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proposal.c
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proposal.c
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/*
* MrBayes 3
*
* (c) 2002-2013
*
* John P. Huelsenbeck
* Dept. Integrative Biology
* University of California, Berkeley
* Berkeley, CA 94720-3140
*
* Fredrik Ronquist
* Swedish Museum of Natural History
* Box 50007
* SE-10405 Stockholm, SWEDEN
*
* With important contributions by
*
* Paul van der Mark ([email protected])
* Maxim Teslenko ([email protected])
*
* and by many users (run 'acknowledgments' to see more info)
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details (www.gnu.org).
*
*/
#include "bayes.h"
#include "best.h"
#include "command.h"
#include "mcmc.h"
#include "model.h"
#include "proposal.h"
#include "utils.h"
const char* const svnRevisionProposalC = "$Rev: 1069 $"; /* Revision keyword which is expanded/updated by svn on each commit/update */
/* debugging compiler statements */
#undef DEBUG_LOCAL
#undef DEBUG_UNROOTED_SLIDER
#undef DEBUG_ParsSPR
#undef DEBUG_ExtSS
#undef DEBUG_CSLIDER
#undef DEBUG_ExtSPRClock
#undef DEBUG_ParsSPRClock
#undef DEBUG_ExtTBR
#undef DEBUG_NNIClock
#undef DEBUG_SPLITMERGE
#undef DEBUG_FBDPR
extern int *chainId;
void TouchAllTreeNodes (ModelInfo *m, int chain);
int Move_Aamodel (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* Change amino acid model for model mixing
amino acid model ID's
AAMODEL_POISSON 0
AAMODEL_JONES 1
AAMODEL_DAY 2
AAMODEL_MTREV 3
AAMODEL_MTMAM 4
AAMODEL_WAG 5
AAMODEL_RTREV 6
AAMODEL_CPREV 7
AAMODEL_VT 8
AAMODEL_BLOSUM 9 */
int i, oldM, newM;
MrBFlt *bs, *subValue;
ModelParams *mp;
/* get model params */
mp = &modelParams[param->relParts[0]];
subValue = GetParamSubVals(param, chain, state[chain]);
/* get old value of model */
newM = oldM = (int)*GetParamVals(param, chain, state[chain]);
/* get a new model ID */
do
{
newM = (int)(RandomNumber(seed) * 10);
} while (newM == oldM);
/* set proposal ratio */
*lnProposalRatio = 0.0;
/* set prior ratio */
*lnPriorRatio = subValue[newM] - subValue[oldM];
/* copy new amino acid model ID back */
*GetParamVals(param, chain, state[chain]) = (MrBFlt)newM;
/* set amino acid frequencies */
bs = GetParamSubVals (modelSettings[param->relParts[0]].stateFreq, chain, state[chain]);
if (newM == AAMODEL_POISSON)
{
for (i=0; i<mp->nStates; i++)
bs[i] = 1.0 / 20.0;
}
else if (newM == AAMODEL_JONES)
{
for (i=0; i<mp->nStates; i++)
bs[i] = jonesPi[i];
}
else if (newM == AAMODEL_DAY)
{
for (i=0; i<mp->nStates; i++)
bs[i] = dayhoffPi[i];
}
else if (newM == AAMODEL_MTREV)
{
for (i=0; i<mp->nStates; i++)
bs[i] = mtrev24Pi[i];
}
else if (newM == AAMODEL_MTMAM)
{
for (i=0; i<mp->nStates; i++)
bs[i] = mtmamPi[i];
}
else if (newM == AAMODEL_WAG)
{
for (i=0; i<mp->nStates; i++)
bs[i] = wagPi[i];
}
else if (newM == AAMODEL_RTREV)
{
for (i=0; i<mp->nStates; i++)
bs[i] = rtrevPi[i];
}
else if (newM == AAMODEL_CPREV)
{
for (i=0; i<mp->nStates; i++)
bs[i] = cprevPi[i];
}
else if (newM == AAMODEL_VT)
{
for (i=0; i<mp->nStates; i++)
bs[i] = vtPi[i];
}
else if (newM == AAMODEL_BLOSUM)
{
for (i=0; i<mp->nStates; i++)
bs[i] = blosPi[i];
}
/* Set update flags for all partitions that share this amino acid model. Note that the conditional
likelihood update flags have been set before we even call this function. */
for (i=0; i<param->nRelParts; i++)
TouchAllTreeNodes(&modelSettings[param->relParts[i]],chain);
/* Set update flags for cijks for all affected partitions. */
for (i=0; i<param->nRelParts; i++)
modelSettings[param->relParts[i]].upDateCijk = YES;
return (NO_ERROR);
MrBayesPrint ("%lf", *mvp); /* just because I am tired of seeing the unused parameter error msg */
}
int Move_AddDeleteCPPEvent (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* add or delete one Poisson process event */
int i, k, addEvent, *nEvents, numEvents;
MrBFlt sigma, m, lognormalLnProb, **position, **rateMultiplier, length, pos, rate;
TreeNode *p, *q;
ModelInfo *model;
Tree *t;
/* get the model settings */
model = &modelSettings[param->relParts[0]];
/* get cpp rate */
rate = *GetParamVals (model->cppRate, chain, state[chain]);
/* get sigma of lognormal of rate multipliers */
sigma = *GetParamVals (model->cppMultDev, chain, state[chain]);
/* get the cpp event data */
nEvents = param->nEvents[2*chain+state[chain]];
position = param->position[2*chain+state[chain]];
rateMultiplier = param->rateMult[2*chain+state[chain]];
/* get tree */
t = GetTree (param, chain, state[chain]);
/* pick a branch */
do
{
p = t->allDownPass[(int)(RandomNumber(seed) * (t->nNodes -2))];
} while (p->anc == NULL || (p->anc->anc == NULL));
/* get number of events for convenience */
numEvents = nEvents[p->index];
/* add or delete ? */
addEvent = NO;
if (numEvents == 0)
addEvent = YES;
else if (RandomNumber(seed) < 0.5)
addEvent = YES;
if (addEvent == NO)
{
/* delete event */
/* choose random event */
k = (int) (RandomNumber(seed) * numEvents);
/* save multiplier to be deleted */
m = rateMultiplier[p->index][k];
/* rearrange and reduce */
for (i=k; i<numEvents-1; i++)
{
position[p->index][i] = position[p->index][i+1];
rateMultiplier[p->index][i] = rateMultiplier[p->index][i+1];
}
if (numEvents-1 > 0)
{
position[p->index] = (MrBFlt *) SafeRealloc ((void *) position[p->index], (numEvents-1)*sizeof(MrBFlt));
rateMultiplier[p->index] = (MrBFlt *) SafeRealloc ((void *) rateMultiplier[p->index], (numEvents-1)*sizeof(MrBFlt));
assert (position[p->index] != NULL && rateMultiplier[p->index] != NULL);
}
else
{
free (position[p->index]);
free (rateMultiplier[p->index]);
position[p->index] = rateMultiplier[p->index] = NULL;
}
/* update number of events */
nEvents[p->index]--;
}
else /* if (addEvent == YES) */
{
/* add event */
/* generate new multiplier */
m = LogNormalRandomVariable (0.0, sigma, seed);
/* generate new position */
pos = RandomNumber(seed);
/* find place in current array */
for (k=0; k<numEvents; k++)
{
if (position[p->index][k] > pos)
break;
}
/* rearrange and insert */
position[p->index] = (MrBFlt *) SafeRealloc ((void *)position[p->index], (numEvents+1)*sizeof(MrBFlt));
rateMultiplier[p->index] = (MrBFlt *) SafeRealloc ((void *)rateMultiplier[p->index], (numEvents+1)*sizeof(MrBFlt));
assert (position[p->index] != NULL && rateMultiplier[p->index] != NULL);
for (i=numEvents; i>k; i--)
{
position[p->index][i] = position[p->index][i-1];
rateMultiplier[p->index][i] = rateMultiplier[p->index][i-1];
}
position[p->index][k] = pos;
rateMultiplier[p->index][k] = m;
/* update number of events */
nEvents[p->index]++;
}
/* the CPP process is relative to expected substitutions */
length = p->length;
lognormalLnProb = LnProbLogNormal(0.0, sigma, m);
if (addEvent == YES)
(*lnPriorRatio) = lognormalLnProb + log (rate);
else
(*lnPriorRatio) = -(lognormalLnProb + log(rate));
if (addEvent == YES)
/* note that nEvents[p->index] now contains k+1 after addition */
(*lnProposalRatio) = log (length / ((double) nEvents[p->index])) - lognormalLnProb;
else
/* note that nEvents[p->index] contains k after deletion */
(*lnProposalRatio) = log ((double)(nEvents[p->index]+1) / length) + lognormalLnProb;
/* take care of asymmetric add and delete probabilities around 0 and 1 events */
if (addEvent == YES && nEvents[p->index] == 1)
(*lnProposalRatio) += log (0.5);
else if (addEvent == NO && nEvents[p->index] == 0)
(*lnProposalRatio) += log (2.0);
/* update evolLengths in subtree above new event */
if (UpdateCppEvolLengths (param, p, chain)==ERROR)
{
abortMove=YES;
return (NO_ERROR);
}
/* set update of cond likes down to root */
/* crown tree update flags set in UpdateCppEvolLengths */
q = p->anc;
while (q->anc != NULL)
{
q->upDateCl = YES;
q = q->anc;
}
return (NO_ERROR);
MrBayesPrint ("%lf", *mvp); /* just because I am tired of seeing the unused parameter error msg */
}
int Move_Adgamma (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* Change correlation parameter (-1, 1) of adgamma model */
int i, isValidP;
MrBFlt oldP, newP, window, minP, maxP, ran, *markovTiValues;
ModelParams *mp;
/* get size of window, centered on current rho */
window = mvp[0];
/* get model params */
mp = &modelParams[param->relParts[0]];
/* get minimum and maximum values for rho */
minP = mp->corrUni[0];
maxP = mp->corrUni[1];
/* get address of markovTi */
markovTiValues = GetParamSubVals (param, chain, state[chain]);
/* get old value of rho */
newP = oldP = *GetParamVals(param, chain, state[chain]);
/* change value for rho */
ran = RandomNumber(seed);
if (maxP-minP < window)
{
window = maxP-minP;
}
newP = oldP + window * (ran - 0.5);
/* check that new value is valid */
isValidP = NO;
do
{
if (newP < minP)
newP = 2* minP - newP;
else if (newP > maxP)
newP = 2 * maxP - newP;
else
isValidP = YES;
} while (isValidP == NO);
/* get proposal ratio */
*lnProposalRatio = 0.0;
/* get prior ratio */
*lnPriorRatio = 0.0;
/* copy new rho value back */
*GetParamVals(param, chain, state[chain]) = newP;
/* fill in new Markov trans probs */
AutodGamma (markovTiValues, newP, mp->numGammaCats);
/* Set update flags for all partitions that share this rho. Note that the conditional
likelihood update flags have been set before we even call this function. */
for (i=0; i<param->nRelParts; i++)
TouchAllTreeNodes(&modelSettings[param->relParts[i]],chain);
/* Update flags for divisions already set */
return (NO_ERROR);
}
int Move_Beta (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* change symmetric Dirichlet variance using multiplier */
int i, j, k, isValidB, isPriorExp, nStates;
MrBFlt oldB, newB, minB, maxB, priorExp=0.0, *bs, ran, factor, tuning,
x, y;
ModelParams *mp;
/* get tuning parameter */
tuning = mvp[0]; /* multiplier tuning parameter lambda */
/* get model paramaters */
mp = &modelParams[param->relParts[0]];
/* get prior, minimum and maximum values for rate */
if (!strcmp(mp->symPiPr,"Uniform"))
{
isPriorExp = NO;
minB = mp->symBetaUni[0];
maxB = mp->symBetaUni[1];
}
else
{
isPriorExp = YES;
priorExp = mp->symBetaExp;
minB = SYMPI_MIN;
maxB = SYMPI_MAX;
}
/* get old value of symDir */
oldB = *GetParamVals(param, chain, state[chain]);
/* change value */
ran = RandomNumber(seed);
factor = exp(tuning * (ran - 0.5));
newB = oldB * factor;
/* check validity */
isValidB = NO;
do
{
if (newB < minB)
newB = minB * minB / newB;
else if (newB > maxB)
newB = maxB * maxB / newB;
else
isValidB = YES;
} while (isValidB == NO);
/* set new value of symDir */
*GetParamVals(param, chain, state[chain]) = newB;
/* get proposal ratio */
*lnProposalRatio = log (newB / oldB);
/* get prior ratio */
if (isPriorExp == YES)
{
*lnPriorRatio = priorExp * (oldB - newB);
}
else
*lnPriorRatio = 0.0;
/* fill in the new betacat frequencies */
bs = GetParamStdStateFreqs(param, chain, state[chain]);
k = mp->numBetaCats;
BetaBreaks (newB, newB, bs, k);
k *= 2;
for (i=k-2; i>0; i-=2)
{
bs[i] = bs[i/2];
}
for (i=1; i<k; i+=2)
{
bs[i] = 1.0 - bs[i-1];
}
/* if there are multistate characters, update prior probability of current pis */
bs += 2 * mp->numBetaCats;
for (i=0; i<param->nSympi; i++)
{
/* get number of states */
nStates = param->sympinStates[i];
/* get prior ratio update */
x = LnGamma(newB*nStates) - nStates*LnGamma(newB);
y = LnGamma(oldB*nStates) - nStates*LnGamma(oldB);
for (j=0; j<nStates; j++)
{
x += (newB-1.0)*log(bs[j]);
y += (oldB-1.0)*log(bs[j]);
}
(*lnPriorRatio) += x - y;
/* update pointer to state freqs */
bs += nStates;
}
/* Set update flags for all tree nodes. Note that the conditional
likelihood update flags have been set for the relevant partitions
before we even call the move function. */
for (i=0; i<param->nRelParts; i++)
TouchAllTreeNodes(&modelSettings[param->relParts[i]],chain);
/* may need to hit update flag for cijks if we have multistate characters */
for (i=0; i<param->nRelParts; i++)
{
if (modelSettings[param->relParts[i]].nCijkParts > 0)
modelSettings[param->relParts[i]].upDateCijk = YES;
}
return (NO_ERROR);
}
int Move_BrLen (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* change one branch length */
MrBFlt tuning, maxV, minV, m, newM, brlensPrExp=0.0;
TreeNode *p;
ModelParams *mp;
Tree *t;
int isVPriorExp;
tuning = mvp[0]; /* Larget & Simon's tuning parameter lambda */
mp = &modelParams[param->relParts[0]];
/* max and min brlen */
if (param->paramId == BRLENS_UNI)
{
minV = mp->brlensUni[0];
maxV = mp->brlensUni[1];
isVPriorExp = NO;
}
else if (param->paramId == BRLENS_GamDir)
{
minV = BRLENS_MIN;
maxV = BRLENS_MAX;
isVPriorExp = 2;
}
else if (param->paramId == BRLENS_iGmDir)
{
minV = BRLENS_MIN;
maxV = BRLENS_MAX;
isVPriorExp = 3;
}
else if (param->paramId == BRLENS_twoExp)
{
minV = BRLENS_MIN;
maxV = BRLENS_MAX;
isVPriorExp = 4;
}
else
{
minV = BRLENS_MIN;
maxV = BRLENS_MAX;
brlensPrExp = mp->brlensExp;
isVPriorExp = YES;
}
/* get tree */
t = GetTree (param, chain, state[chain]);
/* Dirichlet or twoExp prior */
if (isVPriorExp > 1)
(*lnPriorRatio) = -LogDirPrior(t, mp, isVPriorExp);
/* pick a branch */
do {
p = t->allDownPass[(int)(RandomNumber(seed) * t->nNodes)];
}
while (p->anc == NULL || (t->isRooted == YES && p->anc->anc == NULL));
/* determine new length */
m = p->length;
newM = m * exp(tuning * (RandomNumber(seed) - 0.5));
/* reflect new length if necessary */
while (newM < minV || newM > maxV)
{
if (newM < minV)
newM = minV * minV / newM;
else if (newM > maxV)
newM = maxV * maxV / newM;
}
p->length = newM;
/* calculate proposal ratio */
/* must be based on new length after reflection */
(*lnProposalRatio) = log(newM / m);
/* set flags for update of transition probabilities at p */
p->upDateTi = YES;
/* set the update flag for cond likes if p is connected to root in unrooted */
/* tree, if this is not done, cond likes are not updated in this case */
if (t->isRooted == NO && p->anc->anc == NULL)
p->upDateCl = YES;
/* set flags for update of cond likes from p->anc and down to root */
while (p->anc->anc != NULL)
{
p = p->anc;
p->upDateCl = YES;
}
/* update prior if exponential prior on branch lengths */
if (param->paramId == BRLENS_EXP)
(*lnPriorRatio) = brlensPrExp * (m - newM);
/* Dirichlet or twoExp prior */
else if (isVPriorExp > 1)
(*lnPriorRatio) += LogDirPrior(t, mp, isVPriorExp);
return (NO_ERROR);
}
int Move_ClockRate_M (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* change clock rate using multiplier */
int i, j, k, *nEvents;
MrBFlt oldRate, newRate, factor, lambda, nu, igrvar, *brlens, *igrRate, *tk02Rate,
N, newTheta, oldTheta, growth, newLnPrior, oldLnPrior;
Tree *t, *oldT;
TreeNode *p, *q;
Param *treeParam, *subParm;
ModelParams *mp;
ModelInfo *m;
/* get old value of clock rate */
oldRate = *GetParamVals(param, chain, state[chain]);
/* Rely on general algorithm to change the value */
Move_PosRealMultiplier(param, chain, seed, lnPriorRatio, lnProposalRatio, mvp);
if (abortMove == YES)
return NO_ERROR;
/* get new value of clock rate */
newRate = *GetParamVals(param, chain, state[chain]);
/* calculate factor */
factor = newRate / oldRate;
/* clock rate applies to all clock trees */
for (i = 0; i < numTrees; i++)
{
t = GetTreeFromIndex(i, chain, state[chain]);
if (t->isClock == NO)
continue;
if (!strcmp(modelParams[t->relParts[0]].clockPr, "Fixed"))
continue;
oldT = GetTreeFromIndex(i, chain, 1^state[chain]);
treeParam = modelSettings[t->relParts[0]].brlens;
/* adjust the node depths and lengths */
for (j = 0; j < t->nNodes-1; j++)
{
p = t->allDownPass[j];
q = oldT->allDownPass[j];
p->nodeDepth *= factor; /* no harm done if nodeDepth==0.0 (undated tips) */
p->length *= factor; /* no harm done if length==0.0 (root or fossil ancestors)*/
if (p->length < 0.0 || p->length > BRLENS_MAX ||
(q->length > BRLENS_MIN && p->length < BRLENS_MIN) ||
(q->length < TIME_MIN && p->length > TIME_MIN))
{ /* consider ancestral fossil (brl=0) in fossilized bd tree */
abortMove = YES;
return (NO_ERROR);
}
}
/* prior ratio for coalecent tree, as theta is changed */
mp = &modelParams[t->relParts[0]];
if (!strcmp(mp->clockPr,"Coalescence"))
{
m = &modelSettings[t->relParts[0]];
N = *GetParamVals(m->popSize, chain, state[chain]);
if (!strcmp(mp->ploidy, "Diploid"))
N *= 4.0;
else if (!strcmp(mp->ploidy, "Zlinked"))
N *= 3.0;
else
N *= 2.0;
oldTheta = N * oldRate;
newTheta = N * newRate;
if (!strcmp(mp->growthPr, "Fixed"))
growth = mp->growthFix;
else
growth = *GetParamVals(m->growthRate, chain, state[chain]);
if (LnCoalescencePriorPr (oldT, &oldLnPrior, oldTheta, growth) == ERROR)
{
MrBayesPrint ("%s Problem calculating prior for coalescent process\n", spacer);
return (ERROR);
}
if (LnCoalescencePriorPr (t, &newLnPrior, newTheta, growth) == ERROR)
{
MrBayesPrint ("%s Problem calculating prior for coalescent process\n", spacer);
return (ERROR);
}
(*lnPriorRatio) += newLnPrior - oldLnPrior;
}
/* adjust proposal and prior ratio for relaxed clock models */
for (k = 0; k < treeParam->nSubParams; k++)
{
subParm = treeParam->subParams[k];
if (subParm->paramType == P_CPPEVENTS)
{
nEvents = subParm->nEvents[2*chain+state[chain]];
lambda = *GetParamVals (modelSettings[subParm->relParts[0]].cppRate, chain, state[chain]);
/* proposal ratio */
for (j=0; j<t->nNodes-2; j++)
{
p = t->allDownPass[j];
q = oldT->allDownPass[j];
(*lnProposalRatio) += nEvents[p->index ] * log (p->length / q->length);
}
/* prior ratio */
(*lnPriorRatio) += lambda * (TreeLen(oldT) - TreeLen(t));
/* update effective evolutionary lengths */
if (UpdateCppEvolLengths (subParm, t->root->left, chain) == ERROR)
{
abortMove = YES;
return (NO_ERROR);
}
}
else if ( subParm->paramType == P_TK02BRANCHRATES ||
(subParm->paramType == P_MIXEDBRCHRATES && *GetParamIntVals(subParm, chain, state[chain]) == RCL_TK02))
{
if (subParm->paramType == P_TK02BRANCHRATES)
nu = *GetParamVals (modelSettings[subParm->relParts[0]].tk02var, chain, state[chain]);
else
nu = *GetParamVals (modelSettings[subParm->relParts[0]].mixedvar, chain, state[chain]);
tk02Rate = GetParamVals (subParm, chain, state[chain]);
brlens = GetParamSubVals (subParm, chain, state[chain]);
/* no proposal ratio effect */
/* prior ratio and update of brlens */
for (j = 0; j < t->nNodes-2; j++)
{
p = t->allDownPass[j];
q = oldT->allDownPass[j];
if (p->length > 0.0) // not ancestral fossil
{
(*lnPriorRatio) -= LnProbTK02LogNormal (tk02Rate[q->anc->index], nu*q->length, tk02Rate[q->index]);
(*lnPriorRatio) += LnProbTK02LogNormal (tk02Rate[p->anc->index], nu*p->length, tk02Rate[p->index]);
brlens[p->index] = p->length * (tk02Rate[p->anc->index]+tk02Rate[p->index])/2.0;
}
}
}
else if ( subParm->paramType == P_IGRBRANCHRATES ||
(subParm->paramType == P_MIXEDBRCHRATES && *GetParamIntVals(subParm, chain, state[chain]) == RCL_IGR))
{
if (subParm->paramType == P_IGRBRANCHRATES)
igrvar = *GetParamVals (modelSettings[subParm->relParts[0]].igrvar, chain, state[chain]);
else
igrvar = *GetParamVals (modelSettings[subParm->relParts[0]].mixedvar, chain, state[chain]);
igrRate = GetParamVals (subParm, chain, state[chain]);
brlens = GetParamSubVals (subParm, chain, state[chain]);
/* prior ratio and update of brlens */
for (j = 0; j < t->nNodes-2; j++)
{
p = t->allDownPass[j];
q = oldT->allDownPass[j];
if (p->length > 0.0) // not ancestral fossil
{
(*lnPriorRatio) -= LnProbGamma (q->length/igrvar, q->length/igrvar, igrRate[q->index]);
(*lnPriorRatio) += LnProbGamma (p->length/igrvar, p->length/igrvar, igrRate[p->index]);
brlens[p->index] = igrRate[p->index] * p->length;
}
}
}
}
}
return (NO_ERROR);
}
int Move_CPPEventPosition (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* move the position of one CPP event */
int i, j, k, *nEvents;
MrBFlt pos, temp, **position, **rateMultiplier;
TreeNode *p=NULL, *q;
Tree *t;
/* get the cpp event data */
nEvents = param->nEvents[2*chain+state[chain]];
position = param->position[2*chain+state[chain]];
rateMultiplier = param->rateMult[2*chain+state[chain]];
/* get tree */
t = GetTree (param, chain, state[chain]);
/* pick a branch and an event */
for (i=j=0; i<t->nNodes - 2; i++)
{
p = t->allDownPass[i];
j += nEvents[p->index];
}
if (j == 0)
{
abortMove = YES;
return (NO_ERROR);
}
k = (int) (RandomNumber(seed) * j);
for (i=j=0; i<t->nNodes - 2; i++)
{
p = t->allDownPass[i];
j += nEvents[p->index];
if (j > k)
break;
}
if (position[p->index] == NULL)
getchar();
/* find local index */
k = k - (j - nEvents[p->index]);
/* find new position */
pos = RandomNumber(seed);
if (pos < POS_MIN || 1.0 - pos < POS_MIN)
{
abortMove = YES;
return (NO_ERROR);
}
position[p->index][k] = pos;
/* sort events; bubble sort for now */
for (i=0; i<nEvents[p->index]; i++)
{
for (j=i+1; j<nEvents[p->index]; j++)
{
if (position[p->index][j] < position[p->index][i])
{
temp = position[p->index][i];
position[p->index][i] = position[p->index][j];
position[p->index][j] = temp;
temp = rateMultiplier[p->index][i];
rateMultiplier[p->index][i] = rateMultiplier[p->index][j];
rateMultiplier[p->index][j] = temp;
}
}
}
/* calculate prior and proposal ratio */
(*lnPriorRatio) = (*lnProposalRatio) = 0.0;
/* update branch evolution lengths */
if (UpdateCppEvolLengths (param, p, chain) == ERROR)
{
abortMove = YES;
return (NO_ERROR);
}
/* set update of cond likes down to root */
/* update of crowntree set in UpdateCppEvolLengths */
q = p->anc;
while (q->anc != NULL)
{
q->upDateCl = YES;
q = q->anc;
}
return (NO_ERROR);
MrBayesPrint ("%lf", *mvp); /* just because I am tired of seeing the unused parameter error msg */
}
int Move_CPPRate (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* move the CPP rate (lambda) using multiplier */
int i, j, *nEvents, sumEvents;
MrBFlt oldLambda, newLambda, treeLength, tuning;
Model *mp;
TreeNode *p;
Tree *t;
/* get tuning parameter */
tuning = mvp[0];
/* get model params */
mp = &modelParams[param->relParts[0]];
/* get the CPP rate */
oldLambda = *GetParamVals (param, chain, state[chain]);
/* set new value */
newLambda = oldLambda * exp ((0.5 - RandomNumber(seed))*tuning);
/* reflect if necessary */
while (newLambda < CPPLAMBDA_MIN || newLambda > CPPLAMBDA_MAX)
{
if (newLambda < CPPLAMBDA_MIN)
newLambda = CPPLAMBDA_MIN * CPPLAMBDA_MIN / newLambda;
if (newLambda > CPPLAMBDA_MAX)
newLambda = CPPLAMBDA_MAX * CPPLAMBDA_MAX / newLambda;
}
/* store new value */
(*GetParamVals (param, chain, state[chain])) = newLambda;
/* calculate prior ratio */
(*lnPriorRatio) = 0.0;
for (i=0; i<param->nSubParams; i++)
{
nEvents = param->subParams[i]->nEvents[2*chain+state[chain]];
sumEvents = 0;
t = GetTree (param->subParams[i], chain, state[chain]);
treeLength = 0.0;
for (j=0; j<t->nNodes-2; j++)
{
p = t->allDownPass[j];
sumEvents += nEvents[p->index];
treeLength += p->length;
}
(*lnPriorRatio) += (oldLambda - newLambda) * treeLength;
(*lnPriorRatio) += sumEvents * log (newLambda / oldLambda);
}
/* adjust for prior on cppRate */
if (!strcmp(mp->cppRatePr,"Exponential"))
(*lnPriorRatio) += mp->cppRateExp * (oldLambda - newLambda);
/* calculate proposal ratio */
(*lnProposalRatio) = log (newLambda / oldLambda);
/* we do not need to update likelihoods */
for (i=0; i<param->nRelParts; i++)
{
modelSettings[param->relParts[i]].upDateCl = NO;
}
return (NO_ERROR);
}
int Move_CPPRateMultiplier_M (Param *param, int chain, RandLong *seed, MrBFlt *lnPriorRatio, MrBFlt *lnProposalRatio, MrBFlt *mvp)
{
/* move one CPP rate multiplier using multiplier */
int i, j, k, *nEvents;
MrBFlt newRateMultiplier, oldRateMultiplier, tuning, minM, maxM, sigma, **rateMultiplier;
TreeNode *p = NULL;
ModelInfo *m;
Tree *t;
TreeNode *q;
/* get the tuning parameter */
tuning = mvp[0];
/* get the model settings */
m = &modelSettings[param->relParts[0]];
/* get tree */
t = GetTree (param, chain, state[chain]);
/* get CPP event data */
nEvents = param->nEvents[2*chain+state[chain]];
rateMultiplier = param->rateMult[2*chain+state[chain]];
/* get minimum and maximum of CPP rate multiplier */
minM = param->min;
maxM = param->max;
/* pick a branch and a rateMultiplier */
for (i=j=0; i<t->nNodes - 2; i++)
{
p = t->allDownPass[i];
j += nEvents[p->index];
}
if (j == 0)
{
abortMove = YES;
return (NO_ERROR);
}
k = (int) (RandomNumber(seed) * j);
for (i=j=0; i<t->nNodes - 2; i++)
{
p = t->allDownPass[i];
j += nEvents[p->index];
if (j > k)
break;
}
/* find local index */
k = nEvents[p->index] - (j - k);
/* find new rateMultiplier */
oldRateMultiplier = rateMultiplier[p->index][k];
newRateMultiplier = oldRateMultiplier * (exp (0.5 - RandomNumber(seed) * tuning));
/* reflect if necessary */
while (newRateMultiplier < minM || newRateMultiplier > maxM)
{
if (newRateMultiplier < minM)
newRateMultiplier = minM * minM / newRateMultiplier;