1 100644 --- a/man/scatter_chart.Rd +++ b/man/scatter_chart.Rd @@ -53,7 +53,7 @@ Plots a 2d scatter plot of the input data. \section{Inheritance}{ A \code{scatter_chart} object inherits the following \code{struct} classes: \cr\cr -\code{scatter_chart()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[scatter_chart]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/split_data.Rd b/man/split_data.Rd index 7b6941c..74ba3f6 100644 --- a/man/split_data.Rd +++ b/man/split_data.Rd @@ -24,7 +24,7 @@ The data matrix is divided into two subsets.A predefined proportion of the sampl \section{Inheritance}{ A \code{split_data} object inherits the following \code{struct} classes: \cr\cr -\code{split_data()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[split_data]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/stratified_split.Rd b/man/stratified_split.Rd index d1fb64d..723e62f 100644 --- a/man/stratified_split.Rd +++ b/man/stratified_split.Rd @@ -26,7 +26,7 @@ The dataset is divided into two subsets. A predefined proportion of samples from \section{Inheritance}{ A \code{stratified_split} object inherits the following \code{struct} classes: \cr\cr -\code{stratified_split()} ⭢ \code{split_data()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[stratified_split]} >> \verb{[split_data]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/svm_plot_2d.Rd b/man/svm_plot_2d.Rd index f9a2d84..7c0fe63 100644 --- a/man/svm_plot_2d.Rd +++ b/man/svm_plot_2d.Rd @@ -28,7 +28,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{svm_plot_2d} object inherits the following \code{struct} classes: \cr\cr -\code{svm_plot_2d()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[svm_plot_2d]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/tSNE.Rd b/man/tSNE.Rd index 01d45fe..80d45e0 100644 --- a/man/tSNE.Rd +++ b/man/tSNE.Rd @@ -47,7 +47,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{tSNE} object inherits the following \code{struct} classes: \cr\cr -\code{tSNE()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[tSNE]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/tSNE_scatter.Rd b/man/tSNE_scatter.Rd index 0032686..579568f 100644 --- a/man/tSNE_scatter.Rd +++ b/man/tSNE_scatter.Rd @@ -26,7 +26,7 @@ This object makes use of functionality from the following packages:\itemize{ \i \section{Inheritance}{ A \code{tSNE_scatter} object inherits the following \code{struct} classes: \cr\cr -\code{tSNE_scatter()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[tSNE_scatter]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/tic_chart.Rd b/man/tic_chart.Rd index d119fcb..f8e37f4 100644 --- a/man/tic_chart.Rd +++ b/man/tic_chart.Rd @@ -27,7 +27,7 @@ A scatter plot of Total Ion Count (sum of each sample) versus run order. \section{Inheritance}{ A \code{tic_chart} object inherits the following \code{struct} classes: \cr\cr -\code{tic_chart()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[tic_chart]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/ttest.Rd b/man/ttest.Rd index 52432a2..30d8a17 100644 --- a/man/ttest.Rd +++ b/man/ttest.Rd @@ -49,7 +49,7 @@ A t-test compares the means of two factor levels. Multiple-test corrected p-valu \section{Inheritance}{ A \code{ttest} object inherits the following \code{struct} classes: \cr\cr -\code{ttest()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[ttest]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/vec_norm.Rd b/man/vec_norm.Rd index 901f433..9885da1 100644 --- a/man/vec_norm.Rd +++ b/man/vec_norm.Rd @@ -24,7 +24,7 @@ The samples in the data matrix are normalised to account for differences in conc \section{Inheritance}{ A \code{vec_norm} object inherits the following \code{struct} classes: \cr\cr -\code{vec_norm()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[vec_norm]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{ diff --git a/man/wilcox_p_hist.Rd b/man/wilcox_p_hist.Rd index a93b951..5279529 100644 --- a/man/wilcox_p_hist.Rd +++ b/man/wilcox_p_hist.Rd @@ -21,7 +21,7 @@ A histogram of p values for the wilcoxon signed rank test \section{Inheritance}{ A \code{wilcox_p_hist} object inherits the following \code{struct} classes: \cr\cr -\code{wilcox_p_hist()} ⭢ \code{chart()} ⭢ \code{struct_class()} +\verb{[wilcox_p_hist]} >> \verb{[chart]} >> \verb{[struct_class]} } \examples{ diff --git a/man/wilcox_test.Rd b/man/wilcox_test.Rd index f7f182e..a08d547 100644 --- a/man/wilcox_test.Rd +++ b/man/wilcox_test.Rd @@ -48,7 +48,7 @@ A Mann-Whitney-Wilcoxon signed rank test compares ,the ranks of values in two gr \section{Inheritance}{ A \code{wilcox_test} object inherits the following \code{struct} classes: \cr\cr -\code{wilcox_test()} ⭢ \code{model()} ⭢ \code{struct_class()} +\verb{[wilcox_test]} >> \verb{[model]} >> \verb{[struct_class]} } \examples{