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updateassignment.c
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/* MigSelect 2013-2019 Arun Sethuraman, Vitor Sousa, Jody Hey */
/* This code was developed based on IMa2 2009-2010 Jody Hey, Rasmus Nielsen and Sang Chul Choi*/
#if !defined(_WIN32) && !defined(_WIN64) && !defined(WIN32) && !defined(WIN64)
/* cr 110524.1 config.h part of Auto make process. File will not be
* included if the NOCONFIG define is set in the makefile. This change
* only affects build on platforms other than Windows.
*/
//#ifndef NOCONFIG
//#include <config.h>
//#endif /* NOCONFIG */
#endif
#include <search.h>
#undef GLOBVARS
#include "imamp.h"
/* #include "imagsl.h" */
#include "update_gtree_common.h"
#include "utilities.h"
#ifdef STRUCTURAMAREMOTERUN
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <errno.h>
#include <string.h>
#include <sys/types.h>
#include <sys/socket.h>
#include <netinet/in.h>
#include <netdb.h>
#include <arpa/inet.h>
#include <sys/wait.h>
#include <signal.h>
#endif /* STRUCTURAMAREMOTERUN */
#include "updateassignment.h"
extern char *outfilename;
extern char *trueassignment;
/* Class Edgemiginfo */
static struct edgemiginfo saoem;
static struct edgemiginfo saosm;
static struct edgemiginfo sanem;
static struct edgemiginfo sansm;
static struct edgemiginfo saoem2;
static struct edgemiginfo sanem2;
static struct edgemiginfo *saoems;
static struct edgemiginfo *sanems;
static struct edgemiginfo *saosms;
static struct edgemiginfo *sansms;
/* Class Nnminus1 */
static double *snnminus1;
/* Class Sbf */
static im_bfupdate sbfold;
static im_bfupdate sbfnew;
/* Class Ginfo */
static im_ginfo *saGiold;
static im_ginfo *saGioldz1;
static im_ginfo *saGioldz2;
static im_ginfo *saGinew;
static im_ginfo *saGinewz1;
static im_ginfo *saGinewz2;
/* Member sasigned */
static double **sassigned;
/* Class Individuals */
static int snind;
static int snind_known;
static int snind_unknown;
static int *sngenes_ind;
static int ssizePi;
static int **sind2gi;
static int *sinds;
static int sci;
/* Class Ptree */
static im_popntree saC; /* _s_tatic _a_ssignment _C_hain */
/* Class Saved */
static im_savedlocus *saT; /* _s_tatic _a_ssignment _T_ree */
static int snasn;
static int *saasn;
static void imaInitEdgemiginfo ();
static void imaFreeEdgemiginfo ();
static void imaIndInit ();
static void imaIndFree ();
static void imaIndSet ();
static void imaIndSetPairs ();
static void imaGtreeReseti ();
static void imaGtreeCopyi ();
static int imaIndN (int k);
static void imaInitNnminus1 ();
static void imaFreeNnminus1 ();
static int imaSbfInit ();
static int imaSbfFree ();
static void imaGinfoInit (im_ginfo **g);
static void imaGinfoFree (im_ginfo **g);
static void imaGinfoReset (im_ginfo *g);
static void imaInitSagi ();
static void imaFreeSagi ();
static double imaGtreeBranchLength (int ci, int li, int ei);
static int imaGtreeSister (int ci, int li, int ei);
static double imaGtreeTime (int ci, int li, int ei);
static int imaGtreeNmig (int ci, int li, int ei);
static void imaGnodePrint_node (FILE *fp, struct edge *gtree, int e);
static void imaGnodePrint (FILE *fp, struct edge *gtree, int e);
static void imaGnodePrint_nodeseq (FILE *fp, struct edge *gtree, int e, int si);
void imaGnodePrintseq (FILE *fp, struct edge *gtree, int e, int si);
static int findperiodoftime (int ci, double ktime);
static double imaAsnValue_mean (int ci, int li);
static void imaPtreeSetIsland ();
static void imaPtreeSet ();
static void imaPtreeUnset ();
static void imaSavedSaveLocusInfo (int ci, int li);
static void imaSavedRestoreLocusInfo (int ci, int li);
static void imaSavedReset (int li);
static void imaSavedInit ();
static void imaSavedFree ();
static int imaSavedSaveBranch (int ci, int li, int ei);
static void imaSavedRestore (int ci, int li);
/* assertgenealogy */
#ifndef NDEBUG
static void assertgenealogylocdiploid (int ci, int li);
static void assertgenealogyindividual (int ci);
static void assertgenealogyedgelabel (int ci, int li, int ei);
static void assertgenealogylabel (int ci);
static void assertgenealogyloclabel (int ci, int li);
static void assertgenealogyultrametric (int ci);
static void assertgenealogylocultrametric (int ci, int li);
static void assertgenealogylocbranch (int ci, int li);
static void assertgenealogybranch (int ci);
static void IMA_check_popn_up (int kprevperiod, int prevpop, int kperiod, int pop);
static void IMA_check_popn_move (int notpop, int kperiod, int pop);
static void assertgenealogyasn (int ci);
#endif /* NDEBUG */
static void removeSpaces (char *s1, const char *s2);
static int im_event_cmp (const void *a, const void *b);
static double relabel (int ci, int *mpart);
static void IMA_edge_fillmiginfo (int ci, int li, int ei,
struct edgemiginfo *em);
void IMA_edge_copynewmig (int ci, int li, struct edgemiginfo *em);
static double imaRandomPickpopn (int *topop, int ci, int pop, int apop);
static double addmigration_relabel (int ci, int li, int newpop,
int oldmigcount,
int *newmigcount,
struct edgemiginfo *olde,
struct edgemiginfo *newe);
static void copy_probcalc_all (struct probcalc *dest, struct probcalc *srce);
static double bfmove (int ci);
static void bfmove_chooseA1 (int ci, int li, im_bfupdate *pbf);
static double bfmove_selectA1 (int ci, int li, im_bfupdate *pbf, double lq);
static int bfmove_chooseAnEdge (int ci, int li, im_bfupdate *pbf, double ct, int pc);
static int bfmove_selectAnEdge (int ci, int li, im_bfupdate *pbf, im_bfupdate *qbf);
static double bfmove_nextI (int ci, int li,
double lq, im_event *ek,
int np, double rates[],
im_ginfo *gk,
im_bfupdate *pbf,
int *ki,
int z1,
char *is_coalesced1,
int *pc1);
static int bfmove_ratesI (double (*r)[],
im_ginfo *gk,
im_ginfo *gkz1,
im_bfupdate *pbf,
int ki,
int pc1);
static void bfmove_ratesIII (double (*rates)[], im_ginfo *gk, im_bfupdate *pbf,
int ki,
int pc1, int pc3);
static void IMA_genealogy_detach (int ci, int li, im_bfupdate *pbf,
int z1);
static int IMA_sbf_c (int ci, int li, int edge, int pi,
int *seqz,
int *n, int **l, int *a);
static int IMA_sbf_m (int edge, int pi, int pj,
int *n, int **l, int *a);
static int IMA_sbf_nsum (im_bfupdate *pbf,
int pc1, int pc3);
static void IMA_sbf_lineages (im_bfupdate *pbf, int ci, int li, int z1);
static void IMA_intervals_collectsbfnew (int ci, int li, im_edgemiginfo *newm3);
static double bfq (im_bfupdate *pbf, im_bfupdate *qbf,
int ci, int li,
im_ginfo *gk,
im_ginfo *gkz1);
static double IMA_choose_migtopop (int *topop, int ki, int pi, im_ginfo *gk);
static void IMA_edgemiginfo_copymig (im_edgemiginfo *em, int ci, int li, int ei);
static void IMA_edgemiginfo_appendmig (im_edgemiginfo *em, int ci, int li, int ei);
static void IMA_genealogy_copymig (int ci, int li, int ei, im_edgemiginfo *em);
static void IMA_genealogy_appendmig (int ci, int li, int sis, im_edgemiginfo *em,
int edge, int down);
static int IMA_intervals_collect (int ci, int li, double upt, double dnt);
static int IMA_genealogy_derivetheta (char w, int ci, int li, int z1);
int IMA_ginfo_computetheta (im_ginfo *gk);
#ifdef DEBUG
static int ran_discrete (int n, ...);
#endif /* DEBUG */
static int ran_discretea (int n, double pr[]);
static int ran_discreteloga (int n, double pr[]);
static int normalizeLoga (int n, double pr[]);
static char* IMA_getIndividualName (int i);
static int IMA_getGenotype (int ii, int li, int *ig1, int *ig2);
static int imaPtreeNsispop (int ci);
static int imaPtreeSispop (int ci, int **s);
int IMA_rgf_setSnasn (int nind, int np);
int IMA_convertStr2Asn (int ncol, int *a, char *s);
int IMA_io_readp_header (char *fname, char **name, int mc);
int IMA_io_readp (char *fname, int ***m, int *mr, int *mc);
int IMA_gusfield_distanceRemoved (int *A, int **m, int nrow, int ncol, double *r);
int IMA_gusfield_distance (int *A, int **m, int nrow, int ncol);
int IMA_gusfield_squaredDistance (int *A, int **m, int nrow, int ncol);
double IMA_gusfield_varianceDistance (int *A, int **m, int nrow, int ncol, double mean);
/*
static int skip_a_line (FILE *fp);
*/
int IMA_gdistanceRemoved (int n, int *Ai, int *Bi, char *Ci);
int IMA_gdistanceOrderNEW (int n, int *Ai, int *Bi, int m, int *od);
int IMA_gdistanceOrder (int n, int *Ai, int *Bi, int m, int *od);
int IMA_gdistance (int n, int *Ai, int *Bi);
int IMA_gdistanceSimple (int n, int *Ai, int *Bi);
int IMA_max_intarray (int n, int *A);
int IMA_permLexSuccessor (int n, int *p);
int IMA_permLexRank (int n, int *p);
int IMA_permLexUnrank (int *p, int n, int r);
int IMA_permFprintf (FILE *fp, int n, int *p);
int IMA_factorial (int n);
void
recordassignment_header (char *fname, int ci, int bIsPerChain)
{
int li;
int ii;
int ei;
int ki;
int li2;
char strName[FNSIZE];
char *assignfilename;
int lenname;
FILE *assignfile = NULL;
FILE *namefile = NULL;
FILE *fpassigngenealogy = NULL;
/* we find individuals for each locus. */
lenname = 30 + strlen (fname);
assignfilename = malloc (lenname * sizeof (char));
if (bIsPerChain == 0)
{
strcpy (assignfilename, fname);
strcat (assignfilename, ".in.p");
assignfile = fopen (assignfilename, "w");
strcpy (assignfilename, fname);
strcat (assignfilename, ".tex");
namefile = fopen (assignfilename, "w");
strcpy (assignfilename, fname);
strcat (assignfilename, ".asn");
}
else
{
sprintf (assignfilename, "%s.%s.asn", fname, C[ci]->name);
}
fpassigngenealogy = fopen (assignfilename, "w");
if (bIsPerChain == 0)
{
if (assignfile == NULL || namefile == NULL)
{
IM_err (IMERR_CREATEFILEFAIL,
"Assignment output file cannot be created: %s",
assignfilename);
}
fprintf (assignfile, "Gen");
fprintf (assignfile, "\tlnL");
}
fprintf (fpassigngenealogy, "Gen");
if (bIsPerChain == 1)
{
fprintf (fpassigngenealogy, "\tbeta");
for (ki = 0; ki < numsplittimes; ki++)
{
fprintf (fpassigngenealogy, "\tt%d", ki);
}
}
fprintf (fpassigngenealogy, "\tlnL");
if (bIsPerChain == 0)
{
fprintf (namefile, "\\begin{tabular}{l}\n");
}
for (ii = 0; ii < snind; ii++)
{
li = 0;
ei = sind2gi[ii][li];
if (!(ei < 0))
{
removeSpaces (strName, L[li].gNames[ei]);
if (bIsPerChain == 0)
{
fprintf (assignfile, "\tP(%s)", strName);
fprintf (namefile, "%s\\tabularnewline\n", strName);
}
fprintf (fpassigngenealogy, "\tP(%s)", strName);
}
else
{
/* If the individual does not have genes at first locus, we look for
* it from the rest of loci. */
for (li2 = 1; li2 < nloci; li2++)
{
ei = sind2gi[ii][li2];
if (!(ei < 0))
{
removeSpaces (strName, L[li2].gNames[ei]);
if (bIsPerChain == 0)
{
fprintf (assignfile, "\tP(%s)", strName);
fprintf (namefile, "%s\\tabularnewline\n", strName);
}
fprintf (fpassigngenealogy, "\tP(%s)", strName);
break;
}
}
}
}
if (bIsPerChain == 0)
{
fprintf (namefile, "\\end{tabular}\n");
fprintf (assignfile, "\n");
}
fprintf (fpassigngenealogy, "\n");
if (bIsPerChain == 0)
{
fclose (assignfile);
assignfile = NULL;
fclose (namefile);
namefile = NULL;
}
fclose (fpassigngenealogy);
fpassigngenealogy = NULL;
free (assignfilename);
assignfilename = NULL;
return;
}
int
IMA_ninds ()
{
assert (snind > 0);
return snind;
}
int
IMA_nindsunknown ()
{
assert (!(snind_unknown < 0));
return snind_unknown;
}
void
recordassignment (char *fname, int ci, int gen, int bIsPerChain)
{
int li;
int ii;
int ei;
int ki;
FILE *assignfile = NULL;
FILE *fpassigngenealogy = NULL;
char assignfilename[FNSIZE];
double pdg;
int *a = NULL;
int *pa;
a = malloc (snind * sizeof (int));
if (bIsPerChain == 0)
{
strcpy (assignfilename, fname);
strcat (assignfilename, ".in.p");
assignfile = fopen (assignfilename, "a");
if (assignfile == NULL)
{
IM_err (IMERR_APPENDFILEFAIL, "Assignment output file cannot be opened: %s", assignfilename);
}
fprintf (assignfile, "%d", gen);
strcpy (assignfilename, fname);
strcat (assignfilename, ".asn");
}
else
{
sprintf (assignfilename, "%s.%s.asn", fname, C[ci]->name);
}
fpassigngenealogy = fopen (assignfilename, "a");
if (fpassigngenealogy == NULL)
{
IM_err (IMERR_APPENDFILEFAIL, "Raw assignment output file cannot be opened: %s", assignfilename);
}
fprintf (fpassigngenealogy, "%d", gen);
if (bIsPerChain == 1)
{
fprintf (fpassigngenealogy, "\t%lf", beta[ci]);
for (ki = 0; ki < numsplittimes; ki++)
{
fprintf (fpassigngenealogy, "\t%lf", C[ci]->tvals[ki]);
}
}
pdg = C[ci]->allpcalc.pdg;
if (bIsPerChain == 0)
{
fprintf (assignfile, "\t%lf", pdg);
}
fprintf (fpassigngenealogy, "\t%lf", pdg);
/* how do I know individuals of a locus? */
pa = a;
for (ii = 0; ii < snind; ii++)
{
li = saC.indlist[ii][0].li;
ei = saC.indlist[ii][0].ei;
*pa = C[ci]->G[li].gtree[ei].pop;
pa++;
}
/* A raw assignment is printed out without RGF conversion. */
pa = a;
for (ii = 0; ii < snind; ii++)
{
fprintf (fpassigngenealogy, "\t%d", *pa);
pa++;
}
fprintf (fpassigngenealogy, "\n");
/* An assignment is printed out with RGF conversion. */
if (bIsPerChain == 0)
{
IMA_rgs_convert (a, snind);
pa = a;
for (ii = 0; ii < snind; ii++)
{
fprintf (assignfile, "\t%d", *pa);
pa++;
}
fprintf (assignfile, "\n");
}
if (bIsPerChain == 0)
{
fclose (assignfile);
assignfile = NULL;
}
fclose (fpassigngenealogy);
fpassigngenealogy = NULL;
free (a);
a = NULL;
return;
}
void
recordassignmentloci (char *fname, int ci)
{
static int gen = 0;
#ifdef DEBUG
int i;
#endif /* DEBUG */
recordassignment (fname, ci, gen, 0);
#ifdef DEBUG
if (numchains > 1)
{
for (i = 0; i < numchains; i++)
{
recordassignment (fname, i, gen, 1);
}
}
#endif /* DEBUG */
gen++;
return;
}
int
skip_a_line (FILE *fp)
{
char c;
c = 'x';
while (c != '\n')
{
c = fgetc(fp);
}
return 0;
}
int
read_int (FILE *fp)
{
int v;
char c;
char *buf;
int len;
int i;
len = 5;
buf = malloc (len * sizeof (char));
c = fgetc (fp);
i = 0;
while (c != '\t' && c != '\n')
{
buf[i++] = c;
if (i == len)
{
len += 5;
buf = realloc (buf, len * sizeof (char));
}
c = fgetc (fp);
}
buf[i] = '\0';
v = atoi (buf);
free (buf);
buf = NULL;
return v;
}
double
read_double (FILE *fp)
{
double v;
char c;
char *buf;
int len;
int i;
len = 5;
buf = malloc (len * sizeof (char));
c = fgetc (fp);
i = 0;
while (c != '\t' && c != '\n')
{
buf[i++] = c;
if (i == len)
{
len += 5;
buf = realloc (buf, len * sizeof (char));
}
c = fgetc (fp);
}
buf[i] = '\0';
v = atof (buf);
free (buf);
buf = NULL;
return v;
}
int
updateassignmentrelabel (int ci)
{
int accp; /* accept (1) or reject (0) */
double logweight; /* MH ratio */
double logU; /* log uniform */
double tpw; /* log [p(G*)/p(G)] */
double migweight; /* hastings ratio for migration update */
struct genealogy *G; /* locus li */
int mpart;
int li;
int nmigaftertreeweight;
/* declarations must precede any statement for compatibility with Visual C++
* compiler */
G = NULL;
if (assignmentoptions[POPULATIONASSIGNMENTCHECKPOINT] == 1)
{
assertgenealogy (ci);
}
if (ci == 0)
{
for (li = 0; li < nloci; li++)
{
L[li].a_rec->upinf[IM_UPDATE_ASSIGNMENT_RELABEL].tries++;
}
}
Cupinf[ci].upinf[IM_UPDATE_ASSIGNMENT_RELABEL].tries++;
/* save the current state of a chain */
for (li = 0; li < nloci; li++)
{
imaSavedReset (li);
imaSavedSaveLocusInfo (ci, li);
copy_treeinfo (&saT[li].savedgweight, &C[ci]->G[li].gweight);
}
copy_treeinfo (&saC.savedallgweight, &C[ci]->allgweight);
copy_probcalc (&saC.savedallpcalc, &C[ci]->allpcalc);
/* the key proposal function of relabel method */
migweight = relabel (ci, &mpart);
if (migweight < REJECTINFINITESITESCONSTANT + 1.0)
{
/* Reject it. */
accp = 0;
}
else
{
accp = 1;
/* compute Metropolis-ratio */
setzero_genealogy_weights (&C[ci]->allgweight);
for (li = 0; li < nloci; li++)
{
setzero_genealogy_weights (&C[ci]->G[li].gweight);
treeweight (ci, li);
sum_treeinfo (&C[ci]->allgweight, &C[ci]->G[li].gweight);
}
/* check if the number of migration events after the call of treeweight is the
* same as the number of migration events from update */
nmigaftertreeweight = 0;
for (li = 0; li < nloci; li++)
{
nmigaftertreeweight += C[ci]->G[li].mignum;
}
assert (nmigaftertreeweight == mpart);
/* We use allgweight to compute allpcalc */
initialize_integrate_tree_prob (ci, &C[ci]->allgweight, &C[ci]->allpcalc);
/* Log[p(G*)] - Log[p(G)] is [[tpw]] */
tpw = C[ci]->allpcalc.probg - saC.savedallpcalc.probg;
logU = log(uniform ());
logweight = beta[ci] * tpw + migweight;
assert (beta[ci] * tpw + migweight > -1e200
&& beta[ci] * tpw + migweight < 1e200);
}
if (accp == 1 && (logweight > 0.0 || logweight > logU))
{
/* accept the update */
accp = 1;
if (ci == 0)
{
for (li = 0; li < nloci; li++)
{
L[li].a_rec->upinf[IM_UPDATE_ASSIGNMENT_RELABEL].accp++;
}
}
Cupinf[ci].upinf[IM_UPDATE_ASSIGNMENT_RELABEL].accp++;
C[ci]->nasn[sbfold.pop]--;
C[ci]->nasn[sbfnew.pop]++;
}
else
{
accp = 0;
for (li = 0; li < nloci; li++)
{
/* restore edges changed during update */
imaSavedRestore (ci, li);
imaSavedRestoreLocusInfo (ci, li);
copy_treeinfo (&C[ci]->G[li].gweight, &saT[li].savedgweight);
}
copy_probcalc (&C[ci]->allpcalc, &saC.savedallpcalc);
copy_treeinfo (&C[ci]->allgweight, &saC.savedallgweight);
}
if (assignmentoptions[POPULATIONASSIGNMENTCHECKPOINT] == 1)
{
assertgenealogy (ci);
}
return accp;
}
double
relabel (int ci, int *mpart)
{
int li;
int ei;
double logprob;
int newpop;
int oldpop;
int oldmigcount[MAXLOCI];
int newmigcount[MAXLOCI];
struct genealogy *G;
struct edge *gtree;
int ii;
int ij;
int nei;
double t;
int ki;
int minki;
int ni;
int down;
/* Pick an individual to relabel. */
if (modeloptions[NOMIGRATION] == 0)
{
ii = snind_known + randposint (snind_unknown);
}
else
{
ni = 0;
for (ii = snind_known; ii < snind; ii++)
{
nei = sngenes_ind[ii];
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
down = C[ci]->G[li].gtree[ei].down;
if (C[ci]->G[li].gtree[down].pop == C[ci]->G[li].gtree[ei].pop)
{
break;
}
}
if (ij == nei)
{
sinds[ni] = ii;
ni++;
}
}
if (ni == 0)
{
logprob = REJECTINFINITESITESCONSTANT;
return logprob;
}
else
{
ii = sinds[randposint (ni)];
}
}
/* relabel the selected genes: newpop is chosen with logprob */
/* we need a list of edge mig info structures */
li = saC.indlist[ii][0].li;
ei = saC.indlist[ii][0].ei;
G = &C[ci]->G[li];
gtree = G->gtree;
oldpop = gtree[ei].pop;
sbfold.pop = oldpop;
if (modeloptions[NOMIGRATION] == 0)
{
logprob = imaRandomPickpopn (&newpop, ci, oldpop, C[ci]->rootpop);
}
else
{
/* We can only move to descendents of the ancestor. */
minki = npops;
nei = sngenes_ind[ii];
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
t = C[ci]->G[li].gtree[ei].time;
ki = findperiodoftime (ci, t);
if (minki > ki)
{
minki = ki;
}
}
/* pop and minki are used to propose a new pop. */
newpop = oldpop;
while (newpop == oldpop)
{
newpop = randposint (npops);
if (saC.popndown[newpop][minki] != saC.popndown[oldpop][minki])
{
newpop = oldpop;
}
}
logprob = 0.0;
}
sbfnew.pop = newpop;
nei = sngenes_ind[ii];
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
imaSavedSaveBranch (ci, li, ei);
}
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
/* This should work with NOMIGRATION. */
IMA_edge_fillmiginfo (ci, li, ei, &saoems[ij]);
}
for (li = 0; li < nloci; li++)
{
oldmigcount[li] = C[ci]->G[li].mignum;
}
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
C[ci]->G[li].gtree[ei].mig[0].mt = -1;
if (modeloptions[NOMIGRATION] == 0)
{
logprob += addmigration_relabel (ci, li, newpop,
oldmigcount[li],
&newmigcount[li],
&saoems[ij], &sanems[ij]);
}
else
{
/* We check if edge's old pop and new pop share the same ancestral
* population.
* FIXME: this will lead to high rejection rates. We may figure out
* which individual can move to other population. We may have to pick
* individuals that can move.
*/
oldmigcount[li] = 0;
newmigcount[li] = 0;
t = C[ci]->G[li].gtree[ei].time;
ki = findperiodoftime (ci, t);
if (saC.popndown[oldpop][ki] != saC.popndown[newpop][ki])
{
/* Proposed label cannot move. */
logprob = REJECTINFINITESITESCONSTANT;
break;
}
}
oldmigcount[li] = newmigcount[li];
}
*mpart = 0;
if (modeloptions[NOMIGRATION] == 0)
{
for (li = 0; li < nloci; li++)
{
*mpart += oldmigcount[li];
}
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
assert (sanems[ij].edgeid == ei);
assert (sanems[ij].li == li);
/* This should work with NOMIGRATION. */
IMA_edge_copynewmig (ci, li, &sanems[ij]);
}
}
if (logprob > REJECTINFINITESITESCONSTANT)
{
for (ij = 0; ij < nei; ij++)
{
li = saC.indlist[ii][ij].li;
ei = saC.indlist[ii][ij].ei;
gtree = C[ci]->G[li].gtree;
gtree[ei].pop = newpop;
}
}
return logprob;
}
void
IMA_edge_fillmiginfo (int ci, int li, int ei,
struct edgemiginfo *em)
{
int i;
int j;
int down; /* down edge */
struct genealogy *G; /* locus li */
struct edge *gtree; /* genealogy of locus li */
G = &(C[ci]->G[li]);
gtree = G->gtree;
down = gtree[ei].down;
/*******************************************************/
/* oldedgemig */
/*******************************************************/
IMA_reset_edgemiginfo (em);
em->li = li;
em->sisid = -1; /* do we need sisid? */
em->edgeid = ei;
em->upt = imaGtreeTime (ci, li, ei);
em->dnt = gtree[ei].time;
em->pop = gtree[ei].pop;
em->temppop = gtree[ei].pop;
em->fpop = gtree[down].pop;
/* b, e, mtimeavail, and mtall are set. */
fillmiginfoperiods (ci, em);
/* migration events are copied */
em->mig[0].mt = -1.0;
for (j = 0; j <= em->b; j++)
{
em->mp[j] = 0;
}
em->mpall = 0;
i = 0;
j = em->b;
while (gtree[ei].mig[i].mt > -0.5)
{
while (gtree[ei].mig[i].mt > C[ci]->tvals[j])
{
j++;
em->mp[j] = 0;
}
em->mp[j]++;
em->mpall++;
em->mig[i] = gtree[ei].mig[i];
i++;
}
em->mig[i].mt = -1;
return;
}
void
IMA_edge_copynewmig (int ci, int li, struct edgemiginfo *em)
{
int i;
int ei;
struct edge *gtree; /* genealogy of locus li */
ei = em->edgeid;
gtree = C[ci]->G[li].gtree;
i = 0;
while (em->mig[i].mt > 0)
{
checkmigt (i, >ree[ei]);
copymig (&(gtree[ei].mig[i]), &(em->mig[i]));
i++;
}
gtree[ei].mig[i].mt = -1;
return;
}
double
imaRandomPickpopn (int *topop, int ci, int pop, int apop)
{
double v;
int n;
int ip;
int pi;
int nzero;
*topop = pop;
n = saC.npopnlist[apop][0];
assert (!(apop < npops));
while (*topop == pop)
{
ip = randposint (n);
*topop = saC.popnlist[apop][0][ip];
}
assert (n > 1);
/* v = -log ((double) (n - 1)); */
nzero = 0;
for (pi = 0; pi < npops; pi++)
{
if (C[ci]->nasn[pi] == 0)
{
nzero++;
}
}
assert (C[ci]->nasn[pop] > 0);
v = 0.0;
if (C[ci]->nasn[pop] == 1 && nzero > 0 && C[ci]->nasn[*topop] > 0)
{
v = log ((double) (nzero + 1.0));
}
else if (C[ci]->nasn[pop] > 1 && nzero > 1 && C[ci]->nasn[*topop] == 0)
{
v = -log ((double) (nzero));
}