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.
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/whereafter ~/.config/simrisc can be edited to contain local modifications.
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:
# 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: 50 Mammo screeningRound: 74 Mammo
# screening value distribution: systematicError: 0 Normal
# screening value distribution: attendanceRate: 0.8 Normal
beta1: -4.38 Normal beta2: 0.49 Normal beta3: -1.34 Normal beta4: -7.18 Normal
m: 0.136 Normal
# 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
# 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 0.00As 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:
# 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
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 NormalHere 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
# 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
# beta eta s.dev dist. beir7: 0.51 -2.0 0.32 Normal
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)
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
simrisc(1)
too early for that ...