Files in robjohnnoble/demonanalysis
Analysis and plotting of demon data
.DS_Store
.Rhistory
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
R/.DS_Store
R/cor_summary-data.R
R/data-data.R
R/datacollation.R
R/demonanalysis.R
R/depth_wait_cor_summary-data.R
R/driver_matrix-data.R
R/driver_phylo-data.R
R/forecastingplots.R
R/output-data.R
R/output_allele_counts-data.R
R/output_driver_allele_counts-data.R
R/output_driver_genotype_counts-data.R
R/output_genotype_counts-data.R
R/output_passengersgrid-data.R
R/parameters-data.R
R/speedestimates.R
R/sum_df-data.R
R/summary-data.R
R/sweepmetrics.R
R/wait_cor_summary-data.R
README.md
data/.DS_Store
data/.Rapp.history
data/cor_summary.RData
data/data.RData
data/depth_wait_cor_summary.RData
data/driver_matrix.RData
data/driver_phylo.RData
data/output.RData
data/output_allele_counts.RData
data/output_driver_allele_counts.RData
data/output_driver_genotype_counts.RData
data/output_genotype_counts.RData
data/output_passengersgrid.RData
data/parameters.RData
data/sum_df.RData
data/summary.RData
data/wait_cor_summary.RData
inst/.DS_Store
inst/example_batch/.DS_Store
inst/example_batch/log2_K_0/.DS_Store
inst/example_batch/log2_K_0/seed_0/clones.dat
inst/example_batch/log2_K_0/seed_0/demes.dat
inst/example_batch/log2_K_0/seed_0/driver_matrix.dat
inst/example_batch/log2_K_0/seed_0/driver_phylo.dat
inst/example_batch/log2_K_0/seed_0/error_log.dat
inst/example_batch/log2_K_0/seed_0/matrix.dat
inst/example_batch/log2_K_0/seed_0/output.dat
inst/example_batch/log2_K_0/seed_0/output_allele_counts.dat
inst/example_batch/log2_K_0/seed_0/output_birthratesgrid.dat
inst/example_batch/log2_K_0/seed_0/output_deathrates_grid.dat
inst/example_batch/log2_K_0/seed_0/output_diversities.dat
inst/example_batch/log2_K_0/seed_0/output_driver_allele_counts.dat
inst/example_batch/log2_K_0/seed_0/output_driver_genotype_counts.dat
inst/example_batch/log2_K_0/seed_0/output_driver_genotype_properties.dat
inst/example_batch/log2_K_0/seed_0/output_driversgrid.dat
inst/example_batch/log2_K_0/seed_0/output_genotype_counts.dat
inst/example_batch/log2_K_0/seed_0/output_genotype_properties.dat
inst/example_batch/log2_K_0/seed_0/output_migrationratesgrid.dat
inst/example_batch/log2_K_0/seed_0/output_normalcellsgrid.dat
inst/example_batch/log2_K_0/seed_0/output_passengersgrid.dat
inst/example_batch/log2_K_0/seed_0/output_popgrid.dat
inst/example_batch/log2_K_0/seed_0/parameters.dat
inst/example_batch/log2_K_0/seed_0/phylo.dat
inst/example_batch/log2_K_0/seed_0/sample_size_log.dat
inst/example_batch/log2_K_0/seed_1/clones.dat
inst/example_batch/log2_K_0/seed_1/demes.dat
inst/example_batch/log2_K_0/seed_1/driver_matrix.dat
inst/example_batch/log2_K_0/seed_1/driver_phylo.dat
inst/example_batch/log2_K_0/seed_1/error_log.dat
inst/example_batch/log2_K_0/seed_1/matrix.dat
inst/example_batch/log2_K_0/seed_1/output.dat
inst/example_batch/log2_K_0/seed_1/output_allele_counts.dat
inst/example_batch/log2_K_0/seed_1/output_birthratesgrid.dat
inst/example_batch/log2_K_0/seed_1/output_deathrates_grid.dat
inst/example_batch/log2_K_0/seed_1/output_diversities.dat
inst/example_batch/log2_K_0/seed_1/output_driver_allele_counts.dat
inst/example_batch/log2_K_0/seed_1/output_driver_genotype_counts.dat
inst/example_batch/log2_K_0/seed_1/output_driver_genotype_properties.dat
inst/example_batch/log2_K_0/seed_1/output_driversgrid.dat
inst/example_batch/log2_K_0/seed_1/output_genotype_counts.dat
inst/example_batch/log2_K_0/seed_1/output_genotype_properties.dat
inst/example_batch/log2_K_0/seed_1/output_migrationratesgrid.dat
inst/example_batch/log2_K_0/seed_1/output_normalcellsgrid.dat
inst/example_batch/log2_K_0/seed_1/output_passengersgrid.dat
inst/example_batch/log2_K_0/seed_1/output_popgrid.dat
inst/example_batch/log2_K_0/seed_1/parameters.dat
inst/example_batch/log2_K_0/seed_1/phylo.dat
inst/example_batch/log2_K_0/seed_1/sample_size_log.dat
inst/example_batch/log2_K_1/.DS_Store
inst/example_batch/log2_K_1/seed_0/clones.dat
inst/example_batch/log2_K_1/seed_0/demes.dat
inst/example_batch/log2_K_1/seed_0/driver_matrix.dat
inst/example_batch/log2_K_1/seed_0/driver_phylo.dat
inst/example_batch/log2_K_1/seed_0/error_log.dat
inst/example_batch/log2_K_1/seed_0/matrix.dat
inst/example_batch/log2_K_1/seed_0/output.dat
inst/example_batch/log2_K_1/seed_0/output_allele_counts.dat
inst/example_batch/log2_K_1/seed_0/output_birthratesgrid.dat
inst/example_batch/log2_K_1/seed_0/output_deathrates_grid.dat
inst/example_batch/log2_K_1/seed_0/output_diversities.dat
inst/example_batch/log2_K_1/seed_0/output_driver_allele_counts.dat
inst/example_batch/log2_K_1/seed_0/output_driver_genotype_counts.dat
inst/example_batch/log2_K_1/seed_0/output_driver_genotype_properties.dat
inst/example_batch/log2_K_1/seed_0/output_driversgrid.dat
inst/example_batch/log2_K_1/seed_0/output_genotype_counts.dat
inst/example_batch/log2_K_1/seed_0/output_genotype_properties.dat
inst/example_batch/log2_K_1/seed_0/output_migrationratesgrid.dat
inst/example_batch/log2_K_1/seed_0/output_normalcellsgrid.dat
inst/example_batch/log2_K_1/seed_0/output_passengersgrid.dat
inst/example_batch/log2_K_1/seed_0/output_popgrid.dat
inst/example_batch/log2_K_1/seed_0/parameters.dat
inst/example_batch/log2_K_1/seed_0/phylo.dat
inst/example_batch/log2_K_1/seed_0/sample_size_log.dat
inst/example_batch/log2_K_1/seed_1/clones.dat
inst/example_batch/log2_K_1/seed_1/demes.dat
inst/example_batch/log2_K_1/seed_1/driver_matrix.dat
inst/example_batch/log2_K_1/seed_1/driver_phylo.dat
inst/example_batch/log2_K_1/seed_1/error_log.dat
inst/example_batch/log2_K_1/seed_1/matrix.dat
inst/example_batch/log2_K_1/seed_1/output.dat
inst/example_batch/log2_K_1/seed_1/output_allele_counts.dat
inst/example_batch/log2_K_1/seed_1/output_birthratesgrid.dat
inst/example_batch/log2_K_1/seed_1/output_deathrates_grid.dat
inst/example_batch/log2_K_1/seed_1/output_diversities.dat
inst/example_batch/log2_K_1/seed_1/output_driver_allele_counts.dat
inst/example_batch/log2_K_1/seed_1/output_driver_genotype_counts.dat
inst/example_batch/log2_K_1/seed_1/output_driver_genotype_properties.dat
inst/example_batch/log2_K_1/seed_1/output_driversgrid.dat
inst/example_batch/log2_K_1/seed_1/output_genotype_counts.dat
inst/example_batch/log2_K_1/seed_1/output_genotype_properties.dat
inst/example_batch/log2_K_1/seed_1/output_migrationratesgrid.dat
inst/example_batch/log2_K_1/seed_1/output_normalcellsgrid.dat
inst/example_batch/log2_K_1/seed_1/output_passengersgrid.dat
inst/example_batch/log2_K_1/seed_1/output_popgrid.dat
inst/example_batch/log2_K_1/seed_1/parameters.dat
inst/example_batch/log2_K_1/seed_1/phylo.dat
inst/example_batch/log2_K_1/seed_1/sample_size_log.dat
inst/extdata/.DS_Store
inst/extdata/driver_matrix.dat
inst/extdata/driver_phylo.dat
inst/extdata/error_log.dat
inst/extdata/output.dat
inst/extdata/output_allele_counts.dat
inst/extdata/output_birthratesgrid.dat
inst/extdata/output_deathrates_grid.dat
inst/extdata/output_diversities.dat
inst/extdata/output_driver_allele_counts.dat
inst/extdata/output_driver_genotype_counts.dat
inst/extdata/output_driver_genotype_properties.dat
inst/extdata/output_driversgrid.dat
inst/extdata/output_genotype_counts.dat
inst/extdata/output_genotype_properties.dat
inst/extdata/output_migrationratesgrid.dat
inst/extdata/output_normalcellsgrid.dat
inst/extdata/output_passengersgrid.dat
inst/extdata/output_popgrid.dat
inst/extdata/parameters.dat
inst/extdata/sample_size_log.dat
man/T_grow_j.Rd
man/add_columns.Rd
man/add_relative_time.Rd
man/adjust_mig_rate.Rd
man/all_output.Rd
man/all_statuses.Rd
man/ancestry.Rd
man/apply_combinations.Rd
man/apply_combinations_parallel.Rd
man/combine_dfs.Rd
man/corCI_high.Rd
man/corCI_low.Rd
man/cor_pval.Rd
man/cor_summary.Rd
man/count_drivers.Rd
man/count_parameters.Rd
man/count_seeds.Rd
man/create_plots_batch.Rd
man/data.Rd
man/depth_wait_cor_summary.Rd
man/disp_rate.Rd
man/disp_rate_demon.Rd
man/disp_rate_fission.Rd
man/disp_rate_max.Rd
man/disp_rate_min.Rd
man/dominant.Rd
man/driver_geno_div_df_batch.Rd
man/driver_matrix.Rd
man/driver_phylo.Rd
man/filter_by_generation_or_numcells.Rd
man/final_error_message.Rd
man/final_generation.Rd
man/find_correlations.Rd
man/first_inc_moment.Rd
man/geno_dist.Rd
man/get_Variable_cor_summary.Rd
man/get_Variable_cor_summary_FinalSize.Rd
man/get_cor_summary.Rd
man/get_summary.Rd
man/get_tree_from_matrix.Rd
man/get_wait_cor_summary.Rd
man/grid_plot.Rd
man/hist2.Rd
man/image_df_from_grid_file.Rd
man/inv_Simpson_index.Rd
man/lambda.Rd
man/lambda_invasion.Rd
man/make_dir.Rd
man/make_image_file_name.Rd
man/metrics.Rd
man/mig_rate.Rd
man/muller_df_from_file.Rd
man/output.Rd
man/output_allele_counts.Rd
man/output_driver_allele_counts.Rd
man/output_driver_genotype_counts.Rd
man/output_genotype_counts.Rd
man/output_passengersgrid.Rd
man/parameter_names_and_values.Rd
man/parameters.Rd
man/plot_R2_verus_sweep_metric.Rd
man/plot_all_charts.Rd
man/plot_all_images.Rd
man/plot_allelecount_vs_origintime.Rd
man/plot_corr_outcome_versus_period.Rd
man/plot_corr_waiting_time_versus_depth.Rd
man/plot_corr_waiting_time_versus_start_size.Rd
man/plot_counts.Rd
man/plot_cum_dist.Rd
man/plot_curves_faceted.Rd
man/plot_driver_geno_div.Rd
man/plot_figure2.Rd
man/plot_first_inc_moment.Rd
man/plot_logit_freq_dist.Rd
man/plot_mutation_waves.Rd
man/plot_scatter_outcome_diversity.Rd
man/plot_scatter_waiting_time_diversity.Rd
man/plot_trajectories_by_K.Rd
man/plot_trajectories_by_diversity.Rd
man/plot_tree.Rd
man/plot_viol_sweep_metric.Rd
man/prob_successful_migration.Rd
man/quadratic_diversity.Rd
man/read_delim_special.Rd
man/reflect_on_diagonal.Rd
man/refresh_data_files.Rd
man/rho.Rd
man/sum_df.Rd
man/summary.Rd
man/sweep_sequence.Rd
man/sweep_times.Rd
man/time_expected.Rd
man/time_fixation.Rd
man/time_migration.Rd
man/trans_rate.Rd
man/wait_cor_summary.Rd
tests/.DS_Store
tests/testthat.R
tests/testthat/test_demonanalysis.R
