simrisc (15.05.00) * natural death ages < tumor death ages are no longer reported as death by tumors * repaired sudden increases in # tumor cases * avoiding tumor sizes < growth.start sizes * the name 'detectableAge' is confusing: renamed to 'onset', indicating the tumor's start * interval cancers prevent exact 5mm tumor occurrences, caused by spurious onset values -- Frank B. Brokken Mon, 29 Jan 2024 12:40:08 +0100 simrisc (15.04.00) * The params.txt file also contains the cumulative death-proportions if specified (currently: with lung-cancer simulations) -- Frank B. Brokken Thu, 07 Dec 2023 21:10:54 +0100 simrisc (15.03.01) * When reading the cumulative death proportions errors in the specification of the cumulative death proportions are checked (like lines broken at a final '='-character). * Changed the copyright to the Gnu GPL * Cosmetics on the simrisc.xref * The c++std file is no longer used. Instead the ICMAKE_CXXFLAGS environment variable is inspected. -- Frank B. Brokken Sat, 28 Oct 2023 15:08:19 +0200 simrisc (15.03.00) * Repaired survival/cptvsdrow: d_vsdRow was set to S3's row instead of S4's element index, which also resulted in errors in computing, e.g., the number of interval cancers. Because of this bug Simrisc before 15.03.00 should not anymore be used for lung cancer simulations. Using Simrisc for breast cancer simulations is OK. * When using lung cancer simulations the parameters written to file now correctly report the lung cancer parameters. -- Frank B. Brokken Sat, 01 Jul 2023 15:34:15 +0200 simrisc (15.02.00) * Costs values are now stored in size_t instead of in uint16_t variables -- Frank B. Brokken Wed, 14 Jun 2023 16:22:36 +0200 simrisc (15.01.00) * Added a column TNM to the data file containing the TNM categories per case. With breast cancer the 2nd value carries no meaning and is set to 0. * Added specification 'bc:' to the default configuration file defining the tumor diameter boundaries when using breast cancer simulations. * The S3 table in the default configuration specifies increasing (inclusive) boundaries for lung cancer tumer diameters. * Added option --tnm inserting -1,0 in the TNM column of the data file for cases not having tumors. * Fixed handling CT sensitivity computations (in the simulations percentages instead of proportions were used). * Fixed the CT specificity mean (was 99.2, changed to .992). * Added the class Log producing extensive logging when handling cases. * Added option --log "begin end logfile [set] " to log process information for the selected case-index ranges. * Fixed a boundary bug in probgroup/indexof.cc causing indexOf() to return an index value exceeding the width of a cumulative probability vector if the generated probability equals 1. -- Frank B. Brokken Mon, 08 May 2023 10:33:36 +0200 simrisc (15.00.00) * Added option --cancer (-c) which is used to specify the simulation type. By default '--cancer breast' is used, in which case breast cancer simulations are performed. Alternatively, '--cancer female' can be specified in which case lung cancer simulations are performed for women, and '--cancer male' can be specified in which case lung cancer simulations are performed for men. * When performing lung-cancer simulations modality CT must be used (default costs, dose, sensitivity and specificity parameters are defined in the default configuration file in section 'Modalities:' 'CT:'). * Added option --cum-death (-d) which is used to specify the name of a file containing the 101 cumulative death proportions. * Default proportions are provided in the default configuration file at the 'death:' parameter specification of the section 'Scenario:'. * Option --err is still present, but is removed in a future version. It is not mentioned in the current man-page and in simrisc's usage information anymore. * The default configuration file contains parameters used with lung cancer simulations for Costs: Discount: proportion:, Tumor: Growth: start:, Tumor: Growth: lung: (used to specify the selfDetect parameters, for breast cancer simulations Tumor: Growth: breast: is used) Tumor: Growth: DoublingTime: lung: And separate Male: and Female: subsections for Tumor: Incidence: (for breast cancer simulation Tumor: Incidence: Breast: is used) Survival: lung[0-3]: sections to determine the survival parameters, in combination with the new section Tumor: S3: (see the simriscparams(7) man-page for details). * The simrisc(1) and simriscparams(7) manpages were updated. -- Frank B. Brokken Sat, 10 Dec 2022 12:25:10 +0100 simrisc (14.05.01) * Ready for libbobcat6 * Added 'c++std' defining the c++ standard to use for compilation. Compilation commands also use -Werror * Renamed the 'oxref' option in the 'build' script to 'xref' -- Frank B. Brokken Sat, 17 Sep 2022 16:07:04 +0200 simrisc (14.05.00) * Added option --err (-e) to select the previously used but inorrect algorithm for computing the Beir7 risk vector, instead of using the (now default) correct algorithm for computing the risk vector. -- Frank B. Brokken Sat, 22 May 2021 22:09:08 +0200 simrisc (14.04.00) * Modalities support spread-variation. See the simriscparams(7) man-page for a description of how the configuration file was extended wrt the Modality-specifications. When 'spead: true' is specified then Loop::iterate() now calls d_modalities.vary(), calling ModBase vary for the various Modalities. Previously defined 'double' Modality values now use VSDs * Age range specifications do not end in ':'s anymore. E.g., ageGroup: 1 - 50 * Beir7's parameter specification first specifies eta, then beta. * The Case-specific data matrix defines an extra (18th) colum, showing the results of the screening rounds for each simulated case. * When 'spread: true' is specified the actually used and original parameter values are listed in a file, by default 'spread-$.txt', where $ is replaced by the loop iteration index. Use the option '-s' to specify a non-default filename (cf. simrisc(1)); * The man-pages were update -- Frank B. Brokken Sun, 11 Apr 2021 11:00:58 +0200 simrisc (14.03.00) * To specify no screening round ages 'round: none' should be specified. When 'round: none' is specified then the rounds file is not written. -- Frank B. Brokken Sun, 21 Feb 2021 13:30:38 +0100 simrisc (14.02.00) * Option --cases was renamed to --last-case (-l) to avoid confusion with the cases: specification in the configuration file * Default option values are reset at each Analysis: specification. * Analysis files now use (capitalized) Analysis: specifications. * Fixed some specification errors in the simriscparams(7) man-page * Updated the simrisc(1) man-page * Updated the usage info -- Frank B. Brokken Wed, 27 Jan 2021 16:39:02 +0100 simrisc (14.01.00) * 'm:' parameter specifications for the four bi-rad categories were added to the Mammo specifications in the default configuration file * The 'm:' parameter corresponding to the cases bi-rad category given the case's age is used when computing the sensitivity associated with the Mammo modality * The simriscparams(7) man-page was updated accordingly * The simrisc --help info lists the --cases (-c) option instead of --nCases (-n). -- Frank B. Brokken Fri, 22 Jan 2021 11:14:22 +0100 simrsic (14.00.00) * Case-specific data are reproducible when specifying 'generator: fixed' or 'generator: increasing' * Parameter variation when specifying 'spread: true' is available * The organization of the configuration file was drastically modified * The validity of parameter value specifications is checked -- Frank B. Brokken Wed, 20 Jan 2021 20:43:53 +0100 simrsic (13.03.00) * Redefined variables in the Costs class: the discount percentage in fact is a proportion, and its type was adapted accordingly * MRI simulation was incorrectly implemented in the original program. After fixing this error handling False Negatives is now using a standard procedure for all Modalities * The configuration file and the simriscparams man-page were adapted accordingly. * The classes Options, Random, and Error are now singletons. -- Frank B. Brokken Tue, 27 Oct 2020 19:56:12 +0100 simrsic (13.02.01) * Added a Copyright-notice file -- Frank B. Brokken Mon, 12 Oct 2020 09:34:04 +0200 simrsic (13.02.00) * Specifications using multiple analyses no longer overwrite existing files * Added specification 'generator' to the scenario specifications to specify the way the random number generator is initialized * The classes Pool, IDpool, and RandomPool are superfluous * MRI handling is activated. * The loop Status enum now uses 'PRESENT' instead of 'ALIVE' and Status enum values beginning with 'LEFT_' instead of 'NATURAL_' -- Frank B. Brokken Tue, 29 Sep 2020 16:04:26 +0200 simrsic (13.01.00) * Added missing registration of d_roundDetected to loop/maybedetect.cc * loop/selfdetected.cc and loop/treatmentdeath.cc are identical except for used Status values: now inline, calling new function in loop/characteristics.cc * Added a new section OUTPUT to the simrisc(3) man-page, containing descriptions of the content of generated files * By default the id-base option uses value 1 simrsic (13.00.00-pre) * Reorganized config/simrisc, costs associated with Modalities are now defined by the individual modality-specifications * Repaired the computation of d_prePeriod in tumor/reset.cc * Implemented Danielle's code and modified the handling of multiple modalities * Standardized the handling of Modalities by defining one standard interface * Updated the man-pages -- Frank B. Brokken Thu, 16 Jul 2020 13:45:32 +0200 simrsic (12.03.01) * Dropped 'oneAnalysis' and 'showAll' from Options, added specificAges(), fixing a bug in handling specific ages / N-cases specifications -- Frank B. Brokken Fri, 29 May 2020 15:52:30 +0200 simrsic (12.03.00) * Fixed handling of filename specifications in analysis: sections * The --one-analysis option no longer requires command-line arguments * Analysis: specifications may be empty * Minor update of the man-page -- Frank B. Brokken Fri, 29 May 2020 13:39:29 +0200 simrsic (12.02.02) * Changed the content of /usr/share/doc/simrisc: it now contains the README.hierarchy file and the default configuration file (simrisc.gz) -- Frank B. Brokken Tue, 26 May 2020 13:38:10 +0200 simrsic (12.02.01) * Updated the short option letters of the program's usage info -- Frank B. Brokken Tue, 26 May 2020 11:14:14 +0200 simrsic (12.02.00) * Added option --id-base to use id-based random numbers instead of random-pool based random numbers. * All options referring to filesystem entries use capitalized single letter options; all other options are lowercase * Updated the man-pages. * The default parameter specification file is available as the file 'simrisc' in the distribution's .config/ directory -- Frank B. Brokken Mon, 25 May 2020 15:48:49 +0200 simrsic (12.01.01) * New sub-minor release due to a man-page bug. -- Frank B. Brokken Sat, 23 May 2020 21:20:04 +0200 simrsic (12.01.00) * Reorganized the class hierarchy, preparing for multi-threading: see README.hierarcy. * Base directories are created if not available * Output files are provided with a timestamp and optionally analysis labels * Output files are cleaned up: improved table formats, and CSVs for the data files * The file echoing the used parameters is by default not produced. The --parameters option is used to specify the name of that file if requested. * When specifying configuration parameters in the context of an analysis either all, or none of the parameters of a category must be provided. This procedure is used to allow reduction of, e.g., screening rounds. -- Frank B. Brokken Sat, 23 May 2020 19:26:48 +0200 simrsic (12.00.00) * Following a request by Marcel Greuter (m.j.w.greuter@umcg.nl) SimRiSc was completely rewrittin in this release. Earlier specific changelog version information is not available. In the distribution earlier changelog info is available under 'legacy' * This is the initial conversion, offering the basic facilities. The current program produces the same results as the original program, for a single scenario, but specifying 100'000 women is OK. * Lots of work is still required to update the man-pages, and to completely generalize the program. * Debian package construction is (locally) operational. -- Frank B. Brokken Sun, 17 May 2020 17:47:06 +0200