ʻOhana
A suite of software for analyzing population structure and admixture history using unsupervised learning methods.

▼Njade  
Cbasic_agi_controller  A template for a class that encodes and decodes parameters for the NelderMead algorithm. This class uses an admixture graph input file 
Cbasic_agi_reader  A template for a class that reads an AGI (Admixture Graph Input) file. The file provides the following information: A set of branch length variable names, a set of admixture proportion parameter names, a component size (K), and K*(K1)/2 number of expressions representing C matrix entries 
Cbasic_args  A template for a class that helps process commandline arguments 
Cbasic_assertion  A template for a class that asserts valid conditions 
Cbasic_bgl2lgm  A template for a class that converts BEAGLEformatted data to likelihood genotype matrices 
Cbasic_bgl_reader  A template for a class that reads BEAGLE data and is capable of writing it to a stream as a likelihood genotype matrix 
Cbasic_controller  A template for a class that performs the NelderMead optimization. This class implements shared features of the two concrete controllers of this module, one that uses a Newick tree as input and another that does not 
Cbasic_controller_factory  A template for a class that creates controllers that use or do not use Newick trees specified on the command line 
Cbasic_cov2nwk  A template for a class that approximates covariance matrices as Newickformatted trees 
Cbasic_discrete_genotype_matrix  A template for a class implementing operations for a discrete genotype matrix 
Cbasic_error  A template for a class representing an exception thrown from this namespace 
Cbasic_forced_grouping  A template for a class that implements the forced grouping feature 
Cbasic_genotype_matrix  A template for an abstract class implementing operations for a genotype matrix 
Cbasic_genotype_matrix_factory  A template for a class that creates genotype matrices based on files and their file extensions 
Cbasic_improver  A template for a class that improves the Q and F matrices 
▼Cbasic_lemke  A template for a class that implements Lemke's algorithm 
Cstate  Possible states of the algorithm 
Cbasic_likelihood  A template for a class that efficiently computes a loglikelihood based on 1) the log of the determinant for a covariance matrix and 2) the inverse of the covariance matrix. The class caches values based on a [K1 x J] rooted F matrix for major allele frequencies and a [J x 1] mu vector 
Cbasic_likelihood_genotype_matrix  A template class implementing operations for a likelihood genotype matrix type 
Cbasic_matrix  A template class for a matrix 
Cbasic_neighbor_joining  A template for a class that implements the neighbor joining algorithm 
▼Cbasic_neoscan  A template for a class implementing the neoscan algorithm. This algorithm scans for positive selection between ancient and modern data. It can take advantage of the dating for each individual ancient sample 
Coutput  Output for one column 
Cbasic_newick_node  A template class representing a node from a Newick tree 
Cbasic_nwk2cov  A template for a class that converts Newickformatted trees to covariance matrices 
Cbasic_nwk2svg  A template for a class that converts Newickformatted trees to SVG representations 
Cbasic_openblas  A template for a class providing access to OpenBLAS 
Cbasic_optimizer  A template for a class that optimizes the Q and F matrices 
Cbasic_options  A template for a class encapsulating the program options 
Cbasic_ped2dgm  A template for a class that converts PEDformatted data to discrete genotype matrices 
Cbasic_ped_reader  A template for a class that reads PED data 
Cbasic_qpas  A template for a class that implements the Quadratic Programming for Active Set algorithm 
Cbasic_randomizer  A template for a class that randomizes matrices 
Cbasic_rema  A template for a class that reduces columns of matrices given to it. The columns to keep are chosen at random, but their relative order is not changed 
Cbasic_rerooted_tree  A template for a class that maintains a list of paths from all leaf nodes to the rerooted node with the name "0" 
Cbasic_scanner  A template class that parses text and throws meaningful error messages 
Cbasic_selscan  A template for a class implementing the selscan program 
Cbasic_settings  A template for a class encapsulating the settings provided to the optimizer 
Cbasic_shunting_yard  A template for a class that implements the shuntingyard algorithm. The implementation supports '+', '', '*', and '/' operators; the '(' and ')' parentheses; floatingpoint numbers; and variables. After parsing an expression, the instance can evaluate the expression if given a table of variable values 
▼Cbasic_simplex  A template for a class that implements the NelderMead Simplex Method, which attempts to minimize an objective function in a manydimensional space by continually refining a simplex 
Cexecute_args  Arguments to the execute method 
Cexit_condition  An indication of what caused the execute to temrinate 
Clog_args  Arguments passed to the logging function 
Coperation  An operation performed during an iteration 
Coptions  A data structure used to initialize the NelderMead algorithm 
Cstats  Statistics about the behavior of the algorithm 
Cbasic_stopwatch  A template class imlementing a stopwatch 
Cbasic_svg_tree  A template for a class that renders newick trees as SVG 
Cbasic_tree_controller  A template for a class that encodes and decodes parameters for the NelderMead algorithm. This class uses a userspecified Newick tree 
Cbasic_tree_path  A template for a class that maintains a table of nodes indicating a distance to the root of the tree 
Cbasic_treeless_controller  A template for a class that encodes and decodes parameters for the NelderMead algorithm. This class does not use a userspecified Newick tree 
Cbasic_vec2  A template for a class that implements ranktwo vector operations 
Cbasic_verification  A template for a class that performs validation on various types of matrices 
Cbasic_version  A template for a class that displays version and build information 