simrisc(1)

simrisc breast cancer simulation program
(simrisc.13.02.01.tar.gz)

2020

NAME

simrisc - This program performs simulations in the context of breast cancer

SYNOPSIS

simrisc [options] analyses

The analyses argument is the name of the file specifying the analyses to perform. See section ANALYSES for details.

DESCRIPTION

Simrisc was originally designed around 2010 by Marcel Greuter at the University Medical Center Groningen, and thereafter modified in 2015 by Chris de Jonge.

OPTIONS

Short options are provided between parentheses, immediately following their long option equivalents. Several parameters specify the path-names of files produced by simrisc. If a path-name starts with a tilde character (~) then the tilde is replaced by the user's home directory. An initial + is replaced by the program's base directory (see option base). When an analysis uses multiple iterations then `$' characters in filename specifications are replaced by the analysis' interation index.

All single-letter options referring to filesystem entries (directories, filenames) are capitalized, all other single-letter options are lowercase.

ANALYSES

Unless the one-analysis option is used the program's first and only required argument is the name of a file providing the details of the analyses to perform.

Analyses files may define multiple analyses. Each analysis specification must begin with a line containing


    analysis:
        
Following this line the characteristics of the analysis are specified. These specifications may

Analysis: sections not altering configuration parameters use the parameters that are specified in the configuration file.

Lines not containing option-, label- or parameter-specifications are also ignored, but should (to avoid confusion) probably be avoided.

Options are specified using their long option names as keys. E.g.:


    base:   /tmp/
    nCases: 20
    
Actually provided command-line options always overrule options that are specified in analyses files. If a scenario specification merely consists of the line scenario: an analysis is performed using the parameter specifications that are found in the program's configuration file.

Multiple analysis sections should not use identically named output files, as the output files are (re)written for each separate analysis.

Analysis sections are commonly used to alter the default specifications found in the configuration file. E.g., the default the default number of iterations equals 1. By specifying


    iterations: 3
    
the analysis performs perform 3 iterations.

Configuration parameters are either read from the configuration file or they are redefined in analysis: sections. E.g., by default screening rounds are defined for two-year intervals between the ages of 50 and 74. If screening rounds are requested for 5-year intervals between ages 50 and 65 then an analysis: specification could be, e.g.,


    screeningRound:     50  Mammo MRI
    screeningRound:     55  Mammo MRI
    screeningRound:     60  Mammo MRI
    screeningRound:     65  Mammo MRI
    

In addition to options and parameter specifications analysis: sections may contain (multiple) label: lines. The text following label: is written at the top of the output files of those sections.

When using the --one-analysis option parameters may be altered by providing comma-separated parameters specifications as program command-line arguments. E.g., to perform one analysis, writing the data file to /tmp/data, simulating 1000 cases, and 20 for seeding the random number generator the command


simrisc -o -D /tmp/data nWomen: 1000, seed: 20
    
can be issued.

Each analysis: specification starts with the configuration file's parameter specifications. When an analysis: specification modifies parameters, then subsequent analysis: sections again start with the configuration files parameter specifications.

OUTPUT

The first lines of the generated files contain time stamps showing the date and time when the files were written. Here is an example of the time stamp, following the RFC 2822 format:


    Thu, 16 Jul 2020 15:30:45 +0200
    
An empty line follows next, whereafter the file's specific data are written. The data in all files (except for the file listing the actually used parameters (option --parameters (P))) are written using the standard comma-separated format (cf. RFC 4180): the first line lists the comma-separated variable labels, followed by the comma separated data line(s).

Data of simulated cases

For each simulated case the values of the following variables are written to file (one line of comma-separated values per simulated case):

FILES

SEE ALSO

simriscparams(7)

BUGS

too early for that...

COPYRIGHT

This is free software, distributed under the terms of the GNU General Public License (GPL).

AUTHOR

Frank B. Brokken (f.b.brokken@rug.nl),