Man pages for emvolz-phylodynamics/sarscov2Rutils
Scripts to support preparation and analysis of SARS CoV 2 analyses
| add_ggGR_sarscov2skygrowth | Combine growth plots for two skygrowth fits, for example... |
| add_ggR_sarscov2skygrowth | Combine Reff plots for two skygrowth fits, for example... |
| add_starting_trees_to_xml | Make starting trees, insert into beast xml and create ML tree... |
| combine_logs | Combine BEAST log files after removing burnin |
| combine_logs_and_traj | Combine BEAST log AND trajectory files after removing burnin |
| combine_traj | Combine PhyDyn trajectory files after removing burnin |
| compute_spike614genotype | Determine the spike 614 genotype for the given fasta... |
| compute_timports | Computes the time of importation events using a one or more... |
| cutie_treedater | Running treedater on ML trees on HPC or work stations with... |
| exog_sampler1 | Sample exogenous sequence IDs using a time stratified design... |
| exog_sampler2 | Sample exogenous sequence IDs using a time stratified design... |
| filter_hostAndDates | Remove samples from non-human hosts and sequences with... |
| filter_quality0 | Selects a background reference set of sequences with good... |
| filter_quality1 | Selects a background reference set of sequences with good... |
| format_xml0 | Generates a runnable XML by inserting sequence data, a... |
| format_xml_gmrf_exogsir | Generates a runnable XML by inserting sequence data, a... |
| gen_gmrf_betablock | Assemble a XML fragment that will define beta(t) aas a linear... |
| gmrf_exogsir_plot_daily_inf | Plot the daily new infections through time from a GMRF SEIJR... |
| gmrf_exogsir_plot_Rt | Plot reproduction number through time from a SEIJR trajectory... |
| gmrf_exogsir_plot_size | Plot the cumulative infections through time from a SEIJR... |
| GMRF_SEIJR_plot_daily_inf | Plot the daily new infections through time from a GMRF SEIJR... |
| GMRF_SEIJR_plot_reporting | Plot reporting rate through time from SEIJR trajectory sample... |
| GMRF_SEIJR_plot_Rt | Plot reproduction number through time from a SEIJR trajectory... |
| GMRF_SEIJR_plot_size | Plot the cumulative infections through time from a GMRF SEIJR... |
| GMRF_SEIJR_reproduction_number | Compute R0, growth rate and doubling time for the GMRF or... |
| googmobility | Compute time series cross correlations and plots using google... |
| googmobility_skygrowth | Compute time series cross correlations and plots using google... |
| make_starting_tree | Generate a starting tree for beast |
| make_starting_trees | Make starting trees and ML tree plot |
| mcc_col_tree_plot | plotting tree with background sequences labelled |
| mcc_tree_plot | Plot the maximum clade credibility tree and showing HPD node... |
| plot_importations | Plot a errbar of importation times given a data frame from... |
| plot_importationsHist | Plot a histogram of importation times given a data frame from... |
| plot_sample_distribution | Sampling distribution of sequences |
| plot_sample_distribution_spike614 | Plot sample times for D and G genotypes on spike 614 |
| prep_tip_labels_phydyn | Change the name of sequences to recognize numeric time of... |
| prep_tip_labels_seijr | Prepare an alignment of regional and exogenous sequences with... |
| quick_region_treeplot | Plot a rooted tree (may be a time tree) with tips... |
| region_clades | Extact all clades in given tree descended from nodes with... |
| region_sampler1 | Sample sequence IDs from within a region |
| region_time_stratified_sample | Select a random sample from aligment stratified through time... |
| region_time_stratified_sample1 | Select a random sample from aligment stratified through time... |
| s614_phylodynamics | Run skygrowth and treestructure on clades defined by s614... |
| SEIJR_plot_daily_inf | Plot the daily new infections through time from a SEIJR... |
| SEIJR_plot_reporting | Plot reporting rate through time from SEIJR trajectory sample... |
| SEIJR_plot_Rt | Plot reproduction number through time from a SEIJR trajectory... |
| SEIJR_plot_size | Plot the cumulative infections through time from a SEIJR... |
| SEIJR_reproduction_number | Compute R0, growth rate and doubling time for the SEIJR.0.0... |
| skygrowth0 | Compute skygrowth Ne(t) and R(t) estimates for a given list... |
| skygrowth1 | Compute skygrowth Ne(t) and R(t) estimates for a given list... |
| time_stratified_sample | Select a random sample from aligment stratified through time |
| tree_annotator_windows | Tree annotator in Windows |
| tree_combiner_helper | Wrapper for logcombiner |
| write_phylo_metadata_yaml | Automatic generation of metadata.yml You can add more... |
