Man pages for suryakevin/drugcandy
Detecting Punctuated Evolution in Dinosaurs and Viruses
| break_vcv | Break the variance-covariance matrix |
| calc_partialr2 | Calculate partial R^2 |
| calc_r2 | Calculate R^2 |
| calc_vif | Calculate the variance inflation factors (VIFs) |
| compare_models | Compare model fits with BIC |
| create_dmat | Create the normalizing matrix D |
| drugcandy | Detecting punctuated evolution in taxa ranging from dinosaurs... |
| est_node_density | Test for the node-density artifact |
| est_punc_contrib | Estimate the punctuational contribution to the total... |
| export_data | Export dataset to a text file |
| export_data_bt | Export dataset to a text file |
| export_plot_pdf | Export plot to a PDF file |
| export_plot_svg | Export plot to a SVG file |
| export_tree | Export phylogenetic tree to a file |
| fit_punc_model | Detect punctuated evolution |
| get_node_count | Extract node counts |
| get_path_length | Extract phylogenetic path lengths |
| import_data | Import dataset |
| import_data_bt | Import dataset (BayesTraits style) |
| import_data_csv | Import a .csv file |
| import_tree_nex | Import phylogenetic tree (NEXUS format) |
| import_tree_nwk | Import phylogenetic tree (Newick format) |
| plot_data_2d | Create a 2D interactive plot |
| plot_data_3d | Create a 3D interactive plot |
| plot_diagnostics | Plot regression diagnostics |
| plot_node_density | Plot the node-density test |
| plot_punc_model | Plot data with or without a fit line |
| plot_tree | Plot phylogenetic tree |
| plot_tree_color | Plot phylogenetic tree with colored branches |
| print_node_density | Print the node-density test output |
| print_punc_model | Print the output of a regression model |
| reorder_data | Re-order the dataset to follow the tree |
