Input files

File content determination via file name extensions

lmt automatically detects the format of input files by the filename extension. Supported extensions are

• ".csv" for ordinary comma separated values ascii text files
• ".blkcsv" for comma separated value ascii text files in block format
• ".bin" for binary files in block format

".csv" files

".csv" files may contain several commented lines at the top only where the comment character is "#".

The type of the file content is determined by its prospective use, that is

• the data file is supposed to contain only real/float numbers which are transferred to integer if required,
• a file containing an ordinary pedigree is supposed to contain only integer numbers,
• a file containing a missing value indicator matrix is supposed to contain only character strings.

data file

lmt accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:

• file must have at least one commented line where the last commented line must containing the column names separated by comma,
• the column names
  • must be alpha-numeric only
  • must not be quoted
  • must be unique
• below the header the data file must contain only numeric values where the decimal separator is a dot(".").

An example for a data file with three columns is shown below.

#y,mu,id
25.0,1,5
33.1,1,6
36.0,1,7
28.3,1,8

co-variance matrix file

A co-variance matrix files must contain a single full squared symmetric matrix, for instance

1.5,0.8,0.1
0.8,2.1,1.1
0.1,1.1,1.9

missing observations indicator files

The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a boolean data type, and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.

For example a data file

#y1,y2,mu,id
25.0,0.0,1,5
0.0,0.8,1,6
36.0,-1.5,1,7
28.3,0.0,1,8

maybe accompanied by a missing value indicator file

#y1,y2
T,F
F,T
T,T
T,F