coarsen_jsfs {jaatha}

Divides the joint site frequency spectrum (jsfs) into blocks and returns the sum of the jsfs entries for each block.

Description

ja is the jsfs, part a list of vectors specifying for each dimension how ja should be partitioned. If part_hi!=NULL, it is a list spefifying how ja is to be paritioned on the higher end of each dimension. if part or part_hi is not a list, it is turned into a list of the same length as dim(ja), in which each entry is the original part or part_hi e.g. 2,7,9 partitions into 1:2, 3:7, 8:9, 9:N For example, with part=c(1,3) and part_hi=c(1,3) we get the classical jaatha summary statistics. Note, however, that the order in which they appear will be different than in the original jaatha package.

Usage

coarsen_jsfs(ja, part, part_hi = NULL)

Arguments

ja

an array containing the joint site frequency spectrum

part

a vector of integers or a list of vectors of integers. If it is a list, the vector part[[i]] specifies that the i-th dimension of ja should be partitioned into 1:(part[[i]][1]-1), part[[i]][1]:(part[[i]][2]-1), and so on. If part is a vector, it will be used for all dimensions.

part_hi

NULL or a vector of integers or a list of vector of integers indicating the partioning at the higher end of each dimension. This means, if it is a list, the values in the vector dim(ja)[i]-part_hi[[i]] will be appended to the end of part[[i]]. If part_hi is a single vector, it will be used for all dimensions. Thus, with the combination of part=c(1,3) and part_hi=c(1,3), the classical jaatha summary statistics, plus the two values ja[0] and ja[length(ja)]. Note that the order in which they appear will however be different than in the original jaatha summary statistics.

Value

vector of numbers, which are the sums over the blocks of the jsfs for all combinations of partitions

Author(s)

Dirk Metzler & Paul Staab

References

A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose, T. Staedler, W. Stephan, and D. Metzler (2011) Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS One 6(5): e18155