simriscparams(7)

simrisc configuration file organization
(simrisc.13.02.01.tar.gz)

2020

NAME

DESCRIPTION

This page describes the organization of the simrisc configuration files. These files are formatted like standard unix configuration files. Lines are interpreted after removing initial white-space (blanks and tabs). If a line ends in \ (a backslash), then the next line (initial white-space removed) is appended to the current line.

While processing the configuration files trailing blanks and information on lines starting at the first # character are removed.

DEFAULT PARAMETER FILE

A default parameter file is provided as /usr/share/doc/simrisc/simrisc.gz.

Usually this file is unzipped to the ~/.config directory:

    gunzip < /usr/share/doc/simrisc/simrisc.gz > ~/.config/
   

Various parameters specify probability distributions. By default this is the Normal distribution. The program also recognizes the LogNormal, Uniform, and Exponential distributions.

Parameter specifications start with keywords, followed by a colon. The keywords are shown in the following overview. The format of the specifications is also fixed, but white space may be added between elements to improve the specifications' readabilities. And of course end-of-line comment, starting at the # characters, may be used.

The default ~/.config/simrisc file contains the following parameters:

• variableSpread: true
  this parameter is commented out. If specified with the value true then variable spreading is used;

• iterations: 1
  the number of iterations used in a simulation loop;

• generator: random
  the default way to initialize simrisc's random number generator. With this initialization mode the random number generator is initialized once using a random initialization value, and seed (below) is not used. Alternatively, the generator may be initialized with specification fixed, in which case at each iteration the random number generator is initialized with seed's value. Specification increasing can also be used, in which case at each iteration 1 is added to seed;

• seed: 1
  the default value to seed the random number generator with;

• nWomen: 100000
  the number of cases to simulate;

• costs:
  specification of the costs. This specification must consist of a discount age and its associated cost, followed by the cost of a biopsy, followed by pairs of age: cost values specifying the treatment cost starting at the specified age, up to the next pair's age (if specified). The first age must be specified as 0. The default costs specification is

  
  #         discount:             pairs of (increasing) begin-diam: cost
  #         age   cost    biop    (first diameter must be 0)
  costs:    50    0       176     0: 6438  20: 7128  50: 7701
          
  

• screeningRound:
  each screening round specifies an age followed by a list of at least one Modality specification. Currently defined modalities are Mammo, Tomo and MRI. By default 2-year intervals are used, starting at age 50 through age 74. The default screening round specifications specify Mammo. Here are two examples:

  
  screeningRound:     50  Mammo
  screeningRound:     74  Mammo
          
  

• systematicError:
  specifies a value and a probability distribution:

  
  # screening         value   distribution:
  systematicError:    0       Normal
          
  

• attendanceRate:
  specifies a value and probability distribution:

  
  # screening         value   distribution:
  attendanceRate:     0.8     Normal  
          
  

• beta-parameters:
  specify values and probability distributions. The default parameter values are:

  
  beta1:   -4.38   Normal
  beta2:    0.49   Normal
  beta3:   -1.34   Normal
  beta4:   -7.18   Normal
         
  

• m-parameter:
  specifies a value and probability distribution:

  
  m:        0.136  Normal
          
  

• breastDensities:
  breast density values for various age groups, covering ages 0 through 100. By default the following age groups and four associated birads values are provided:

  
  #                   agegroup    birads1 birads2 birads3 birads4
  breastDensities:    0  - 40     0.05    0.30    0.48    0.17
  breastDensities:    40 - 50     0.06    0.34    0.47    0.13
  breastDensities:    50 - 60     0.08    0.50    0.37    0.05
  breastDensities:    60 - 70     0.15    0.53    0.29    0.03
  breastDensities:    70 - 100    0.18    0.54    0.26    0.02
         
  

• modalities:
  Currently three modalities are supported: Mammo, Tomo and MRI. Mammo and Tomo define specificity age groups (age groups 0-40 and 40-100) and define treatment costs and four birads doses and sensitivities. For MRI only costs is specified as no birads and agegroups apply to MRI, but sensitivity and specificity are specified. Here is the default specification:

  
  #                       birads  birads              (agegroups: values)
  # modalities id    cost dose    sensitivity         specificity
  #                       1..4    1..4                            
  modality:    Mammo 64   3 3 3 3 0.87 0.84 0.73 0.65 0-40: 0.961 40-100: 0.965
  modality:    Tomo  64   3 3 3 3 0.87 0.84 0.73 0.65 0-40: 0.961 40-100: 0.965
  modality:    MRI   64           0.00                0.00
         
  

  As an illustration of how MRI can also be specified: for one of the specifications used when constructing simrisc we used

  
  modality:    MRI   280 0.94 0.95
         
  

Tumor parameters:

• incidence parameters:
  Max. three carrier names can be provided: Normal, BRCA1 and BRCA2. Each having a certain probability, summing up to 1. By default only the Normal carrier is used. Each incidence specification defines a lifetime risk, a mean age and a std. dev., each having a mean, and std. deviation and a specified distribution. The default Normal incidence parameter specification is:

  
  #                             lifeTimeRisk         mean age          std. dev.
  #               carier        -------------------  ----------------- -----------------
  #               name    prob. mean  s.dev  dist.   mean s.dev dist.  mean s.dev dist.   
  tumorIncidence: Normal  1     0.226 0.0053 Normal  72.9 0.552 Normal 21.1 0.048 Normal  
         
  

• growth parameters:
  tumor growth parameters consist of two separate specification types: on the one hand the growth start diameter and self-detection parameters, each consisting of a mean, std. dev. and probability distribution, and on the other hand tumor doubling times, specified for various age groups using means, std. dev. and distribution types for the means and standard deviations of the doubling times.

  The default start diameter and self detect parameters are:

  
  #                                       self detect diameter
  #                              -----------------------------------
  #            start diam.            mean             std. dev.        
  #            ----------------- ----------------- -----------------    
  #            mean s.dev dist.  mean s.dev dist.  mean s.dev dist.     
  tumorGrowth: 5    0     Normal 2.92 0.084 Normal 0.70 0     Normal  
          
  

  Here are the default doubling time parameters for the agegroup 1-50:

  
  #                                mean             std. dev.        
  #                           ----------------- -----------------    
  #doublingTime:  agegroup:   mean s.dev dist.  mean s.dev dist.     
  tumorGrowth:    1-50        4.38 0.43  Normal 0.61 0     Normal  
          
  

• survival parameters:
  four types of survival parameters (a..d) are required. Each parameter type specifies a distribution type, its mean, and its std. dev.. The default parameter specifications are:

  
  #               type    mean        s.dev       dist.
  tumorSurvival:  a       0.00004475  0.000004392 Normal  
  tumorSurvival:  b       1.85867     0.0420      Normal
  tumorSurvival:  c       -0.271      0.0101      Normal
  tumorSurvival:  d       2.0167      0.0366      Normal
          
  

• BEIR (tumor induction) parameters
  currently only tumor induction type 7 (i.e., beir7) is used. The default specifications for beir 7 are:

  
  #       beta    eta     s.dev   dist. 
  beir7:  0.51    -2.0    0.32    Normal  
         
  

PARAMETER RESPECIFICATION

Parameters can be respecified by defining a separate parameter configuration file or by providing alternate parameter specifications in analyses: sections of the program's input file, or by providing alternative parameter specifications as command-line arguments (cf. the simrisc(3) man-page)

FILES

By default configuration files is expected in ~/.config/simrisc.

The default configuration file provided in the distribution is found in /usr/share/docs/simrisc/simrisc.gz

SEE ALSO

simrisc(1)

BUGS

too early for that ...

COPYRIGHT

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