RIDL-drive modeling project

Content

.
├── README.md
├── data
│   ├── processed
│   │   ├── RIDL-drive_discrete
│   │   ├── RIDL-drive_heterozygotes_survival
│   │   ├── RIDL-drive_mosquito
│   │   ├── RIDL-drive_mosquito_LDGR
│   │   ├── RIDL-drive_mosquito_fitness
│   │   ├── RIDL-drive_resistance
│   │   ├── RIDL_mosquito_LDGR
│   │   ├── RIDL_mosquito_fitness
│   │   ├── SIT_discrete
│   │   ├── SIT_mosquito
│   │   ├── SIT_mosquito_LDGR
│   │   └── SIT_mosquito_fitness
│   └── raw
│       ├── RIDL-drive_discrete
│       ├── RIDL-drive_heterozygotes_survival
│       ├── RIDL-drive_mosquito
│       ├── RIDL-drive_mosquito_LDGR
│       ├── RIDL-drive_mosquito_fitness
│       ├── RIDL-drive_resistance
│       ├── RIDL_mosquito_LDGR
│       ├── RIDL_mosquito_fitness
│       ├── SIT_discrete
│       ├── SIT_mosquito
│       ├── SIT_mosquito_LDGR
│       └── SIT_mosquito_fitness
└── models
    ├── discrete.slim
    ├── mosquito.slim
    └── mosquito_het_survival.slim

SLiM Model description

• discrete.slim: panmictic discrete generation model
• mosquito.slim: basic panmictic mosquito (overlapping generation) model
• mosquito_het_survival.slim: panmictic mosquito (overlapping generation) model considering the heterozygotes survival rate

Data description

The *.csv files in the raw data adhere to the following naming convention:

[Transgene type]_[Param 1]-[Param 1 value]-[Param 2]-[Param 2 value]-..._[Repetition number].csv

where:

• [Transgene type] indicates the type of transgene element applied in the simulation. It should be RIDL-drive, RIDL, or SIT.
• [Param]s and [Param value]s indicate some important parameters and their values in the simulation. Here are some [Param]s:
  • drop: drop ratio (a positive float number in)
  • eff: drive efficiency (a float number in $[0.0,1.0]$)
  • fit: drive (RIDL/SIT) homozygotes fitness (a float number in $[0.5,1.0]$)
  • ldgr: low-density growth rate (a float positive number)
  • r2: germline resistance rate (a float number in $[0.0,0.5]$)
  • hets: heterozygotes survival rate (a float number in $[0.0,0.5]$)
  • curve: density-dependent growth curve type ( concave / linear / convex )
  • type: rescue drive type ( normal / haplolethal / recessivelethal )
• [Repetition number] is a positive integer (1~20), representing one of the 20 simulations with identical parameters.

Errata

• There is a fertile_female_size column in *.csv files from some mosquito model simulations. The values are always 1 due to a wrong output. These columns are not used in our project, because all females are fertile in the mosquito model. The female_size columns give the total number (and also, the correct number of fertile ones) of females. This error is fixed in the current version of models.