ʻOhana
Population structure, admixture history, and selection using learning methods.
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▼Njade | |
Cbasic_agi_controller | A template for a class that encodes and decodes parameters for the Nelder-Mead 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*(K-1)/2 number of expressions representing C matrix entries |
Cbasic_args | A template for a class that helps process command-line arguments |
Cbasic_assertion | A template for a class that asserts valid conditions |
Cbasic_bgl2lgm | A template for a class that converts BEAGLE-formatted 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_blas | A template for a class providing access to BLAS |
Cbasic_controller | A template for a class that performs the Nelder-Mead 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 Newick-formatted 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_lapack | A template for a class providing access to LAPACK |
▼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 log-likelihood 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 [K-1 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 Newick-formatted trees to covariance matrices |
Cbasic_nwk2svg | A template for a class that converts Newick-formatted trees to SVG representations |
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 PED-formatted 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 shunting-yard algorithm. The implementation supports '+', '-', '*', and '/' operators; the '(' and ')' parentheses; floating-point 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 Nelder-Mead Simplex Method, which attempts to minimize an objective function in a many-dimensional 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 Nelder-Mead 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 Nelder-Mead algorithm. This class uses a user-specified 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 Nelder-Mead algorithm. This class does not use a user-specified Newick tree |
Cbasic_vec2 | A template for a class that implements rank-two 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 |