46 #include <Bpp/Numeric/Prob/DiscreteDistribution.h> 47 #include <Bpp/Numeric/Parameter.h> 92 addParameter_(
new Parameter(
"TS98.s1", s1, &Parameter::R_PLUS_STAR));
93 addParameter_(
new Parameter(
"TS98.s2", s2, &Parameter::R_PLUS_STAR));
100 #ifndef NO_VIRTUAL_COV 108 std::string
getName()
const {
return "TS98"; }
119 double s1 = getParameterValue(
"s1");
120 double s2 = getParameterValue(
"s2");
virtual void updateMatrices()
void updateRatesModel()
Update the rates vector, generator and equilibrium frequencies.
Interface for reversible substitution models.
RowMatrix< double > rates_
Tuffley and Steel's 1998 covarion model.
double getRate() const
Get the rate.
Partial implementation of the Markov-modulated class of substitution models.
std::string getName() const
Get the name of the model.
TS98(ReversibleSubstitutionModel *model, double s1=1., double s2=1., bool normalizeRateChanges=false)
Build a new TS98 substitution model.
void setRate(double rate)
Set the rate of the model (must be positive).
RowMatrix< double > ratesExchangeability_