Name		Name	Last commit message	Last commit date
parent directory ..
README.md		README.md
TPT_aux.py		TPT_aux.py
TPT_clsFactCheck.py		TPT_clsFactCheck.py
TPT_crunchData.sh		TPT_crunchData.sh
TPT_debug.py		TPT_debug.py
TPT_downloadData.sh		TPT_downloadData.sh
TPT_downloadPlots.sh		TPT_downloadPlots.sh
TPT_factChecks.py		TPT_factChecks.py
TPT_functions.py		TPT_functions.py
TPT_gene.py		TPT_gene.py
TPT_gene_HUM.py		TPT_gene_HUM.py
TPT_gene_INC.py		TPT_gene_INC.py
TPT_gene_LDR.py		TPT_gene_LDR.py
TPT_incidenceFix.py		TPT_incidenceFix.py
TPT_preProcess.py		TPT_preProcess.py
TPT_preTraces.py		TPT_preTraces.py
TPT_preTracesInfectious.py		TPT_preTracesInfectious.py
TPT_processFull.sh		TPT_processFull.sh
TPT_pstFraction.py		TPT_pstFraction.py
TPT_pstProcess.py		TPT_pstProcess.py
TPT_pstTraces.py		TPT_pstTraces.py

README.md

TP-13 DA Files

To generate the whole analysis set for the paper, run:

TPT_crunchData.sh $USR

Upon the output of the simulation defined in these MGDrive scripts (which make use of the cubeHoming LDR)

This will generate the required plots and summary files for:

ECO: Gene frequencies
HLT: Dominant transgene presence in female mosquitos
HUM: Susceptible versus prevalence in humans
INC: Human incidence analysis

Originally, the paths are set to be:

/RAID5/marshallShare/TP13
/RAID5/marshallShare/TP13

But this can be changed in the aux file if needed.

The experiments' filename key is E_ren_rer_rsg_gsv_fch_fcb_fcr_hrm_hrf where:

ren: number of releases
rer: size of the releases
rsg: resistance generation
gsv: genetic standing variation
fch: fitness cost on homing allele
fcb: fitness cost on broken allele
fcr: fitness cost on resistant allele
hrm: homing rate on males
hrf: homing rate on females