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