Snitkin-Lab-Umich regentrans issues

Snitkin-Lab-Umich / regentrans

regentrans: R package for investigating regional pathogen transmission using genomic data

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Question about Estimating Pairwise SNV Threshold Using Mutation Rate

#60 Tonny-zhou opened 1 year ago
1
Incorporate Rcpp get_genetic_flow() functions

#59 shoffm opened 2 years ago
0
Add code to get pairwise day differences between isolates

#58 zenalapp closed 2 years ago
1
Provide example in vignette of intra versus inter patient SNV distance plots

#57 zenalapp opened 3 years ago
0
Add functionality to include multiple patient isolates to calculate Fsp

#56 zenalapp closed 2 years ago
1
Include functionality or example of including multiple patient samples for SNV distance analysis

#55 zenalapp closed 2 years ago
1
Fix `check_locs()`

#54 zenalapp closed 2 years ago
1
Update website to include link to preprint

#53 zenalapp closed 2 years ago
1
Create preprocessing vignette

#52 zenalapp opened 3 years ago
0
Make `get_patient_flow()` faster

#51 zenalapp opened 3 years ago
0
Create first release of regentrans

#50 zenalapp closed 3 years ago
0
Make SNV threshold <= instead of <

#49 zenalapp closed 3 years ago
0
Update README

#48 zenalapp closed 3 years ago
0
Don't flip anything in `get_pair_types()`, just flip in the summary function

#47 zenalapp closed 3 years ago
0
More flexible input for `get_patient_flow()`

#46 zenalapp opened 3 years ago
0
Change some variable names

#45 zenalapp closed 3 years ago
0
Rename `get_snv_dists`

#44 zenalapp closed 3 years ago
0
Update vignette

#43 zenalapp closed 3 years ago
0
Fix environmental sample example in vignette

#42 zenalapp closed 3 years ago
0
Decrease runtime of `get_facility_fsp` function & tests

#41 zenalapp closed 2 years ago
1
Simplify inputs to `get_frac_intra` and `get_patient_transfers`

#40 zenalapp closed 3 years ago
0
Have the user remove duplicate patients etc. beforehand

#39 zenalapp closed 3 years ago
0
Rename output columns for some functions

#38 zenalapp closed 3 years ago
0
Save data using `usethis::use_data`

#37 zenalapp closed 3 years ago
0
Update DESCRIPTION

#36 zenalapp closed 3 years ago
0
Clean up extras directory

#35 zenalapp closed 3 years ago
0
Beef up function documentation

#34 zenalapp closed 3 years ago
0
Allow more flexibility when `get_pair_types()` used as input

#33 zenalapp opened 3 years ago
0
Export only user-facing functions

#32 zenalapp closed 3 years ago
1
Refactor patient flow function to separate out getting flow and finding number of closely related pairs

#31 zenalapp closed 3 years ago
0
Set up automatic package check & code reformatting on GitHub

#30 zenalapp opened 3 years ago
0
Add code coverage and other stats/info to GitHub page

#29 zenalapp opened 3 years ago
0
Fix errors, warnings, and notes from `devtools::check()`

#28 zenalapp closed 3 years ago
0
Update vignette to show manuscript figures

#27 zenalapp closed 3 years ago
0
Add unit tests for pureness and bootstrap options in get_largest_subtree

#26 zenalapp closed 3 years ago
0
Add unit tests for checks

#25 zenalapp closed 3 years ago
0
Remove duplicate pairs before returning get_snv_dists

#24 zenalapp closed 3 years ago
0
Fix get_frac_intra

#23 zenalapp closed 3 years ago
0
Change first word of all functions to verbs

#22 zenalapp closed 3 years ago
0
Add code to patient_transfer function to fill in missing source and/or destination facilities

#21 zenalapp closed 3 years ago
0
Add check for patient_flow that no multiple rows with same source and destination facility

#20 zenalapp closed 3 years ago
0
[Add to vignette] Code to assign each isolate to a cluster based on the get_clusters output

#19 kylegontjes closed 3 years ago
0
Add code to plot SNVs vs. time between samples to vignette

#18 sthiede closed 2 years ago
4
design vignette

#17 shoffm closed 3 years ago
0
Return subtrees for get_clusters

#16 zenalapp closed 3 years ago
0
Write tests for outputs

#15 shoffm closed 3 years ago
0
Write tests for checks

#14 shoffm closed 3 years ago
0
function to subset to one of each pair from get_snv_dists results

#13 shoffm closed 3 years ago
0
Profile get_facility_fsp

#12 shoffm closed 3 years ago
0
Create R package

#11 shoffm closed 3 years ago
0