philliplab yasss issues

philliplab / yasss

Yet Another Short Sequence Simulator

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Design vignette - the write-up of the identifiers do not belong in the dsum section - find a new home for them

#160 philliplab opened 5 years ago
0
BUG: recombine_gen can currently introduce multiple breakpoints in a single generation - this is not allowed

#159 philliplab closed 5 years ago
1
Update the design vignette: The write-up motivating the choice of recomb_muts is bad

#158 philliplab closed 5 years ago
0
Add write-up of clara2 clustering in summarize_dmat into design vignette

#157 philliplab closed 6 years ago
0
Figure out what is up with the identifiers variable in check_dcollection

#156 philliplab opened 6 years ago
0
Add meny_pop specific settings into output: many_pop_arguments

#155 philliplab opened 6 years ago
0
Add fitness_processing_metrics_to_df function

#154 philliplab closed 6 years ago
1
Add reporting on within / between cluster distances to sim_proc_many_pops

#153 philliplab closed 6 years ago
2
migrate genealogy_summary_table from quasispecies reports into yasss

#152 philliplab opened 6 years ago
0
migrate sim_pop_arg_formatter from quasispecies_reports into yasss

#151 philliplab opened 6 years ago
0
Expand linkage function to handle tied most frequent nucleotides by computing both

#150 philliplab opened 6 years ago
2
Why is the computation of D_prome failing for V2 in linkage tests?

#149 philliplab closed 6 years ago
1
Modify linkage section in design vignette replace p1 and p2 where referring to positions with L1 and L2 (loci) to prevent confusion with the p1/p2 frequency variables

#148 philliplab closed 6 years ago
0
Add tests for linkage_diseq

#147 philliplab closed 6 years ago
0
Add test data structures for linkage diseq

#146 philliplab closed 6 years ago
0
Add in linkage_diseq function

#145 philliplab closed 6 years ago
0
Add in consensusMatrix function

#144 philliplab closed 6 years ago
0
Think about the implications of calculating linkage disequilibrium

#143 philliplab closed 6 years ago
0
Add a test that actually tests the breakpoint and LHS/RHS in recombine_gen

#142 philliplab closed 5 years ago
0
Think: The double chance of being a recombinant - see the design vignette

#141 philliplab opened 6 years ago
0
Add recombination tests for sim_pop

#140 philliplab closed 6 years ago
0
Integrate recombination into sim_pop

#139 philliplab closed 6 years ago
0
Add functionality and tests recombine_gen

#138 philliplab closed 6 years ago
0
Add functionality and tests for recombine_seqs

#137 philliplab closed 6 years ago
0
BIG: Move all the recombination metrics out of the genealogy and into a separate data structure

#136 philliplab opened 6 years ago
0
Write design notes about adding recombination into yasss

#135 philliplab closed 6 years ago
0
Add more tests fo dcollection_to_df

#134 philliplab opened 6 years ago
2
Find a better home for fitness_processing_metrics and its tests

#133 philliplab opened 6 years ago
0
Migrate design notes from README to design vignette

#132 philliplab closed 6 years ago
0
Fix bandwidth selection in sim_proc_many_pops

#131 philliplab opened 6 years ago
2
sim_proc_many_pops: Track the number of sequences removed by get_fit_offspring

#130 philliplab closed 6 years ago
0
Add functionality into sim_proc_many_pops that produce a summary of the arg_collection and fitness_processing - is the fact that I need to add lots of logic into sim_proc_many_pops to achieve this a design flaw?

#129 philliplab opened 6 years ago
0
move dcollection_to_df function into yasss from quasi reports / comp_sim_chunk.Rmd

#128 philliplab closed 6 years ago
0
update get_fit_offspring to preserve the sim_id and label columns (also sampling?)

#127 philliplab opened 6 years ago
0
sim_proc_many_pops: Add support for empty genealogies (due to too strict fitness requirements)

#126 philliplab opened 6 years ago
0
Add check into sim_proc_many_pops: if fitness processing is not none, then required fitness must be in all arg_sets

#125 philliplab closed 6 years ago
0
include summarize_gen in the design_vignette

#124 philliplab opened 6 years ago
0
What do I call the function that computes a dmat on a generation and summarizes the dmat and add in the identifiers?

#123 philliplab closed 6 years ago
1
Add n_seqs element into dsums

#122 philliplab opened 6 years ago
1
Add max_dmat_size argument to sim_proc_many_pops

#121 philliplab closed 6 years ago
0
Add fit_unfit_pair option to sim_proc_many_pops

#120 philliplab closed 6 years ago
0
Add check_all_dmats + tests (dsum.R)

#119 philliplab opened 6 years ago
0
Add check_identified_dmat function + tests (dsum.R)

#118 philliplab opened 6 years ago
0
Expand functionality of sim_proc_many_pops: output full genealogies

#117 philliplab opened 6 years ago
0
Expand functionality of sim_proc_many_pops: output dmats

#116 philliplab closed 6 years ago
0
Expand functionality of sim_proc_many_pops : n_sims argument

#115 philliplab closed 6 years ago
0
sim_proc_many_pops: ADD test cases for broken dcollection

#114 philliplab closed 6 years ago
0
add a check_many_pops function to check the results of sim_proc_many_pops

#113 philliplab closed 6 years ago
0
Add label requirement into arg_sets

#112 philliplab opened 6 years ago
0
Add check for arg_collection: label must be unique

#111 philliplab closed 6 years ago
0