Data_files

Data files

The ASCII model data files *.dat, *.csv or *.txt are used for model fitting and the data can be delimited by a space, a comma, or a tab. The first row should identify the column names and must be preceded by ##. For example, the first row of the example Theophylline dataset listed below looks like this:

     ## id, wt, dose, time, conc.

Only the period “.” character is an acceptable decimal separator.

Note: When using Phoenix, the column header line in a PML dataset must be preceded by ## or Phoenix will not recognize the column headers.

Each subsequent row must contain data for each field. Use a period “.” to represent a null value. The data for the first subject in the example Theophylline dataset thbates.dat (found in …\Examples\NLME\Command Line\Model 3 or Model 4) are shown below.

     thbates.dat 
       ## xid  wt  dose time   yobs
           1  79.6 4.02    0    .74
           1  79.6 4.02   .25  2.84
           1  79.6 4.02   .57  6.57
           1  79.6 4.02  1.12 10.5
           1  79.6 4.02  2.02  9.66
           1  79.6 4.02  3.82  8.58
           1  79.6 4.02  5.1   8.36
           1  79.6 4.02  7.03  7.47
           1  79.6 4.02  9.05  6.89
           1  79.6 4.02 12.12  5.94
           1  79.6 4.02 24.37  3.28

Dataset row limitations

Most of the memory is allocated and de-allocated dynamically as needed. In most cases, peak total memory demands for the engines are easily accommodated within the memory available on modern computers (typically at least one gigabyte of memory per processor). However, there are still several static limits on model parameters.

Maximum number of subjects=120,000 (This limit applies to all engines except the nonparametric engine, where the maximum number of subjects is 1000.)

Maximum number of observations per subject=unlimited (See limit on total number of observations below.)

Maximum total number of observations=480,000

Maximum number of thetas (fixed effects)=1000 (This includes both fixed effects that are frozen to a user-specified value, as well as free fixed effects that are included in the likelihood optimization, which is given below as 401.)

Maximum number of etas (random effects)=101 (This is also the maximum dimension of the Omega matrix in the diagonal case. Although, if Omega has a full or partial block structure, the maximum dimension will be less (see remarks below for free parameters).)

Maximum number of free parameters to be optimized=401 (This includes both free fixed effect, residual error model, and Omega parameters. Only non-zero Omega parameters on and below the diagonal are counted against this limit. Thus, a full block matrix with Neta random effects will consume Neta*(Neta+1)/2 of these parameters, while a diagonal matrix will only consume Neta parameters. Omega matrices with a block diagonal structure will fall somewhere in between as determined by the particular block structure.

Maximum number of QRPEM samples=no limit (Large values (e.g., > 100,000) may cause difficulties with total static+dynamic peak memory demands. Typical values of QRPEM sample size range between 300 and 10,000 and should cause no problems.

Maximum number of iterations=10,000.

Maximum number of covariate categories or occasions=40.

Depending on the available memory and actual combination of model and run parameters, it is possible for very large models technically within the above static limits to require more dynamically allocated memory than is available. However, this should be an extremely rare occurrence and the majority of population NLME models should easily fit.