ChronoModel 2.0 (February 2019)

for Mac OS X : Supported by 10.13 (High Sierra) and later ; for Windows 64 bits : Supported by Windows 10 ; for Linux : Supported by Ubuntu 18

User Manual
Release notes

New features

Model Window

  • Relocation and modification of the function of the STUDY PERIOD button. The button is now situated above both scenes.
  • Addition of visualization of the loading progress for large models.
  • Relocation of the button to display the properties of EVENTS and BOUNDS to the toolbar of the EVENTS scene, tools panel on the left.
  • Relocation of the button to display the “Import Data” window to the toolbar in the EVENTS scene, tools panel on the left.
  • Modification of the action of the “Grid” button, which helps to attach the items just like a magnetic grid.
  • Addition of the possibility of modifying the size of the icons in the tool panels, this choice can be made through the menu in the application’s preferences.
  • Removal of the slot option for BOUNDS.
  • Modification of the size of the BOUNDS to match the lengths of the miniatures in BOUNDS with the lengths of the calibration miniatures in EVENTS.
  • Improvement of the display of miniatures.
Events Scene
  • Modification of the plugin name from “Typo” to “Unif”.
  • Addition of the use of “Wiggle-Matching” in the “Gauss” plugin.
  • Addition in the search tool “OverView” (eye) of the possibility of finding a piece of Data by name, as for EVENTS.
Phases Scene
  • Modification of the method for attributing and removing an EVENT in a PHASE. Addition of two buttons (‘input’ and ‘output’ arrows) that appear when you hover over the PHASE items.
  • Removal of the ‘eye’ tool which was included in the PHASE items and replacement by a process of shading of the non-selected elements, on the side of the EVENTS scene and on the side of the PHASES scene.
  • Addition of order classification of EVENTS in the PHASES items in relation to their vertical layout in the EVENTS scene.
  • Addition of a question mark on the constraints of the successions between PHASES. This appears when you hover over with the constraint arrow, to indicate that you can have access to the dialog box on the constraint.
Import Data
  • Modification of the file format to import Data, to be able to directly assign a piece of Data to an existing or not yet existing EVENT.
  • Addition of import Data per packet into the EVENTS scene.
  • Addition of the possibility of importing a BOUND from a same CSV file as the Data.
Multi-Calibration Window
  • NEW: Addition of a visualization function for several individual calibrations (before modeling) simultaneously in a “Multi-Calibration View” window.
Calibration Window
  • Addition of a toolbar on the left side of the Calibration Window.
  • Deletion of the scale "slider" and of the "ruler" that allowed modification of the position on the time axis. Now, the time graduation scale can be modified using four boxes “Start”, “End”, “Maj. Int.” and “Min. Cnt” corresponding to the values of the start and end of the desired interval, and to the main division and to the number of subdivisions of this last value, respectively.
  • Modification of the HPD interval calculation which is now carried out only on the STUDY PERIOD interval.
  • Improvement in the precision of the HPD interval calculation and of the surface (%).
MCMC Parameter Window
  • Removal of the modification box of the “Mixing Level”, because this value is never modified.
  • Addition of control during parameter input.
Results Window
  • NEW: Addition of calculation and display of the “Phase Tempo” and “Phase Activity” curves under the"TEMPO" tab.
  • NEW: Addition of the “Time Phase Range” bar above the probability curves of start and end of phase.
  • Modification of the presentation of tools in the right-hand panel, with the introduction of tabs to organize the sub-menus.
  • Addition of a “Study Period Display” button to return to the default interval.
  • Addition of the possibility of exploring outside the STUDY PERIOD, to visualize calibrations outside the study interval.
  • Addition of the bar representing the Credibility Interval above the “duration” distribution.
  • NEW: Relocation of the EVENTS, PHASES and TEMPO tabs to the right.
  • Relocation of the “Duration” button to the sub-menu that appears with the “TEMPO” tab.
  • Relocation of the figure export tools to the menus on the right.
  • Relocation of the statistical results window to the right of the graphs.
  • Addition of the possibility of selecting the figures to export.
  • Addition of the BCE/CE timeline. The choice is made via the preferences menu of the application.
  • Addition of the possibility of modifying the graduations of the time axis, by adding the two boxes “Maj. Int.” and “Min. Cnt” corresponding to the value of the main scale and to the number of subdivisions of this scale.
  • Addition of management of figures per “Page”.
  • Addition of the memorization of the display parameters on X (min and max intervals, zoom, Major Interval and Minor Interval Count) for each type of curve.
  • Addition of the possibility of choosing the EVENTS and PHASES that you wish to see in the results, by selecting them directly in the “MODEL” window.
Log Window
  • Modification of the layout of results, with the results of the Phases being placed first (orange color), then according to the information on the succession between Phases (green color), on Events (blue color) and on Data (black color).
  • Replacement of the terms “alpha” and “beta” of the PHASES by “Begin” and “End”.
  • Modification of the term “PhaseConstraint” to “Succession” in the “MCMC Initialization” tab.
  • NEW: Addition of the result of the “Phase Time Range” of each PHASE.
  • NEW: Addition of the results of calculations linked to the presence of a succession between phases, ie.e.: “Transition Range” and “Gap Range”.
Calculation
  • Modification of the calculation initialization algorithm.
  • Addition of the indication of the constraint path in the case of a blockage due to a circularity of the model detected between the EVENTS scene and the PHASES scene.
Many other minor improvements!

Bug fixes

  • Memory overrun during the creation and calculation of large models. This problem cannot be resolved on 32-bit systems.
  • Recalculation of calibration curves during modification of the time scale unit.
  • Recalculation is compulsory in the case of a change in color or the name of a PHASE.
  • Display overflow of the scale values on the graphs.
  • The random string changes for a same kernel between run 1 and run 2. The chain value sequence becomes identical from run 3.
  • Software crashes when stopped during the calibration process.
  • Maximum scale at 39 instead of 40 in Autocorrelation.
  • Exporting scenes: size of characters not respected.

Known issues

  • The dark theme of OSX hides texts in the toolbar (black on black).
  • In the case of a problem when opening a project from a former version of ChronoModel, you should delete the associated \*.cal file. If this does not work, you should also delete the \*.res file. Take note that this leads to deletion of the results of the calculations that have been performed.

ChronoModel 1.5 (March 2016)

Supported : 10.9 (Mavericks), 10.10 (Yosemite), Windows XP, Windows Vista, Windows 7, Windows 8

User Manual
Release notes

New features

  • Individual Dates can be evaluated outside the study period but the curves of posterior[1]  are plotted on the study period).
  • Calibration view shows "out of bounds" regions if calibrated density is outside study period.
  • Data are marked as "not computable" if the calibration process gives no result on the whole reference curve definition (whatever the study period).
  • Memory usage improvement.
  • MCMC: All events and data methods can be reset to their default values from the "MCMC" Menu.
  • MCMC settings: New "Mixing Level" parameter. This is related to the ability to find solutions outside the study period for dates.
  • Settings Dialog (Preferences): New dialog layout combining app settings and data method settings.
  • Application Settings (Preferences): "Language" fixes the decimal separator "." or "," depending on the country. For instance French ',' and UK '.'
  • Application Settings (Preferences): new image export parameters to control pixel, ratio, DPM and compression factor (quality).
  • Application Settings (Preferences): date/time formats can be BC/AD, CalBP, Cal B2K for displaying Results and Calibration Views. WARNING: The modeling[2]  (Study Period and stratigraphic constraints) is always in BC/AD!
  • Data Method Settings (Preferences): Reference curves can be added or deleted for 14C, Gauss and AM.
  • New "Actions" menu in menu bar to perform grouped actions on selected events (change name, color, method).
  • Unzooming on events scene hides calibrated dates thumbnail AND bounds thumbnail.
  • Search box on event's scene is shown only if overview is visible.
  • Data Method Gauss: now possible to use custom curves!
  • General layout improved.
  • "CTRl-c" and "Esc" keyboard shortcuts can toggle Calibration window.
  • Results view: "Fill opacity" can be controlled.
  • Results view: Better text log for numerical results.
  • Results view: CSV exports improved with all history plots and numerical results
  • Many other minor improvements ! (see commits on GitHub for more details)

Bug fixes

  • "About" dialog can be closed correctly.
  • When quitting, the app asks to save the current project only once.
  • MCMC doesn't crash anymore when cancelling dialog progress box.

Known issues

  • Running MCMC on large models can freeze the application on computers with not enough RAM (Random Access Memory). The MCMC process goes all the way to the end on most cases but the results cannot be displayed because graphical representations are memory consumming. We currently work on a new architecture of the code to solve this issue.
  • The red rectangle corresponding to the zoom on the scene overview can appear shifted on large models.
  • Using pixel ratio > 1 in export image preferences could scale text fonts unappropriatly (depends on platforms)
  • Many improvements on graphs display and zooming performances (nothing "visible" though...)
  • Event properties' view layout improved with better enable/disable states of controls.
  • Data Method Gauss : using the "equation" mode with first parameter not null (the t^2 factor) can break the calibration display on large study period : Y scale is very large and cannot be displayed correctly.

ChronoModel 1.1 (January 2015)

Supported : 10.9 (Mavericks), 10.10 (Yosemite), Windows XP, Windows Vista, Windows 7, Windows 8

User Manual
Release notes

New features

  • Search field added on the events scene.
  • When exporting the model's data as CSV, data are grouped by event and comments with event names added in the CSV file.
  • FFTW library version for Mac downgraded from 3.3.4 to 3.2.2 to ensure Mac OS X 10.7 support.
  • PNG image size is 4 times bigger than screen resolution.
  • In results view, when browsing by phases, you can now also display data under phases and events by unfolding the results.
  • Duration graph added for phases.
  • CSV import: comments in CSV source file are now displayed in Chronomodel's user interface.
  • When drag-and-dropping data from CSV import to the scene, the data name is used as the newly created event's name.
  • HPD multi-intervals displayed with their respective percentage.
  • Calculation improvements.

Bug fixes

  • Better event merge, solving a bug that occurred sometimes when merging...
  • Graph data export fixed on posterior densities.
  • Calculation issues for models using bounds solved.

Known issues

  • There is calculation problem using a "Wiggle Matching" of type "Range" on C14 data.
  • The red square on the model overview tool may appear shifted from its real position and thus not correspond exactly to the currently viewed area. This happens on large models only.
  • If a warning appears during calculations: simply relaunch it. This limitation is due to a numerical overflow when dealing with extreme values. We are currently working on a fix!

Get source code

Chronomodel is an open source project. You can download the source code and compile everything yourself from scratch. It is built on Qt 5 and uses FFTW library. The only pre-requisite to build it yourself is to have Qt 5 installed on your system. The project is hosted on GitHub.com. You can clone the repository by typing :

git clone https://github.com/Chronomodel/chronomodel.git