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ʻOhana
Population structure, admixture history, and selection using learning methods.
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ʻOhana
Population structure, admixture history, and selection using learning methods.
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| Cjade::basic_agi_reader< TValue > | 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 |
| Cjade::basic_args< TChar > | A template for a class that helps process command-line arguments |
| Cjade::basic_assertion< TChar > | A template for a class that asserts valid conditions |
| Cjade::basic_bgl2lgm< TValue > | A template for a class that converts BEAGLE-formatted data to likelihood genotype matrices |
| Cjade::basic_bgl_reader< TValue > | A template for a class that reads BEAGLE data and is capable of writing it to a stream as a likelihood genotype matrix |
| Cjade::basic_blas< TValue > | A template for a class providing access to BLAS |
| ▼Cjade::basic_controller< TValue > | 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 |
| Cjade::basic_agi_controller< TValue > | A template for a class that encodes and decodes parameters for the Nelder-Mead algorithm. This class uses an admixture graph input file |
| Cjade::basic_tree_controller< TValue > | A template for a class that encodes and decodes parameters for the Nelder-Mead algorithm. This class uses a user-specified Newick tree |
| Cjade::basic_treeless_controller< TValue > | 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 |
| Cjade::basic_controller_factory< TValue > | A template for a class that creates controllers that use or do not use Newick trees specified on the command line |
| Cjade::basic_cov2nwk< TValue > | A template for a class that approximates covariance matrices as Newick-formatted trees |
| Cjade::basic_forced_grouping< TValue > | A template for a class that implements the forced grouping feature |
| ▼Cjade::basic_genotype_matrix< TValue > | A template for an abstract class implementing operations for a genotype matrix |
| Cjade::basic_discrete_genotype_matrix< TValue > | A template for a class implementing operations for a discrete genotype matrix |
| Cjade::basic_genotype_matrix_factory< TValue > | A template for a class that creates genotype matrices based on files and their file extensions |
| Cjade::basic_improver< TValue > | A template for a class that improves the Q and F matrices |
| Cjade::basic_lapack< TValue > | A template for a class providing access to LAPACK |
| Cjade::basic_lemke< TValue > | A template for a class that implements Lemke's algorithm |
| Cjade::basic_likelihood< TValue > | 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 |
| Cjade::basic_likelihood< value_type > | |
| Cjade::basic_likelihood_genotype_matrix< TValue > | A template class implementing operations for a likelihood genotype matrix type |
| Cjade::basic_matrix< TValue > | A template class for a matrix |
| Cjade::basic_matrix< genotype > | |
| Cjade::basic_matrix< value_type > | |
| Cjade::basic_neighbor_joining< TValue > | A template for a class that implements the neighbor joining algorithm |
| Cjade::basic_neoscan< TValue > | 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 |
| Cjade::basic_newick_node< TValue > | A template class representing a node from a Newick tree |
| Cjade::basic_nwk2cov< TValue > | A template for a class that converts Newick-formatted trees to covariance matrices |
| Cjade::basic_nwk2svg< TValue > | A template for a class that converts Newick-formatted trees to SVG representations |
| Cjade::basic_optimizer< TValue > | A template for a class that optimizes the Q and F matrices |
| Cjade::basic_options< TValue > | A template for a class encapsulating the program options |
| Cjade::basic_options< value_type > | |
| Cjade::basic_ped2dgm< TValue > | A template for a class that converts PED-formatted data to discrete genotype matrices |
| Cjade::basic_ped_reader< TValue > | A template for a class that reads PED data |
| Cjade::basic_qpas< TValue > | A template for a class that implements the Quadratic Programming for Active Set algorithm |
| Cjade::basic_randomizer< TValue > | A template for a class that randomizes matrices |
| Cjade::basic_randomizer< value_type > | |
| Cjade::basic_rema< TChar > | 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 |
| Cjade::basic_rerooted_tree< TValue > | A template for a class that maintains a list of paths from all leaf nodes to the rerooted node with the name "0" |
| Cjade::basic_rerooted_tree< value_type > | |
| Cjade::basic_scanner< TChar > | A template class that parses text and throws meaningful error messages |
| Cjade::basic_selscan< TValue > | A template for a class implementing the selscan program |
| Cjade::basic_settings< TValue > | A template for a class encapsulating the settings provided to the optimizer |
| Cjade::basic_shunting_yard< TFloat > | 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 |
| Cjade::basic_simplex< TValue > | 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 |
| Cjade::basic_stopwatch< TClock > | A template class imlementing a stopwatch |
| Cjade::basic_stopwatch< std::chrono::high_resolution_clock > | |
| Cjade::basic_svg_tree< TValue > | A template for a class that renders newick trees as SVG |
| Cjade::basic_tree_path< TValue > | A template for a class that maintains a table of nodes indicating a distance to the root of the tree |
| Cjade::basic_tree_path< value_type > | |
| Cjade::basic_vec2< TValue > | A template for a class that implements rank-two vector operations |
| Cjade::basic_vec2< value_type > | |
| Cjade::basic_verification< TValue > | A template for a class that performs validation on various types of matrices |
| Cjade::basic_version< TChar > | A template for a class that displays version and build information |
| ▼Cstd::exception | STL class |
| Cjade::basic_error< TChar > | A template for a class representing an exception thrown from this namespace |
| Cjade::basic_simplex< TValue >::execute_args | Arguments to the execute method |
| Cjade::basic_simplex< TValue >::exit_condition | An indication of what caused the execute to temrinate |
| Cjade::basic_simplex< TValue >::log_args | Arguments passed to the logging function |
| Cjade::basic_simplex< TValue >::operation | An operation performed during an iteration |
| Cjade::basic_simplex< TValue >::options | A data structure used to initialize the Nelder-Mead algorithm |
| Cjade::basic_neoscan< TValue >::output | Output for one column |
| Cjade::basic_lemke< TValue >::state | Possible states of the algorithm |
| Cjade::basic_simplex< TValue >::stats | Statistics about the behavior of the algorithm |