| Cbmtable | BioMarker Table |
| Cclasssplitter | Used by parse_classmaps.m |
| Cgridsearchparam | |
| ▼Chandle | |
| Cclassmap | Scans IRootLab directories and build hierarchical class maps |
| Cgencode | MATLAB code generation to create, boot, train and use blocks |
| Cmapitem | Map item |
| ▼Cirobj | Base class |
| Cbiocomparer | |
| ▼Cblock | Base Block class |
| ►Cas | Analysis Session (AS) base class |
| Cas_crossc | Cross-calculation Analysis Session |
| Cas_dsperc_x_rate | (dataset %) x (classification rate) curve |
| ►Cas_fsel | Analysis Session that produces a log_as_fsel |
| Cas_fsel_eclass | EClass-based feature selection |
| Cas_fsel_forward | Forward Feature Selection |
| Cas_fsel_grades | Feature Selection based on a "grades" vector |
| Cas_fsel_grades_super | "Super-object" encapsulating both a as_fsel_grades and a as_grades_data object |
| Cas_fsel_lasso | LASSO feature selection |
| ►Cas_grades | Analysis Session that outputs a log_grades |
| Cas_grades_fsg | Calculates grades using a Feature Subset Grader (FSG) object |
| Cas_grades_loadings | Loadings vector becomes the grades vector |
| Cfactorscurve | Used to calculate (number of factors)x(performance) curves |
| Cfselrepeater | Analysis Session - Feature Selection Repeater |
| Cgridsearch | Grid Search |
| Covrcurves | One-Versus-Reference calculation of grades curves |
| Crater | "Rater" class |
| ►Creptt | REPeated Train-Test |
| Creptt_bag | REPTT for bagging classifiers |
| Creptt_blockcube | REpeated Train-Test - Block Cube |
| Creptt_hiesplit | Hierarchical split |
| Creptt_incr | Incremental learning curve - to test incremental classifiers |
| ►Cblbl | Other blocks |
| Cblbl_extract_cv | Extracts cluster vectors from block |
| Cblbl_extract_ds_from_sovalues | Extracts dataset from sovalues |
| Csubsetsprocessor | Processor of a set of subsets of features |
| ►Cblmisc | Miscellaneous block |
| ►Cblmisc_classes | Base class for blocks that change a dataset classes |
| Cblmisc_classes_from_clus | Assign classes from one data column from an irdata_clus object |
| Cblmisc_classes_random | Randomizes classes |
| ►Cblmisc_classlabels | Base class for blocks that change a dataset class labels |
| Cblmisc_classlabels_hierarchy | Select some given class levels |
| Cblmisc_classlabels_rename | Renames class labels |
| Cblmisc_classlabels_sort | Sorts dataset class labels renumbering classes accordingly |
| Cblmisc_fearange | Re-sets the x-axis of a dataset using 2-element range vector provided |
| ►Cblmisc_image | Image operations base class |
| Cblmisc_image_transpose | Switches direction between 'hor' or 'ver' |
| ►Cblmisc_merge | Base class for dataset mergers |
| Cblmisc_merge_cols | Merges datasets parallelly (column-wise) |
| Cblmisc_merge_rows | Merges datasets serially (row-wise) |
| ►Cblmisc_rows | Base class for blocks that change a dataset row order |
| Cblmisc_rows_inliers | Select inliers only |
| Cblmisc_rows_shuffle | Shuffles rows keeping spectra from the same group together or not |
| ►Cblmisc_split | Base class for blocks that split one dataset into many |
| Cblmisc_split_classes | Splits dataset into many according to classes |
| Cblmisc_split_groups | Splits dataset per group, one dataset per group |
| Cblmisc_split_ovo | One-Versus-One dataset split class combination |
| Cblmisc_split_ovr | One-Versus-Reference dataset split class combination |
| Cblmisc_split_proportion | Splits dataset in two according to proportion specified |
| ►Cblmisc_rowsout | Outlier Removal base class |
| Cblmisc_rowsout_multistage | Multi-Stage Complex Outlier Removal |
| ►Cblmisc_rowsout_uni | Univariate Outlier removal |
| ►Cblmisc_rowsout_distr | Distribution-Based Outlier Removal |
| Cblmisc_rowsout_hist | Outlier removal by Histogram |
| Cblmisc_rowsout_kernel | Outlier removal by Kernel distribution estimation |
| Cblmisc_rowsout_ranges | Outlier removal by Ranges |
| ►Crowaggr | |
| ►Cesag | Estimation Aggregator - combines estimato objects together |
| Cesag_linear1 | Estimation Aggregator - Linear Combination of datasets |
| Cesag_wta | Estimation Aggregator - Winner takes all |
| ►Cgrag | Group Aggregator - combines data rows outputting one row per group |
| ►Cgrag_classes | Group Aggregator - classes |
| Cgrag_classes_first | Group Aggregator - Classes - First row |
| Cgrag_classes_vote | Group Aggregator - Classes - Vote |
| Cgrag_classes_votew | Group Aggregator - Classes - Weighted Vote |
| Cgrag_mean | Group Aggregator - averages rows per group |
| Crowaggr_means | |
| Crowaggr_nmean | |
| Cblock_bypass | Bypass block |
| ►Cblock_cascade_base | Cascade block: sequence of blocks represented by a block |
| Cblock_cascade | Cascade block: final instantializable class |
| Ccascade_cbn | Cascade: fsel -> pre_bc_rubber -> pre_norm |
| Ccascade_decidergrag | Cascade block: decider -> grag_classes_vote |
| Ccascade_diffvn | Cascade block: pre_diff_sg -> pre_norm_vector |
| Ccascade_fsel_grades_fsg | Cascade block: as_grades_fsg->as_fsel_grades->(extract_fsel) |
| Ccascade_gragdecider | Cascade block: grag_mean -> decider |
| Ccascade_pcalda | Cascade block: fcon_pca -> fcon_lda |
| Ccascade_stdhie | Demo cascade block: pre_norm_std -> blmisc_classlabels_hierarchy |
| ►Cclssr | Classifiers base class |
| ►Caggr | Base class for all ensemble classifiers |
| Caggr_adaboost | Adaboost |
| Caggr_bag | Bagging ensemble |
| Caggr_hiesplit | Class-Hierarchical Training Data Split |
| Caggr_mold | Fixed, pre-determined components |
| Caggr_obsidxs | Pre-determined dataset splits |
| Caggr_ova | One-versus-all classifier |
| Caggr_ovc | One-versus-"control" classifier |
| Caggr_pairs | Pairwise classifier |
| Cclssr_ann | Neural Network Classifier. This is a wrapper to MATLAB's Neural Networks Toolbox |
| Cclssr_d | Linear and Quadratic discriminant |
| Cclssr_dist | Least-Distance-to-Class-Mean Classifier |
| Cclssr_incr | Base class for Incremental Classifiers |
| Cclssr_knn | K-Nearest Neighbours Classifier |
| Cclssr_lasso | Lasso Classifier |
| Cclssr_ls | Least-squares classifier |
| Cclssr_mnr | Logistic Regression Classifier |
| Cclssr_svm | Support Vector Machine Classifier using LibSVM |
| Cclssr_tree | Binary Decision Tree Classifier |
| Cdecider | Block that resolves estimato posterior probabilities into classes |
| ►Cfext | Feature Extraction (Fext) base class |
| ►Cfcon | Feature Construction (FCon) base class |
| ►Cclus | Clustering base class |
| Cclus_hca | Hierarchical Clustering |
| Cfcon_feaavg | Decimation - makes averages of adjacent features |
| ►Cfcon_linear | Feature Construction - Linear Transformations base class |
| Cfcon_lda | Fisher's Linear Discriminant Analysis |
| Cfcon_linear_fixed | Loadings vector specified directly |
| Cfcon_mcr | Multivariate Curve Resolution |
| Cfcon_pca | Principal Component Analysis |
| Cfcon_pls | Partial Least Squares Transformation aka PLSDA |
| Cfcon_slda | Sparse LDA |
| Cfcon_spline | B-Splines Decomposition |
| Cfcon_maxminpos | Maxima/minima detection |
| ►Cfcon_mea | Measure: calculates one scalar per dataset row |
| Cfcon_mea_area | Area |
| Cfcon_mea_maha | Mahalanobis distance |
| Cfcon_mea_max | Maximum over all features |
| Cfcon_mea_mean | Mean |
| Cfcon_mea_min | Minimum over all features |
| Cfcon_mea_norm | Norm |
| Cfcon_mea_pick | Picks region area, region peak, or value at fixed x-position |
| Cfcon_mea_ratio | Ratio between the X matrix of two datasets |
| Cfcon_resample | Resampling - uses MATLAB's DSP Toolbox resample() function |
| Cfext_parallel | Combines features extracted from two or more blocks in parallel |
| Cfsel | Feature Selection (FSel) class |
| Clogrecorder | Used to record a ttlog based on test and estimation data |
| Cmethodcaller | Calls a method from input block |
| Cmutant | "Mutant" block / metablock |
| ►Cpre | Pre-processing block base class |
| Cpre_abs | Takes absolute value of data X |
| Cpre_abs2atr | Converts AB -> ATR |
| ►Cpre_bc | Baseline Correction base class |
| Cpre_bc_asls | Asymmetric Least-Squares Baseline Correction |
| Cpre_bc_poly | Polynomial Baseline Correction |
| Cpre_bc_rmiesc | Paul Bassan's Resonant Mie Scattering Correction |
| Cpre_bc_rubber | Convex Polygonal Line (Rubberband-like) Baseline Correction |
| Cpre_deconv | Deconvolution |
| Cpre_diff | Simple differentiation using MATLAB diff() function |
| Cpre_diff_sg | Savitsky-Golay (SG) Differentiation |
| Cpre_flip_refmean | Flips the means around a reference class |
| ►Cpre_norm_base | Normalization - base class |
| Cpre_meanc | Mean-centering (trained) |
| Cpre_norm | Normalization - final class |
| Cpre_norm_amide1 | Normalization - Amide I peak |
| Cpre_norm_amide2 | Normalization - Amide II peak |
| Cpre_norm_meanc | Normalization - Mean-centering |
| Cpre_norm_std | Normalization - std Normalization - backward compatibility |
| Cpre_norm_vector | Normalization - Vector Normalization |
| Cpre_std | Standardization (trained) |
| Cpre_sigwindow | Applies sigmoid window to curves |
| Cpre_sub_refmean | Subtracts the mean of a reference class from all the rows |
| Cpre_trimneg | Trim Negatives to zero |
| Cpre_wden | Wavelet De-noising block |
| ►Cvis | Visualization base class |
| ►Cirreport | Report base class |
| Creport_default | |
| Creport_estlog | estlog 's HTML (confusion matrices) |
| Creport_log_fselrepeater_hist | Single histogram report |
| Creport_log_gridsearch | Shows best parameters at each |
| ►Creport_soitem | Base for all reports that operate on a soitem object |
| Creport_log_fselrepeater_histcomp | Histograms and biomarkers comparison using various subsetsprocessor objects |
| Creport_soitem_fhg_hist | Single histogram report. Passes on to report_log_fselrepeater_hist |
| Creport_soitem_fhg_histcomp | Passes on to report_log_fselrepeater_histcomp |
| Creport_soitem_foldmerger_fitest | Passes on to report_estlog, to show confusion matrices |
| Creport_soitem_fs | Plots the (nf)x(rates) curve |
| Creport_soitem_items | Shows curves or images from foldmerge of some model selection (e.g. clarchsel or fearchsel) |
| Creport_soitem_merger_fhg | Histograms ane Biomarkers comparison tables - Several set-ups (including stabilizations). Comparisons using histograms, biomarker comparison tables/(heat maps) |
| Creport_soitem_merger_merger_fhg | |
| Creport_soitem_merger_merger_fitest | |
| Creport_soitem_merger_merger_fitest_1d | 1D comparison table |
| Creport_soitem_sovalues | Comparison and p-values tables |
| Creport_sovalues_comparison | Comparison and p-values tables |
| Creport_testtable | |
| Creport_ttlog | ttlog 's HTML (confusion matrices |
| Creport_ttlog_generic | ttlog_generic 's HTML (confusion matrices) |
| Creportmerger | Merges contents of many log_html |
| Cvis_3dhist | Visualization - Per-Feature Histogram 3D |
| Cvis_alldata | Visualization - All curves in dataset |
| Cvis_as_fsel_hist_entropy | Draws entropy curves based on a as_fsel_hist object |
| Cvis_balls | Visualization - Balls visualization for Confusion Matrices |
| Cvis_blmisc_rowsout_uni | Visualization for blmisc_rowsout_uni objects. Invokes the outlier removal Preview dialog |
| Cvis_clssr2d | Classification Domain - classification regions etc |
| Cvis_cov | Covariance matrix |
| Cvis_crossloadings | Loadings vector of an as_crossc |
| Cvis_curvefit | 1D Scatterplot with x-axis values associated to classes and curve fit |
| Cvis_cv | Visualization - Cluster Vectors |
| Cvis_featuregrades | Feature Grades using a fsg object to grade the features |
| Cvis_hachures | Hachures showing intervals |
| Cvis_hists | Visualization - Histograms from log_hist |
| Cvis_image | Image map |
| Cvis_image_cat | Image map for non-ordered, discrete features (e.g. from clustering) |
| Cvis_loadings | Visualization - Loadings plots or Peak Location plots for loadings vectors |
| Cvis_log_as_fsel | Visual representation of selected features |
| Cvis_log_celldata | Visualization - Histograms from log_celldata |
| Cvis_log_grades | Visualization - Grades vector calculated by any as_grades |
| Cvis_log_ovrcurves | Visualization of Grades Curves stored inside a log_ovrcurves object |
| Cvis_means | Visualization - Class means |
| Cvis_scatter1d | 1D Scatterplot |
| Cvis_scatter2d | 2D Scatterplot |
| Cvis_scatter3d | 3D Scatterplot |
| Cvis_scatter3d2 | Visualization - 3D Scatterplot - Ellipse Walls |
| Cvis_scatter3dgif | GIF animation showing rotation of a 3D scatterplot |
| Cvis_sovalues_drawimage | Draws image from a sovalues object |
| Cvis_sovalues_drawplot | Draws plot from a sovalues object |
| Cvis_sovalues_drawsubplot | Draws plot from a sovalues object |
| Cvis_stackedhists | Visualization - Stacked histograms |
| ▼Cbmart | Art stuff for BioMarker Tables |
| Cbmart_circle | Art stuff |
| Cbmart_diamond | Art stuff |
| Cbmart_pentagram | Art stuff |
| Cbmart_square | Art stuff |
| ▼Cbmunit | Representation of a Unit |
| Cbmunit_au | Unit - Arbitrary |
| Cbmunit_hist | Unit - HistogramSame as Integer, but plots as histogram (stem plot). Affects bmtable |
| Cbmunit_int | Unit - Integer |
| Cbmunit_perc | Unit - percentage |
| ▼Cdataio | Dataset loader/saver common class |
| Cdataio_db | Dataset loader/saver for the SHEWare database |
| Cdataio_mat | Dataset loader/saver for mat files |
| Cdataio_opus_nasse | Dataset loader for OPUS "0" files |
| ►Cdataio_txt_basic | Basic TXT loader/saver |
| Cdataio_txt_basic_image | Derives from dataio_txt_basic to match uip_dataio_txt_basic.m |
| Cdataio_txt_dpt | DPT TXT loader only |
| ►Cdataio_txt_irootlab | IRootLab TXT loader/saver |
| Cdataio_txt_irootlab2 | IRootLab TXT that saves classes column as labels, not numbers |
| Cdataio_txt_libsvm | Saver in LIBSVM format (loading currently not implemented) |
| ►Cdataio_txt_pir | "Pirouette" TXT loader/saver |
| Cdataio_txt_pir_image | Derives from dataio_txt_pir; just sets flag_params to open GUI when opening file |
| ▼Cfsg | FSG - Feature Subset Grader |
| Cfsg_clssr | FSG that uses classifier to grade the subsets |
| ►Cfsg_test | Feature subset grader that uses a statistical test |
| Cfsg_test_anova | Feature subset grader - ANOVA |
| Cfsg_test_fisher | |
| Cfsg_test_manova | Feature subset grader - MANOVA |
| Cfsg_test_t | Feature subset grader - t-test |
| Cfsg_test_u | Feature subset grader - Mann-Whitney "U"-test |
| Cfsg_test_var | Feature subset grader - variance |
| ▼Cfsgt | |
| Cfsgt_fisher | |
| Cfsgt_infgain | |
| Cfsgt_maxentr | |
| ▼Cirdata | Dataset class |
| Cestimato | Dataset representing estimation |
| Cirdata_clus | Dataset class - cluster data |
| ▼Cirlog | Log base class |
| Circonfusion | Class representing a Confusion matrix |
| Clog_as_crossc | Log generated by an as_crossc |
| ►Clog_as_fsel | Log generated by an as_fsel class |
| Clog_as_fsel_forward | Log generated by a as_fsel_forward |
| Clog_as_fsel_grades | Log generated by as_fsel_grades |
| Clog_blmisc_rowsout_multistage | Log for the blmisc_rowsout_multistage block activity |
| Clog_celldata | Learning curve: (percent dataset used for training)x(classification rate) |
| Clog_cube | Log generated by a reptt_blockcube |
| Clog_fselrepeater | Generated by fselrepeater, carries subsets of features |
| ►Clog_grades | Generated by a as_grades object, carries a "grades" vector; usually |
| Clog_hist | Generated by subsetsprocessor, carries a histogram |
| Clog_gridsearch | Log generated by a gridsearch |
| Clog_html | Generated by irreport, carries HTML contents |
| Clog_ovrcurves | Stores set of grades as a matrix |
| ►Cttlog | Train-Test Log |
| ►Cestlog | Estimation logs base class |
| Cestlog_classxclass | Records (test class)x([rejected, estimation class]) hits |
| Cestlog_groupxclass | Records (test group)x([rejected, estimation class]) hits |
| Cestlog_rightwrong | Records (1)x([rejected, right, wrong]) hits |
| Cttlog_props | Records properties from a block |
| Cpeakdetector | Peak Detector |
| ▼Csgs | Base Sub-dataset Generation Specification (SGS) class |
| Csgs_crossval | K-Fold Cross-Validation |
| Csgs_one_class_out | One-class-out SGS |
| ►Csgs_randsub_base | Random Sub-sampling base class |
| Csgs_randsub | Random Sub-sampling |
| Csgs_weighted | Weighted Sub-Sampling |
| ▼Cvectorcomp | Paired Vector Comparer base class |
| Cvectorcomp_difference | |
| Cvectorcomp_ttest | Vector Comparer - t-test |
| Cvectorcomp_ttest_right | Vector Comparer - paired t-test right tail |
| Cvectorcomp_utest | |
| Cvectorcomp_xornorm | |
| Cplotter12 | |
1.8.9.1 
