Man pages for emvolz-phylodynamics/variantAnalysis
sarscov2 variant analysis
| beast-parser | read.beast |
| cluster_muts | Computes mutations for sequences within specified clusters |
| cluster_muts_new | mutation_plots |
| cluster_origin_comparison | Compute cumulative proportion of samples descended from... |
| cluster_origin_comparison2 | Compute cumulative proportion of samples descended from... |
| cluster_sizes | Compute cluster sizes only counting clusters with first... |
| clusterwise_logistic | Estimate rate that clusters increase or decrease in frequency... |
| compute_genotypes | Compute AA genotype at specified postions in alignment |
| dedup_data | Functions required to output scanner markdown figures |
| hier_bayes_exponentialGrowth_frequency | Hierarchical Bayesian inference of cluster-wise selection... |
| hier_bayes_pairwiseLogistic_frequency | too slow |
| matched_sample | Matched sample by time (week) and UTLA |
| matched_sample2 | Matched sample by time (week) and UTLA for each sampled tree... |
| mutations_plots | mutation plots |
| plot_maps | plot_maps |
| plpg | Performs a simple logistic model fit and make a frequency... |
| recurrent_mutations | Identify recurrent mutations in a tree and quantify offspring... |
| report_table | Table for scanner report |
| sample_lineage | Produce a random sample of given global lineage and sample... |
| scanner2 | Compute scanner statistics for nodes in tree. |
| scanner_output | Output a markdown for scanner results, including full written... |
| sim_cluster_growth | Simulate cluster trajectories |
| sim_importation_time | Simulate time and number of importation events for clusters... |
| sim_powerDetectionPrevalence_logisticGrowth | Simple power calculation for detecting growth of variant with... |
| sim_replicate | Simulate entire pipeline: importation, growth, sampling |
| sim_replicate2 | Uses hier bayes model for identifying growth |
| sim_replicate3 | Three methods: gam adjusted for imports; simple logistic;... |
| sim_sampling_cluster | Simulate sampling times given cluster trajectory and sample... |
| variable_frequency_day_report | GAM outputs |
| variable_frequency_epiweek | Simple log odds freqency plot for given variable. Does not... |
| variantAnalysis-package | sarscov2 variant analysis |
