1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
/*
* modelunrest.cpp
*
* Created on: 24/05/2016
* Author: mdw2
*/
#include "modelunrest.h"
ModelUnrest::ModelUnrest(PhyloTree *tree, string model_params)
: ModelMarkov(tree, false)
{
num_params = getNumRateEntries() - 1;
model_parameters = new double [num_params];
for (int i=0; i< num_params; i++) model_parameters[i] = 1;
setRates();
if (model_params != "") {
cout << "WARNING: Supplying model params to constructor not yet properly implemented -- ignored" << endl;
// TODO: parse model_params into model_parameters, then call setRates().
}
name = "UNREST";
full_name = "Unrestricted model (non-reversible)";
ModelMarkov::init(FREQ_ESTIMATE);
}
/* static */ bool ModelUnrest::validModelName(string model_name) {
return (model_name == "UNREST");
}
void ModelUnrest::setBounds(double *lower_bound, double *upper_bound, bool *bound_check) {
int i, ndim = getNDim();
for (i = 1; i <= ndim; i++) {
lower_bound[i] = 0.01;
upper_bound[i] = 100.0;
bound_check[i] = false;
}
}
/*
* Set rates from model_parameters
*/
void ModelUnrest::setRates() {
// For UNREST, parameters are simply the off-diagonal rate matrix entries
// (except [4,3] = rates[11], which is constrained to be 1)
memcpy(rates, model_parameters, num_params*sizeof(double));
rates[num_params]=1;
}
|
