tek2
|
Classes | |
struct | tek::HaploidParams |
Parameters for Haploid class. More... | |
struct | tek::PopulationParams |
Parameters for Population class. More... | |
struct | tek::TransposonParams |
Parameters for Transposon class. More... | |
Functions | |
clipp::group | tek::program_options (nlohmann::json *vm) |
clipp::group | tek::population_options (nlohmann::json *vm, PopulationParams *p) |
clipp::group | tek::haploid_options (nlohmann::json *vm, HaploidParams *p) |
clipp::group | tek::transposon_options (nlohmann::json *vm, TransposonParams *p) |
Variables | |
static constexpr double | tek::Haploid::INDEL_RATIO_ = 0.2 |
\(\phi\), relative rate of indels to point mutation | |
static constexpr double | tek::Haploid::TAU_ = 1.5 |
\(\tau\), constant for the intensity of copy number selection | |
static constexpr double | tek::Haploid::PROP_FUNCTIONAL_SITES_ = 0.75 |
\(p\), proportion of non-neutral sites | |
static double | tek::Haploid::MUTATION_RATE_ = 0.0 |
\(L\mu = L\theta / 4N\), mutation rate per TE | |
static double | tek::Haploid::INDEL_RATE_ = 0.0 |
\(L\phi\mu\), absolute indel rate per TE | |
static double | tek::Haploid::RECOMBINATION_RATE_ = 0.0 |
\(c = \rho / 4N\), recombination rate per genome | |
static constexpr double | tek::Population::THETA = 0.01 |
\(\theta = 4N\mu\), population mutation rate | |
static constexpr double | tek::Population::RHO = 20000 |
\(\rho = 4Nc\), population recombination rate | |
static constexpr uint_fast32_t | tek::Transposon::NUM_SYNONYMOUS_SITES = LENGTH / 3u |
number of synonymous sites | |
static constexpr uint_fast32_t | tek::Transposon::NUM_NONSYNONYMOUS_SITES = LENGTH - NUM_SYNONYMOUS_SITES |
number of nonsynonymous sites | |
static constexpr double | tek::Transposon::MAX_TRANSPOSITION_RATE = 0.01 |
\(u_0\), maximum transposition rate | |
|
inline |
Command line option | Symbol | Variable |
---|---|---|
--xi | \(\xi\) | HaploidParams::XI |
--nu | \(\nu\) | HaploidParams::EXCISION_RATE |
--lambda | \(\lambda\) | HaploidParams::MEAN_SELECTION_COEF |
|
inline |
Command line option | Symbol | Variable |
---|---|---|
--sample | PopulationParams::SAMPLE_SIZE | |
-j,--parallel | PopulationParams::CONCURRENCY | |
-c,--coexist | PopulationParams::MAX_COEXISTENCE |
|
inline |
Command line option | Symbol | Variable ----------------— | ----— | ----------------------— -n,--popsize
| \(N\) | -q,--initial
| | -g,--generations
| | -s,--split
| | -i,--interval
| | -r,--record
| | -o,--outdir
| |
|
inline |
Command line option | Symbol | Variable |
---|---|---|
-a,--alpha | \(\alpha\) | TransposonParams::ALPHA |
-b,--beta | \(\beta\) | TransposonParams::BETA |
-l,--lower | \(d_l\) | TransposonParams::LOWER_THRESHOLD |
-u,--upper | \(d_u\) | TransposonParams::UPPER_THRESHOLD |