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AFS.c
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AFS.c
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/* AFS.c
These are definitions / methods of the AFS object for a markov chain representation
of the AFS statespace during the coalecsent process
A. Kern 2012
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_matrix_int.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_sf.h>
#include "AFS.h"
#include "adkGSL.h"
//#include "cmc_island_mle.h"
#include "multimin.h"
#include "sites.h"
#include "cs.h"
#include "adkCSparse.h"
#include <glib.h>
afsObject *afsObjectNew(int n1, int n2){
int i;
afsObject *tmp;
tmp = (afsObject *)malloc(sizeof(afsObject));
tmp->popMats =(gsl_matrix_int **) malloc(2* sizeof(gsl_matrix_int));
tmp->popMats[0] = (gsl_matrix_int *) gsl_matrix_int_alloc(n1+1,n2+1);
tmp->popMats[1] = (gsl_matrix_int *) gsl_matrix_int_alloc(n1+1,n2+1);
tmp->npops=2; //unneeded right now but maybe will generalize in the future
tmp->matString = malloc(sizeof(char) * ((n1+1)*(n2+1)*2) + 1);
for(i=0;i<(n1*n2*2);i++){tmp->matString[i] ='\0';}
return(tmp);
}
//afsObjectNewFrom-- creates a deep copy of an afsObject
afsObject *afsObjectNewFrom(afsObject *v){
afsObject *tmp;
tmp = (afsObject *) malloc(sizeof(afsObject));
tmp->popMats = (gsl_matrix_int **) malloc(2* sizeof(gsl_matrix_int));
tmp->popMats[0] = (gsl_matrix_int *)gsl_matrix_int_alloc(v->popMats[0]->size1,v->popMats[0]->size2);
tmp->popMats[1] = (gsl_matrix_int *)gsl_matrix_int_alloc(v->popMats[1]->size1,v->popMats[1]->size2);
tmp->npops=v->npops;
gsl_matrix_int_memcpy(tmp->popMats[0],v->popMats[0]);
gsl_matrix_int_memcpy(tmp->popMats[1],v->popMats[1]);
tmp->nalleles=afsObjectCount(tmp);
tmp->matString = malloc(sizeof(char) * ((v->popMats[0]->size1 +1) * (v->popMats[0]->size2 +1) * 2) + 1);
// for(i=0;i<(v->popMats[0]->size1 * v->popMats[0]->size2 * 2);i++){tmp->matString[i] ='\0';}
tmp->matString[0] ='\0';
return(tmp);
}
void afsObjectFree(afsObject *v){
gsl_matrix_int_free(v->popMats[0]);
gsl_matrix_int_free(v->popMats[1]);
free(v->popMats);
free(v->matString);
free(v);
}
//sets up the initial sample of size n1 from population 1 and size n2 from
// population 2
void afsObjectInit(afsObject *v, int n1, int n2){
int i, j;
char c[1000];
gsl_matrix_int_set_zero(v->popMats[0]);
gsl_matrix_int_set_zero(v->popMats[1]);
gsl_matrix_int_set(v->popMats[0],1,0,n1);
gsl_matrix_int_set(v->popMats[1],0,1,n2);
v->aCounts[0]=n1;
v->aCounts[1]=n2;
v->nalleles = n1 + n2;
for(i=0;i<= n1;i++){
for(j=0;j<=n2;j++){
itoa(gsl_matrix_int_get(v->popMats[0],i,j),c);
strcat(v->matString, c);
itoa(gsl_matrix_int_get(v->popMats[1],i,j),c);
strcat(v->matString, c);
}
}
//printf("from within afsObjInit: %s\n",v->matString);
}
void afsObjectPrint(afsObject *v){
int i, j;
int m1, m2;
m1 = v->popMats[0]->size1;
m2 = v->popMats[0]->size2;
for(i=0;i<m1;i++){
for(j=0;j<m2;j++) printf("%d ",gsl_matrix_int_get(v->popMats[0],i,j));
printf("|| ");
for(j=0;j<m2;j++) printf("%d ",gsl_matrix_int_get(v->popMats[1],i,j));
printf("\n");
}
}
int nDescPop1(afsObject *v){
int sum, i, j;
int m1, m2;
m1 = v->popMats[0]->size1;
m2 = v->popMats[0]->size2;
sum=0;
for(i=0;i<m1;i++){
for(j=0;j<m2;j++){
sum+= gsl_matrix_int_get(v->popMats[0],i,j) * i;
sum+= gsl_matrix_int_get(v->popMats[1],i,j) * i;
}
}
return(sum);
}
int nDescPop2(afsObject *v){
int sum, i, j;
int m1, m2;
m1 = v->popMats[0]->size1;
m2 = v->popMats[0]->size2;
sum=0;
for(i=0;i<m1;i++){
for(j=0;j<m2;j++){
sum+= gsl_matrix_int_get(v->popMats[0],i,j) * j;
sum+= gsl_matrix_int_get(v->popMats[1],i,j) * j;
}
}
return(sum);
}
/*
void gsl_matrix_prettyPrint(gsl_matrix *m){
int i, j;
for(i=0;i<m->size1;i++){
for(j=0;j<m->size2;j++){
printf("%f ",gsl_matrix_get(m,i,j));
}
printf("\n");
}
printf("///////////\n");
}
*/
//compatibleAfsGivenInitial tests if correct number of ancestral lineages
// are present and if each entry is >= 0, i.e. no bogus negative afs cells
int compatibleAfsGivenInitial(afsObject *v, int m1, int m2){
if (nDescPop1(v) == m1 && nDescPop2(v) == m2 && gsl_matrix_int_min(v->popMats[0]) >= 0
&& gsl_matrix_int_min(v->popMats[1]) >= 0)
return(1);
else
return(0);
}
//nonZeroEntries -- fills a 2D list of coords for nonZero entries in matrix
void nonZeroEntries(gsl_matrix_int *m, int **coords, int *count){
int i, j;
*count = 0;
for(i=0;i<m->size1;i++){
for(j=0;j<m->size2;j++){
if(gsl_matrix_int_get(m,i,j) != 0){
coords[*count][0]=i;
coords[*count][1]=j;
*count+=1;
}
}
}
}
//countNegativeEntries-- returns the count of matrix entries < 0
int countNegativeEntries(gsl_matrix_int *m){
int i, j, sum=0;
for(i=0;i<m->size1;i++){
for(j=0;j<m->size2;j++){
if(gsl_matrix_int_get(m,i,j) < 0)
sum+=1;
}
}
return(sum);
}
//entriesGreaterThan -- fills a 2D list of coords for nonZero entries in matrix
void entriesGreaterThan(gsl_matrix_int *m, int **coords, int *count, int cut){
int i, j;
*count = 0;
for(i=0;i<m->size1;i++){
for(j=0;j<m->size2;j++){
if(gsl_matrix_int_get(m,i,j) > cut){
coords[*count][0]=i;
coords[*count][1]=j;
*count+=1;
}
}
}
}
//entriesLessThan -- fills a 2D list of coords for nonZero entries in matrix
void entriesLessThan(gsl_matrix_int *m, int **coords, int *count, int cut){
int i, j;
*count = 0;
for(i=0;i<m->size1;i++){
for(j=0;j<m->size2;j++){
if(gsl_matrix_int_get(m,i,j) < cut){
coords[*count][0]=i;
coords[*count][1]=j;
*count+=1;
}
}
}
}
/* factorials */
double xchoosey(int n, int k){
if(n<k) return(0);
if(n == k || k == 0) return(1);
if(k == 1) return(n);
if(k==2) return((float)n*(n-1.0)/2.0);
return(gsl_sf_choose(n,k));
}
//matrixSum -- just convenience function
int matrixSum(gsl_matrix_int *m){
int i,j, sum=0;
for(i=0;i<m->size1;i++)
for(j=0;j<m->size2;j++)
sum+= gsl_matrix_int_get(m,i,j);
return(sum);
}
//matrixSumDouble -- just convenience function
double matrixSumDouble(gsl_matrix *m){
int i,j;
double sum=0;
for(i=0;i<m->size1;i++)
for(j=0;j<m->size2;j++)
sum+= gsl_matrix_get(m,i,j);
return(sum);
}
//matrixAllGTZ-- again a silly convenience function
int matrixAllGTZ(gsl_matrix_int *m){
int i,j;
for(i=0;i<m->size1;i++)
for(j=0;j<m->size2;j++)
if(gsl_matrix_int_get(m,i,j) <=0)
return(0);
return(1);
}
//afsObjectsEqual -- compares objects based on matrices and nothing more
int afsObjectsEqual(afsObject *a, afsObject *b){
if(gsl_matrix_int_equal(a->popMats[0],b->popMats[0])
&& gsl_matrix_int_equal(a->popMats[1],b->popMats[1]))
return(1);
else
return(0);
}
int afsObjectQsortCompare(const void *p1, const void *p2){
afsObject **x = (afsObject **)p1;
afsObject **y = (afsObject **)p2;
if((*x)->nalleles < (*y)->nalleles)
return 1;
else if ((*x)->nalleles > (*y)->nalleles)
return -1;
else
return 0;
}
//subtracts matrices from one another to aid in ID of operations
afsObject *afsObjectDelta(afsObject *a, afsObject *b){
afsObject *tmp;
tmp = afsObjectNewFrom(a);
gsl_matrix_int_memcpy(tmp->popMats[0],a->popMats[0]);
gsl_matrix_int_memcpy(tmp->popMats[1],a->popMats[1]);
gsl_matrix_int_sub(tmp->popMats[0],b->popMats[0]);
gsl_matrix_int_sub(tmp->popMats[1],b->popMats[1]);
return(tmp);
}
//subtracts matrices from one another to aid in ID of operations
void afsObjectDeltaPre(afsObject *a, afsObject *b,afsObject *tmp){
gsl_matrix_int_memcpy(tmp->popMats[0],a->popMats[0]);
gsl_matrix_int_memcpy(tmp->popMats[1],a->popMats[1]);
gsl_matrix_int_sub(tmp->popMats[0],b->popMats[0]);
gsl_matrix_int_sub(tmp->popMats[1],b->popMats[1]);
}
//afsObjectCount-- returns the total number of lineages in the afs state
int afsObjectCount(afsObject *a){
return(matrixSum(a->popMats[0])+matrixSum(a->popMats[1]));
}
afsStateSpace *afsStateSpaceNew(){
afsStateSpace *tmp;
tmp =(afsStateSpace *) malloc(sizeof(afsStateSpace));
tmp->nstates=0;
tmp->states = (afsObject **) malloc(MAXSTATES * sizeof(afsObject));
tmp->stateHash = g_hash_table_new(g_str_hash, g_str_equal);
return(tmp);
}
afsStateSpace *afsStateSpaceCopy(afsStateSpace *S){
int i;
afsStateSpace *tmp;
tmp =(afsStateSpace *) malloc(sizeof(afsStateSpace));
tmp->nstates=S->nstates;
tmp->states = (afsObject **) malloc(MAXSTATES * sizeof(afsObject));
for(i=0;i<S->nstates;i++) tmp->states[i] = S->states[i];
// tmp->stateHash = g_hash_table_new(g_str_hash, g_str_equal);
return(tmp);
}
void afsStateSpaceFree(afsStateSpace *a){
int i;
for(i=0;i<a->nstates;i++)afsObjectFree(a->states[i]);
free(a->states);
// for(i=0;i<MAXSIZE;i++){
// free(a->nstateArray[i]);
// for(j=0;j<MAXSIZE;j++){
// free(a->tmpStorage[i][j]);
// }
// free(a->tmpStorage[i]);
// }
// free(a->tmpStorage);
// free(a->nstateArray);
g_hash_table_destroy(a->stateHash);
free(a);
}
//afsStateSpaceContainsState-- linear search for state
int afsStateSpaceContainsState(afsStateSpace *S, afsObject *aState){
int i;
for(i = S->nstates -1 ; i > - 1;i--){
if(S->states[i]->nalleles == aState->nalleles)
if(S->states[i]->aCounts[0] == aState->aCounts[0])
if(afsObjectsEqual(S->states[i],aState))
return(1);
}
return(0);
}
/////// Below is not needed with hash implementation
//afsStateSpaceContainsStateTmpStorage-- same as above but works off of stateSpace->tmpStorage
// int afsStateSpaceContainsStateTmpStorage(afsStateSpace *S, afsObject *aState){
// int i;
// for(i = S->nstateArray[aState->nalleles][aState->aCounts[0]] -1 ; i > - 1;i--){
// if(afsObjectsEqual(S->tmpStorage[aState->nalleles][aState->aCounts[0]][i],aState))
// return(1);
// }
// return(0);
// }
//afsStateSpaceRemoveAbsorbing-- removes all absorbing states
void afsStateSpaceRemoveAbsorbing(afsStateSpace *S){
int i,ii;
afsObject *tmp;
i = 0;
while(i < S->nstates){
if(S->states[i]->nalleles == 1){
tmp = S->states[i];
for(ii=i;ii<S->nstates - 1;ii++) S->states[ii] = S->states[ii+1];
S->nstates--;
i-=1;
afsObjectFree(tmp);
}
i+=1;
}
}
//afsStateSpaceMapPopn-- returns a vector mapping each state to its state if popn1 collapsed into popn0
void afsStateSpaceMapPopn(afsStateSpace *S, int *map){
int i, j,valCount,valInd[S->nstates / 2];
afsObject *tmp, *test;
tmp = afsObjectNewFrom(S->states[0]);
gsl_matrix_int_set_zero(tmp->popMats[1]);
//find and count valid states
valCount = 0;
for(i=0;i<S->nstates;i++){
if(S->states[i]->aCounts[1]==0){
valInd[valCount]=i;
valCount++;
}
}
for(i=0;i<S->nstates;i++){
if(S->states[i]->aCounts[1]==0){
map[i]=i;
}
else{
//create folded state in tmp
gsl_matrix_int_memcpy(tmp->popMats[0],S->states[i]->popMats[0]);
gsl_matrix_int_add(tmp->popMats[0],S->states[i]->popMats[1]);
//go through valid ones to find it
for(j=0;j<valCount;j++){
test= S->states[valInd[j]];
if(S->states[i]->nalleles == test->nalleles)
if(gsl_matrix_int_equal(tmp->popMats[0],test->popMats[0]))
map[i]=valInd[j];
}
}
}
}
//afsStateSpaceMapAndReducePopn-- returns a vector mapping each state to its state if popn1 collapsed into popn0 (map)
//adds valid states to new reducedSpace, also fills reverseMap to larger space indexing
//reducedSpace is passed as ptr, assumed to be empty, initial stateSpace
void afsStateSpaceMapAndReducePopn(afsStateSpace *S, int *map, afsStateSpace *reducedSpace, int *reverseMap){
int i, j,valCount,valInd[S->nstates / 2];
afsObject *tmp, *test;
tmp = afsObjectNewFrom(S->states[0]);
gsl_matrix_int_set_zero(tmp->popMats[1]);
//find and count valid states
valCount = 0;
for(i=0;i<S->nstates;i++){
if(S->states[i]->aCounts[1]==0){
valInd[valCount]=i;
reverseMap[valCount]=i;
reducedSpace->states[valCount]=S->states[i];
reducedSpace->nstates++;
valCount++;
}
}
for(i=0;i<S->nstates;i++){
if(S->states[i]->aCounts[1]==0){
map[i]=i;
}
else{
//create folded state in tmp
gsl_matrix_int_memcpy(tmp->popMats[0],S->states[i]->popMats[0]);
gsl_matrix_int_add(tmp->popMats[0],S->states[i]->popMats[1]);
//go through valid ones to find it
for(j=0;j<valCount;j++){
test= S->states[valInd[j]];
if(S->states[i]->nalleles == test->nalleles)
if(gsl_matrix_int_equal(tmp->popMats[0],test->popMats[0]))
map[i]=valInd[j];
}
}
}
afsObjectFree(tmp);
}
//afsStateSpaceRemovePopulation-- removes all states with members in specified popn
void afsStateSpaceRemovePopulation(afsStateSpace *S, int popn){
int i,ii;
afsObject *tmp;
i = 0;
while(i < S->nstates){
if(S->states[i]->aCounts[1] > 0){
tmp = S->states[i];
for(ii=i;ii<S->nstates - 1;ii++) S->states[ii] = S->states[ii+1];
S->nstates--;
i-=1;
afsObjectFree(tmp);
}
i+=1;
}
}
afsStateSpace *afsStateSpaceImportFromFile(const char *fileName){
int m1,m2,ns;
int i,j,l,c;
char *tmp;
FILE *infile;
afsStateSpace *newStateSpace;
// afsObject *newObj;
int linebuf = 10000;
char line[linebuf+1],*token, search[]=" ";
//open file
infile = fopen(fileName, "r");
if (infile == NULL){
fprintf(stderr,"Error opening infile! ARRRRR!!!!\n");
exit(1);
}
//initialization
//define state space size and shape
c=fscanf(infile,"n1: %d n2: %d nstates: %d", &m1, &m2, &ns);
newStateSpace = afsStateSpaceNew();
newStateSpace->nstates = ns;
tmp=fgets(line,linebuf,infile);
if (tmp == NULL || c == 0){
fprintf(stderr,"Error peaking in infile!\n");
exit(1);
}
for(l=0;l<ns;l++){
newStateSpace->states[l] = afsObjectNew(m1,m2);
for(i=0;i<m1+1;i++){
tmp=fgets(line,linebuf,infile);
// printf("%s\n",line);
// printf("----\n");
token = strtok(line,search);
gsl_matrix_int_set(newStateSpace->states[l]->popMats[0],i,0,atoi(token));
for(j=1;j<m2+1;j++){
token = strtok(NULL,search);
// printf("%s\n",token);
gsl_matrix_int_set(newStateSpace->states[l]->popMats[0],i,j,atoi(token));
}
token = strtok(NULL,search);
for(j=0;j<m2+1;j++){
token = strtok(NULL,search);
gsl_matrix_int_set(newStateSpace->states[l]->popMats[1],i,j,atoi(token));
}
}
tmp=fgets(line,linebuf,infile);
newStateSpace->states[l]->aCounts[0] = matrixSum(newStateSpace->states[l]->popMats[0]);
newStateSpace->states[l]->aCounts[1] = matrixSum(newStateSpace->states[l]->popMats[1]);
newStateSpace->states[l]->nalleles = afsObjectCount(newStateSpace->states[l]);
// afsObjectPrint(newStateSpace->states[l]);
// printf("+++++\n");
}
fclose(infile);
return(newStateSpace);
}
//mcMatsImportFromFile -- reads in the Topology and MoveType matrices output by cmc_printMCMats program
// this function only fills preallocated arrays and sets nnz
void mcMatsImportFromFile(const char *fileName,int *nnz,double *topol, int *moveA, int *dim1, int *dim2){
int i,c;
FILE *infile;
//open file
infile = fopen(fileName, "r");
if (infile == NULL){
fprintf(stderr,"Error opening infile! ARRRRR!!!!\n");
exit(1);
}
//initialization
c=fscanf(infile,"nnz: %d", nnz);
for(i=0;i<*nnz;i++){
c=fscanf(infile,"%lf\t%d\t%d\t%d\n",&topol[i],&moveA[i],&dim1[i],&dim2[i]);
}
fclose(infile);
}
//acceptOrRejectProposedState-- tests if candidate state in valid and not yet represented
// in the afsStateSpace object. Adds to array if true and iterates nstates. Free's candidate if
// false
void acceptOrRejectProposedState(afsStateSpace *S, afsObject *child, int n1, int n2){
int i,j;
char c[10];
child->nalleles=afsObjectCount(child);
child->aCounts[0]=matrixSum(child->popMats[0]);
child->aCounts[1]=matrixSum(child->popMats[1]);
for(i=0;i <= n1;i++){
for(j=0;j <= n2;j++){
itoa(gsl_matrix_int_get(child->popMats[0],i,j),c);
strcat(child->matString, c);
itoa(gsl_matrix_int_get(child->popMats[1],i,j),c);
strcat(child->matString, c);
}
}
// printf("%s\n",child->matString);
//Below block is the old way. new way is hash implementation
// if(compatibleAfsGivenInitial(child, n1,n2) == 1
// && afsStateSpaceContainsStateTmpStorage(S,child) == 0){
// //add in new state
//
// S->states[S->nstates]=child;
// S->nstates++;
// S->tmpStorage[child->nalleles][child->aCounts[0]][S->nstateArray[child->nalleles][child->aCounts[0]]] = child;
// S->nstateArray[child->nalleles][child->aCounts[0]]++;
//check to make sure state array can keep up!
// if(S->nstates==MAXSTATES){
// MAXSTATES = 2*MAXSTATES;
// S->states = realloc(S->states, MAXSTATES * sizeof(child));
// }
if(g_hash_table_lookup(S->stateHash, child->matString) == NULL
&& compatibleAfsGivenInitial(child, n1,n2) == 1){
//add in new state
S->states[S->nstates]=child;
S->nstates++;
g_hash_table_insert(S->stateHash, child->matString, "TRUE");
//recurse!
preorderEvolveState(S, child, n1,n2);
}
else{
afsObjectFree(child);
}
}
//preorderEvolveState -- this is the workhorse that fills the entire state space
// currently this only handles coalescent and migration events for 2 populations
void preorderEvolveState(afsStateSpace *S, afsObject *aState, int n1, int n2){
int i,j, nlin1,nlin2, tmp1, tmp2;
int **activePos1, **activePos2; //first dimension here relates to 2 popns
afsObject *child;
activePos1 = malloc(100*sizeof(int *));
activePos2 = malloc(100*sizeof(int *));
for(i=0;i<100;i++){
activePos1[i] = malloc(2*sizeof(int));
activePos1[i][0] = activePos1[i][1] = 0;
activePos2[i] = malloc(2*sizeof(int));
activePos2[i][0] = activePos2[i][1] = 0;
}
nonZeroEntries(aState->popMats[0], activePos1, &nlin1);
nonZeroEntries(aState->popMats[1], activePos2, &nlin2);
//coalescent in Popn 1?
if(matrixSum(aState->popMats[0]) > 1){
//coalescent is possible; permutations of lineages
for(i=0;i<nlin1;i++){
for(j=0;j<nlin1;j++){
if( i != j || gsl_matrix_int_get(aState->popMats[0],activePos1[i][0],activePos1[i][1]) > 1){
child = afsObjectNewFrom(aState);
//get and set below is ugly... basically subtract one from each of coal lineages add one
//to new lineage
gsl_matrix_int_set(child->popMats[0],activePos1[i][0],
activePos1[i][1], gsl_matrix_int_get(child->popMats[0],
activePos1[i][0],activePos1[i][1]) - 1);
gsl_matrix_int_set(child->popMats[0],activePos1[j][0],
activePos1[j][1], gsl_matrix_int_get(child->popMats[0],
activePos1[j][0],activePos1[j][1]) - 1);
tmp1 = activePos1[i][0] + activePos1[j][0];
tmp2 = activePos1[i][1] + activePos1[j][1];
gsl_matrix_int_set(child->popMats[0],tmp1,
tmp2, gsl_matrix_int_get(child->popMats[0],
tmp1,tmp2) + 1);
//now check state for compatibilty
acceptOrRejectProposedState(S,child, n1, n2);
}
}
}
}
//coalescent in Popn 2?
if(matrixSum(aState->popMats[1]) > 1){
//coalescent is possible; permutations of lineages
for(i=0;i<nlin1;i++){
for(j=0;j<nlin1;j++){
if( i != j || gsl_matrix_int_get(aState->popMats[1],activePos2[i][0],activePos2[i][1]) > 1){
child = afsObjectNewFrom(aState);
//get and set below is ugly... basically subtract one from each of coal lineages add one
//to new lineage
gsl_matrix_int_set(child->popMats[1],activePos2[i][0],
activePos2[i][1], gsl_matrix_int_get(child->popMats[1],
activePos2[i][0],activePos2[i][1]) - 1);
gsl_matrix_int_set(child->popMats[1],activePos2[j][0],
activePos2[j][1], gsl_matrix_int_get(child->popMats[1],
activePos2[j][0],activePos2[j][1]) - 1);
tmp1 = activePos2[i][0] + activePos2[j][0];
tmp2 = activePos2[i][1] + activePos2[j][1];
gsl_matrix_int_set(child->popMats[0],tmp1,
tmp2, gsl_matrix_int_get(child->popMats[0],
tmp1,tmp2) + 1);
//now check state for compatibilty
acceptOrRejectProposedState(S,child, n1, n2);
}
}
}
}
//migration from Pop1 to Popn 2
for(i=0;i<nlin1;i++){
child = afsObjectNewFrom(aState);
gsl_matrix_int_set(child->popMats[0],activePos1[i][0],
activePos1[i][1], gsl_matrix_int_get(child->popMats[0],
activePos1[i][0],activePos1[i][1]) - 1);
gsl_matrix_int_set(child->popMats[1],activePos1[i][0],
activePos1[i][1], gsl_matrix_int_get(child->popMats[1],
activePos1[i][0],activePos1[i][1]) + 1);
//now check state for compatibilty
//now check state for compatibilty
acceptOrRejectProposedState(S,child, n1, n2);
}
//migration from Pop2 to Popn 1
for(i=0;i<nlin2;i++){
child = afsObjectNewFrom(aState);
gsl_matrix_int_set(child->popMats[1],activePos2[i][0],
activePos2[i][1], gsl_matrix_int_get(child->popMats[1],
activePos2[i][0],activePos2[i][1]) - 1);
gsl_matrix_int_set(child->popMats[0],activePos2[i][0],
activePos2[i][1], gsl_matrix_int_get(child->popMats[0],
activePos2[i][0],activePos2[i][1]) + 1);
//now check state for compatibilty
//now check state for compatibilty
acceptOrRejectProposedState(S,child, n1, n2);
}
//cleanup and free
for(i=0;i<100;i++){
free(activePos1[i]);
free(activePos2[i]);
}
free(activePos1);
free(activePos2);
}
/////coalMarkovChainTopologyMatrix -- using a previously calculated state space
//this fills a matrix of topological moves possible in the markov chain,
//along with a lookup table of moves that are parameter dependant
//
// codes for lookup ::
// -1 : absorb
// 0 : coal popn0
// 1 : coal popn1
// 2 : mig popn0
// 3 : mig popn2
// 666: incompatible move
void coalMarkovChainTopologyMatrix(afsStateSpace *S,gsl_matrix *topol, gsl_matrix_int *moveType, int n1, int n2){
int i,j,k,steps,x,y;
double top,bottom;
afsObject *delta;
int **activePos1, **activePos2; //first dimension here relates to 2 popns
int nlin1,nlin2,compat;
if(S->nstates != topol->size1 || S->nstates != moveType->size1){
fprintf(stderr,"Error: StateSpace and matrices are not of equal size\n");
exit(1);
}
//arrays for finding positions of entries
activePos1 = malloc(100*sizeof(int *));
activePos2 = malloc(100*sizeof(int *));
for(i=0;i<100;i++){
activePos1[i] = malloc(2*sizeof(int));
activePos1[i][0] = activePos1[i][1] = 0;
activePos2[i] = malloc(2*sizeof(int));
activePos2[i][0] = activePos2[i][1] = 0;
}
for(i=0;i<S->nstates;i++){
for(j=0;j<S->nstates;j++){
gsl_matrix_int_set(moveType,i,j,666);
//is ith state root state?
if(S->states[i]->nalleles == 1){
//set correct absorbing conditions
if(i==j){
gsl_matrix_set(topol,i,j,1.0);
gsl_matrix_int_set(moveType,i,j,-1);
}
else{
gsl_matrix_set(topol,i,j,0.0);
gsl_matrix_int_set(moveType,i,j,-1);
}
}
else{ //ith not root; what is the move?
delta = afsObjectDelta(S->states[i],S->states[j]);
steps = S->states[i]->nalleles - S->states[j]->nalleles ;
// printf("i:%d j:%d steps:%d\n",i,j,steps);
switch(steps){
case 0:
// 0 "steps", so no changes in nalleles between two
//check counts and positions
if(abs(matrixSum(delta->popMats[0])) == 1){
nonZeroEntries(delta->popMats[0], activePos1, &nlin1);
nonZeroEntries(delta->popMats[1], activePos2, &nlin2);
//exit(1);
//migration?
if(nlin1 == nlin2 && activePos1[0][0] == activePos2[0][0] &&
(gsl_matrix_int_min(delta->popMats[0]) >= 0 || gsl_matrix_int_min(delta->popMats[1]) >= 0))
{
//migration popn1?
if(matrixSum(delta->popMats[0]) == 1){
gsl_matrix_set(topol,i,j,
(double) gsl_matrix_int_get(S->states[i]->popMats[0],
activePos1[0][0], activePos1[0][1]) / S->states[i]->aCounts[0]);
gsl_matrix_int_set(moveType,i,j,2);
}
else{ //migration popn2
// printf("here %d %d %d\n",activePos2[0][0],activePos2[0][1], S->states[i]->aCounts[1]);
gsl_matrix_set(topol,i,j,
(double) gsl_matrix_int_get(S->states[i]->popMats[1],
activePos2[0][0],activePos2[0][1]) / S->states[i]->aCounts[1]);
gsl_matrix_int_set(moveType,i,j,3);
}
}
}
break;
case 1://coalescent?
//coal popn1?
if(matrixSum(delta->popMats[0]) == 1 && countNegativeEntries(delta->popMats[1]) == 0 && S->states[j]->aCounts[0] >= 1
/*((matrixAllGTZ(delta->popMats[0]) || matrixAllGTZ(delta->popMats[1]))) */ ){
// afsObjectPrint(S->states[i]);
// printf("1///////////\n");
// afsObjectPrint(S->states[j]);
// printf("2///////////\n");
entriesGreaterThan(delta->popMats[0], activePos1, &nlin1,0);//old lineages
entriesLessThan(delta->popMats[0], activePos2, &nlin2,0);//new lineages
if(nlin2 != 0 && nlin2 < 2){
compat=0;
if(nlin1 == 1){
if(2*activePos1[0][0] == activePos2[0][0] && 2*activePos1[0][1] == activePos2[0][1])
compat = 1;
}
if(nlin1==2){
if(activePos1[0][0] + activePos1[1][0] == activePos2[0][0] &&
activePos1[0][1] + activePos1[1][1] == activePos2[0][1])
compat = 1;
}
if(compat != 1){
gsl_matrix_set(topol,i,j,0.0);
gsl_matrix_int_set(moveType,i,j,666);
}
else{
top = 1.0;
bottom = S->states[i]->aCounts[0] * (S->states[i]->aCounts[0]-1) /2.0 ;
for(k=0;k<nlin1;k++){
x = activePos1[k][0];
y = activePos1[k][1];
top *= (float) xchoosey(gsl_matrix_int_get(S->states[i]->popMats[0],x,y),
gsl_matrix_int_get(delta->popMats[0],x,y));
// printf("x: %d y: %d bottom: %0.2f top:%0.2f aCounts[0]: %d delta: %d foo:%d choose: %lf\n",x,y,bottom,top,S->states[i]->aCounts[0],gsl_matrix_int_get(delta->popMats[0],x,y),gsl_matrix_int_get(S->states[i]->popMats[0],x,y),xchoosey(3,2));
}
gsl_matrix_set(topol,i,j,top/bottom);
gsl_matrix_int_set(moveType,i,j,0);
}
}
}
else{
if(matrixSum(delta->popMats[1]) == 1 && countNegativeEntries(delta->popMats[0]) == 0 && S->states[j]->aCounts[1] >= 1
/*((matrixAllGTZ(delta->popMats[0]) || matrixAllGTZ(delta->popMats[1]))) */ ){
// afsObjectPrint(S->states[i]);
// printf("1///////////\n");
// afsObjectPrint(S->states[j]);
// printf("2///////////\n");
entriesGreaterThan(delta->popMats[1], activePos1, &nlin1,0);//old lineages
entriesLessThan(delta->popMats[1], activePos2, &nlin2,0);//new lineages
if(nlin2 != 0 && nlin2 < 2){
compat=0;
if(nlin1 == 1){
if(2*activePos1[0][0] == activePos2[0][0] && 2*activePos1[0][1] == activePos2[0][1])
compat = 1;
}
if(nlin1==2){
if(activePos1[0][0] + activePos1[1][0] == activePos2[0][0] &&
activePos1[0][1] + activePos1[1][1] == activePos2[0][1])
compat = 1;
}
if(compat != 1){
gsl_matrix_set(topol,i,j,0.0);
gsl_matrix_int_set(moveType,i,j,666);
}
else{
top = 1.0;
bottom = S->states[i]->aCounts[1] * (S->states[i]->aCounts[1]-1) /2.0 ;
for(k=0;k<nlin1;k++){
x = activePos1[k][0];
y = activePos1[k][1];
top *= xchoosey(gsl_matrix_int_get(S->states[i]->popMats[1],x,y),
gsl_matrix_int_get(delta->popMats[1],x,y));
// top *= gsl_matrix_int_get(S->states[i]->popMats[1],x,y);
// printf("x: %d y: %d bottom: %0.2f top:%0.2f aCounts[1]: %d delta: %d\n",x,y,bottom,top,S->states[i]->aCounts[1],gsl_matrix_int_get(delta->popMats[1],x,y));
}
gsl_matrix_set(topol,i,j,top/bottom);
gsl_matrix_int_set(moveType,i,j,1);
}
}
}
}
break;
}
afsObjectFree(delta);
}
}
}
//cleanup and free
for(i=0;i<100;i++){
free(activePos1[i]);
free(activePos2[i]);
}
free(activePos1);
free(activePos2);
}
//fills and transition matrix along with a vector of rates for use with calculating expected times
void fillTransitionMatrix(afsStateSpace *S, gsl_matrix *topol, gsl_matrix_int *moveType, gsl_matrix *transMat, gsl_vector *rates,
double theta1, double theta2, double mig1, double mig2){
int i, j;
double c0r,c1r,m0r,m1r,totR;
gsl_matrix_set_zero(transMat);
for(i=0;i<topol->size1;i++){
c0r = S->states[i]->aCounts[0] * (S->states[i]->aCounts[0]-1) / theta1 ;
c1r = S->states[i]->aCounts[1] * (S->states[i]->aCounts[1]-1) / theta2;
m0r = S->states[i]->aCounts[0] * mig1 ;
m1r = S->states[i]->aCounts[1] * mig2 ;
totR = c0r + c1r + m0r + m1r;
if(S->states[i]->nalleles > 1 && c0r >= 0 && c1r >= 0)
gsl_vector_set(rates,i,1.0/totR);
else
gsl_vector_set(rates,i,0);
for(j=0;j<topol->size2;j++){
switch(gsl_matrix_int_get(moveType,i,j)){
// case 666:
// gsl_matrix_set(transMat,i,j,0);
break;
case 0: //coal pop0
gsl_matrix_set(transMat,i,j,c0r / totR * gsl_matrix_get(topol,i,j));
break;
case 1: //coal pop1
gsl_matrix_set(transMat,i,j,c1r / totR * gsl_matrix_get(topol,i,j));
break;
case 2: //mig pop0
gsl_matrix_set(transMat,i,j,m0r / totR * gsl_matrix_get(topol,i,j));
break;
case 3: //mig pop1
gsl_matrix_set(transMat,i,j,m1r / totR * gsl_matrix_get(topol,i,j));
// printf("case3 -- tot:%f c0r: %f c1r: %f m0r: %f m1r: %f res:%f\n",
// totR,c0r,c1r,m0r,m1r,gsl_matrix_get(transMat,i,j));
break;
case -1: //absorb state
gsl_matrix_set(transMat,i,j, gsl_matrix_get(topol,i,j));
break;
}
}
}
}
//fills up an AFS matrix using expected times
void fillExpectedAFS(afsStateSpace *S, gsl_matrix *transMat,gsl_vector *rates, gsl_matrix *expAFS, int m1, int m2){
int i, j, k, l, its, count;
gsl_matrix *tmIt, *tmp, *times;
gsl_vector *means;
double tmpRes,max = 0.0;
its = 30;
//set up matrices make copy of transMat
tmIt = gsl_matrix_alloc(transMat->size1,transMat->size2);
tmp = gsl_matrix_alloc(transMat->size1,transMat->size2);
times = gsl_matrix_alloc(transMat->size1, its);
means = gsl_vector_alloc(its);