GenerateMigrationIndividualsOneAtATime: Generate a single a priori PHRAPL model (MigrationIndividual)
In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description Usage Arguments Details Author(s) References Examples

This function creates a single a priori model (migrationIndividual) for a given collapse, n0multiplier, growth, and migration history.

1 2	GenerateMigrationIndividualsOneAtATime(collapseList, n0multiplierList = NULL, growthList = NULL, migrationList = NULL)

`collapseList`	List of collapse histories in the model
`n0multiplierList`	List of population size scalars in the model (if NULL, all are set to 1)
`growthList`	List of growth rate scalars in the model (if NULL, all are set to 0)
`migrationList`	List of migration rate matrices in the model (if NULL, all are set to 0)

The four inputs for this function - collapseList, n0multiplierMap, growthMap, and migrationList - specify parameter indexes for the four major demographic components that can be modeled using PHRAPL.

CollapseList is the only set of parameters that must be specified. This gives a list of collapse history vectors, one vector for each coalescent event in the tree. So, collapseList = list(c(1,1,0),c(2,NA,2)) means that there are two coalescent events: in the first event, population 1 and 2 coalesce while population 3 does not; in the second event, ancestral population 1-2 coalesces with population 3.

The remaining three parameters may be specified or not specified. If not specified, (i.e., set to NULL),then null matrices will be automatically constructed in which all n0multipliers are set to one, and all growth and migration parameters are set to zero.

If specifying n0multiplierList and/or growthList, the format for these is the same as for collapseList, and the available parameters for these must match the splitting history depicted in the collapseList.

MigrationList is a list of migration matrices. There will be one migration matrix for the present generation, plus any historical matrices that apply (there will be as many matrices as there are collapse events). So, in the three population scenario, if there is symmetrical migration between populations 1 and 2 and no historical migration, migrationList will be:

migrationList<-list(
t(array(c(
NA, 1, 0,
1, NA, 0,
0, 0, NA),
dim=c(3,3))),

t(array(c(
NA, NA, 0,
NA, NA, NA,
0, NA, NA),
dim=c(3,3))))

Note that in R, arrays are constructed by reading in values from column 1 first then from column 2, etc. However, it is more intuitive to construct migration matrices by rows (i.e., first listing values for row 1, then row 2, etc). Thus, in the example above, arrays are entered as rows, and then transposed (using "t"). Also, spacing and hard returns can be used to visualize these values in the form of matrices.

Nathan Jackson and Brian O'Meara

O'Meara, B.C., N. Jackson, A. Morales-Garcia, and B. Carstens (2014) Phrapl in prep.

# ##Four population example (with coalescence, growth, and migration parameters)
#
# #Create list of collapse histories
# collapse_1<-c(0,0,1,1)
# collapse_2<-c(2,2,0,NA)
# collapse_3<-c(3,NA,3,NA)
# collapseList<-list(collapse_1,collapse_2,collapse_3)
#
# #Create list of growth histories
# growth_1<-c(0,0,1,1)
# growth_2<-c(0,0,0,NA)
# growth_3<-c(0,NA,0,NA)
# growthList<-list(growth_1,growth_2,growth_3)
#
# #Create list of migration matrices
# migration_1<-t(array(c(
# 	NA, 0, 0, 0,
# 	0, NA, 0, 0,
# 	0, 0, NA, 1,
# 	0, 0, 1, NA),
# dim=c(4,4)))
#
# migration_2<-t(array(c(
# 	NA, 0, 0, NA,
# 	1, NA, 0, NA,
# 	0, 0, NA, NA,
# 	NA,NA,NA, NA),
# dim=c(4,4)))
#
# migration_3<-t(array(c(
# 	NA, NA, 0, NA,
# 	NA, NA, NA,NA,
# 	0,  NA, NA,NA,
# 	NA, NA, NA,NA),
# dim=c(4,4)))
#
# migrationList<-list(migration_1,migration_2,migration_3)
#
# #Run function
# migrationIndividual<-GenerateMigrationIndividualsOneAtATime(collapseList=collapseList,
# growthList=growthList, migrationList=migrationList)



# ##Three population Example (with coalescence and migration parameters)
#
# #Create list of collapse histories
# collapse_1<-c(1,1,0)
# collapse_2<-c(2,NA,2)
# collapseList<-list(collapse_1,collapse_2)
#
# #Create list of migration matrices
# migration_1<-t(array(c(
# 	NA, 2, 1,
# 	2, NA, 1,
# 	1, 1, NA),
# dim=c(3,3)))
#
# migration_2<-t(array(c(
# 	NA, NA, 3,
# 	NA, NA, NA,
# 	3,  NA, NA),
# dim=c(3,3)))
#
# migrationList<-list(migration_1,migration_2)
#
# #Run function
# migrationIndividual<-GenerateMigrationIndividualsOneAtATime(collapseList=collapseList,
# 	migrationList=migrationList)