Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

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
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
Cbiocomparer
Cblbl	Other blocks
Cblbl_extract_cv	Extracts cluster vectors from block
Cblbl_extract_ds_from_sovalues	Extracts dataset from sovalues
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_rowsout	Outlier Removal base class
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_multistage	Multi-Stage Complex Outlier Removal
Cblmisc_rowsout_ranges	Outlier removal by Ranges
Cblmisc_rowsout_uni	Univariate Outlier removal
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
Cblock	Base Block class
Cblock_bypass	Bypass block
Cblock_cascade	Cascade block: final instantializable class
Cblock_cascade_base	Cascade block: sequence of blocks represented by a block
Cbmart	Art stuff for BioMarker Tables
Cbmart_circle	Art stuff
Cbmart_diamond	Art stuff
Cbmart_pentagram	Art stuff
Cbmart_square	Art stuff
Cbmtable	BioMarker Table
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
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
Cclassmap	Scans IRootLab directories and build hierarchical class maps
Cclasssplitter	Used by parse_classmaps.m
Cclssr	Classifiers base class
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
Cclus	Clustering base class
Cclus_hca	Hierarchical Clustering
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
Cdecider	Block that resolves estimato posterior probabilities into classes
Cesag	Estimation Aggregator - combines estimato objects together
Cesag_linear1	Estimation Aggregator - Linear Combination of datasets
Cesag_wta	Estimation Aggregator - Winner takes all
Cestimato	Dataset representing estimation
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
Cfactorscurve	Used to calculate (number of factors)x(performance) curves
Cfcon	Feature Construction (FCon) base class
Cfcon_feaavg	Decimation - makes averages of adjacent features
Cfcon_lda	Fisher's Linear Discriminant Analysis
Cfcon_linear	Feature Construction - Linear Transformations base class
Cfcon_linear_fixed	Loadings vector specified directly
Cfcon_maxminpos	Maxima/minima detection
Cfcon_mcr	Multivariate Curve Resolution
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_pca	Principal Component Analysis
Cfcon_pls	Partial Least Squares Transformation aka PLSDA
Cfcon_resample	Resampling - uses MATLAB's DSP Toolbox resample() function
Cfcon_slda	Sparse LDA
Cfcon_spline	B-Splines Decomposition
Cfext	Feature Extraction (Fext) base class
Cfext_parallel	Combines features extracted from two or more blocks in parallel
Cfsel	Feature Selection (FSel) class
Cfselrepeater	Analysis Session - Feature Selection Repeater
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
Cgencode	MATLAB code generation to create, boot, train and use blocks
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
Cgridsearch	Grid Search
Cgridsearchparam
Circonfusion	Class representing a Confusion matrix
Cirdata	Dataset class
Cirdata_clus	Dataset class - cluster data
Cirlog	Log base class
Cirobj	Base class
Cirreport	Report base class
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_gridsearch	Log generated by a gridsearch
Clog_hist	Generated by subsetsprocessor, carries a histogram
Clog_html	Generated by irreport, carries HTML contents
Clog_ovrcurves	Stores set of grades as a matrix
Clogrecorder	Used to record a ttlog based on test and estimation data
Cmapitem	Map item
Cmethodcaller	Calls a method from input block
Cmutant	"Mutant" block / metablock
Covrcurves	One-Versus-Reference calculation of grades curves
Cpeakdetector	Peak Detector
Cplotter12
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_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_base	Normalization - base class
Cpre_norm_meanc	Normalization - Mean-centering
Cpre_norm_std	Normalization - std Normalization - backward compatibility
Cpre_norm_vector	Normalization - Vector Normalization
Cpre_sigwindow	Applies sigmoid window to curves
Cpre_std	Standardization (trained)
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
Crater	"Rater" class
Creport_default
Creport_estlog	estlog 's HTML (confusion matrices)
Creport_log_fselrepeater_hist	Single histogram report
Creport_log_fselrepeater_histcomp	Histograms and biomarkers comparison using various subsetsprocessor objects
Creport_log_gridsearch	Shows best parameters at each
Creport_soitem	Base for all reports that operate on a soitem object
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
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
Crowaggr
Crowaggr_means
Crowaggr_nmean
Csgs	Base Sub-dataset Generation Specification (SGS) class
Csgs_crossval	K-Fold Cross-Validation
Csgs_one_class_out	One-class-out SGS
Csgs_randsub	Random Sub-sampling
Csgs_randsub_base	Random Sub-sampling base class
Csgs_weighted	Weighted Sub-Sampling
Csubsetsprocessor	Processor of a set of subsets of features
Cttlog	Train-Test Log
Cttlog_props	Records properties from a block
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
Cvis	Visualization base class
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