tek2
Classes | Functions | Variables
Parameters

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
 

Detailed Description

Function Documentation

◆ haploid_options()

clipp::group tek::haploid_options ( nlohmann::json *  vm,
HaploidParams p 
)
inline
Command line option Symbol Variable
--xi \(\xi\) HaploidParams::XI
--nu \(\nu\) HaploidParams::EXCISION_RATE
--lambda \(\lambda\) HaploidParams::MEAN_SELECTION_COEF

◆ population_options()

clipp::group tek::population_options ( nlohmann::json *  vm,
PopulationParams p 
)
inline
Command line option Symbol Variable
--sample PopulationParams::SAMPLE_SIZE
-j,--parallel PopulationParams::CONCURRENCY
-c,--coexist PopulationParams::MAX_COEXISTENCE

◆ program_options()

clipp::group tek::program_options ( nlohmann::json *  vm)
inline

Command line option | Symbol | Variable ----------------— | ----— | ----------------------— -n,--popsize | \(N\) | -q,--initial | | -g,--generations | | -s,--split | | -i,--interval | | -r,--record | | -o,--outdir | |

◆ transposon_options()

clipp::group tek::transposon_options ( nlohmann::json *  vm,
TransposonParams p 
)
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