Output files

lmt generates various output files. The files described below are those maybe relevant to the user. Other output files can be safely deleted after the run.

General output files

lmt.log

General log file always generated. Provides information of the current state of operation.

Operation dependent output files

Solving the mixed model equation system

results.csv

The file contains the solutions for the mixed model equation system. The file has four columns:

• factor name,
• sub-factor name,
• factor level id, and
• solution.

Note that factor name s are derived according to the lmt factor naming convention, and sub-factor name s are user-defined and are extracted from the equation system. Further, the factor level id is the original as provided by the data, pedigree, etc. For variables undergoing polynomial expansions, e.g. sub-factor c in

 y=x*b+age(t(co(p(1,2))))*c+id*u(v(my_var(1)))

the sub-factor name will be expanded as well to sub-factor name_id , where "id" is the polynomial id. For the above example c would be expanded to c_1 and c_2 .

The file has as many records the system has equations. Fixed factor levels which have been omitted due to rank deficiencies are not printed.

PCG solver output files

so_conv.csv

Contains the iteration statistics with columns

• iteration number
• alpha
• beta
• $$||r_i M r_i||$$, where $$M$$ is the preconditioner matrix and $$r_i=Cx_i-b$$ for a system $$Cx=b$$
• convergence criterion CD
• convergence criterion CR
• second per iteration

Intermediate output files

Files from processing pedigrees

"u.d. pedigree name"_sorted.csv

File contains a 3(ordinary pedigree) or 4(probabilistic pedigree) column matrix containing the sorted and renumbered pedigree generated from the original pedigree.

"u.d. pedigree name"_crossref.csv

File contains a vector of original ids of individuals in "u.d. pedigree name"_sorted.csv. That is, the original id individual #1 in "u.d. pedigree name"_sorted.csv is located in record 1 of this file, etc.

"u.d. pedigree name".bin

Block file in binary format containing for blocks:

• a: real vector of diagonal elements of $$A$$
• ai: real vector of diagonal elements of $$A^{-1}$$
• m: real vector of mendelian sampling terms
• pe: 3 column integer matrix of the sorted and renumbered pedigree underlying $$A$$