NEWS.md
(GitHub issue/PR numbers in parentheses)
This new version includes implementations linked to GMACS version 2.10.01, which involved changes to the read/write functions of GMACS input files, implementation of a new workflow to update/upgrade Gmacs (development module). This version also includes a better documentation of most functions with examples.
clean_Inputfiles (): clean Gmacs input files in a folder.get_Param_name(): get the name of all parameters. Useful to write .par/.pin files.getInpOutFiles(): read all the Gmacs input files (‘gmacs.dat’, ‘model.dat’, ‘model.ctl’, ‘model.prj’) and and if they exist, the Gmacs output files (‘Gmacsall.out’, ‘gmacs.par’, ‘gmacs.rep’, ‘simdata.out’).set_DevStruct(): Set up structure folder for the development of a new code version of Gmacs.CompareCodeVersion(): run tests of comparison between two code versions of Gmacs.clean_files(): add the possibility to give specific file names and improve the process of deletion.copy_GMACSinputs(): improve the process for copying files and checks.readGMACS.dat(): add the read of the units.readGMACSallOUT(): add new implementation of Gmacs and names for all parameters.readGMACSctl(): add the maturity probability.readGMACSpar(): add the description of each parameter and update stuff about maturity probability, environmental impact on selex.writeGmacs.dat(): add stuff related to the development module.writeGmacsctlfile(): add stuff related to the development module and the maturity probability.writeGmacsdatfile(): add stuff related to the development module and new format for catch, size frequency and survey data frames.writeGmacsPAR(): update to account for the number of digits when writing the ‘.par’/‘.pin’ files.writeGmacsprjfile(): add stuff related to the development module.write_Gmacs_InputFiles(): write all the stock-specific Gmacs input files.GetGmacsExe(): add the possibility to specify the path to the repertory that holds the ‘.tpl’ file.insertTime();insertTime2(): add a development option.NewGMACSFeat(): improve the way of adding new features in the ‘gmacsbase.tpl’.UpdateGMACS(): change the header to update/upgrade Gmacs, add cleaning options related to the development module.write_TPL(): add stuff about the development module.(GitHub issue/PR numbers in parentheses)
This new version includes implementations linked to GMACS version 2.01.M.09, which involved changes to the read/write functions of GMACS input files. Changes have also been made to the GMACS compilation functions to create a temporary folder when compiling GMACS, making it easier to resolve errors in the code (#26).
read_GMACS_dat(): incorporating 1) stock specification (weight unit and stock name), 2) other controls settings (maximum phase, number of function calls, calculation of reference points, use of pin file, and verbose).readGMACSctl(): 1) incorporating the maturity specific length-weight relationship, 2) the functional maturity terminally molting, 3) removing the other controls settings (maximum phase, number of function calls, calculation of reference points, use of pin file, and verbose).readGMACSdat(): incorporating the option for the new format of input catch, relative abundance indices and size composition.readGMACSprj(): incorporating 1) new options for the projection specifications controls (number of state strategies and F range), and 2) new options for the Harvest Control rules settings (Apply strategies [OFL, ABC], Apply the state strategy, Number of state parameters).writeGmacs_dat(): account for stock specification and other controls settings.writeGmacsctlfile(): account for the maturity specific length-weight relationship, 2) the functional maturity terminally molting, and 3) removing the other controls settings.writeGmacsdatfile(): account for the new format of input catch, relative abundance indices and size composition.writeGmacsprjfile(): account for the new options for 1) the projection specifications controls, and 2) the Harvest Control rules settings.The updates improve the workflow for updating GMACS.
GetGmacsExe(): A temporary folder is now created when compiling GMACS. If errors when converting ‘gmacs.tpl’ to gmacs.cpp or compiling gmacs, either a “Error_convertion.txt” or a “Error_compilation.txt” file is created and indicates the source of the errors.clean_root: delete (if applicable) the “Error_convertion.txt” and/or “Error_compilation.txt” files when updating GMACS.(GitHub issue/PR numbers in parentheses)
This new release includes implementations related to the incorporation of i) environmental impacts and possibility of random walk in the vulnerability parameters (selectivity and retention parameters) (#24).
readGMACSdat(): incorporating the read of environmental indices.readGMACSctl(): 1) change in the selectivity and retention matrices to allow environmental impacts and random walk; 2) Now read phase for random walk deviations; 3) new internal function to count the number of random deviation parameters to be estimated.readGMACSpar(): Accounting for the environmental parameters.readGMACSallOUT(): Reading environmental parameters and deviations in vulnerability.writeGmacsctlfile(): account for environmental parameters and random walk deviations + formatting.writeGmacsdatfile(): account for environmental data and formatting.writeGmacsPAR(): account for environmental parameters and deviations in vulnerability + formatting.The updates improve the workflow for updating GMACS. * Do_Comp() * Do_GMACS() * GMACS() * UpdateGMACS() * getVerGMACS() * NewGMACSFeat()
(GitHub issue/PR numbers in parentheses)
This new release includes implementations related to the CPT modelling workshop hold in January 2023. Major implementations includes updates of i) plotting functions, ii) functions allowing to read and write GMACS input/output files, and iii) functions used when implementing and releasing a new version of GMACS (#20).
BaseThemeGMR(): Specify the basic theme of gmr when plotting outputsreadGMACSallOUT(): reads the gmacsall.out filereadGMACSrep(): read the gmacs.rep file*NewGMACSFeat(): creates a summary file detailing the latest implementations in the gmacsbase.TPL file, when they’ve been done and by whom.
(GitHub issue/PR numbers in parentheses)
This new release comes with the PR (#19) and updates the function to read the control file and the one to realize simulations.
readGMACSctl(): Number of nodes for cubic spline or number of step-changes for option 3 (#18)SaveSimFiles(): Save outputs of the simulation approach (#18)(GitHub issue/PR numbers in parentheses)
This new release allows to run the simulation under Linux.
(GitHub issue/PR numbers in parentheses)
This new release incorporates a new function to plot the basic outputs from GMACS and give the possibility to specify a given file to set the directories needed to call ADMB within R.
plot_basicOutput(): function to plot the basic outputs of GMACS (#15)createGmacsExe(): add the ADMBpaths argument in the function (#16)(GitHub issue/PR numbers in parentheses)
This is a minor version update of gmr that includes new functions to i) work with the simulation module of GMACS, ii) read input and some output files of GMACS and, iii) write the GMACS input files.
readGMACSfiles(): Function to read all the GMACS input filesreadGMACS.dat(): Function to read the gmacs.dat filereadGMACSdat(): Function to read the the data filereadGMACSctl(): Function to read the control filereadGMACSprj: Function to read the projection fileAll these functions return the input files as a named list.
writeGmacs.dat(): function to write the gmacs.dat file writeGmacsdatfile(): function to write data file writeGmacsctlfile(): function to write the control file writeGmacsprjfile(): function to write the projection file writeGmacsPAR(): function to write the gmacs.par file GMACSversion(): Function to extract the Version number of GMACS
prepSim(): function to get the original input files for the simulation approach GenSimFiles(): function to get generate the input files to get the simulated data for each simulation SimData(): Function to generate the data SaveSimFiles(): Function to save the outputs of each simulation-estimation run Gen_GmacsSim(): Function to generates the simulated data for a set of simulation RunGmacsSim(): Function to run the GMACS simulation-estimation *clean_bat_Sim(): Function to clean gmacs simulation-estimation approach
Do_GMACS()read_GMACS.dat()Do_Comp()(GitHub issue/PR numbers in parentheses)
This is a minor version update that includes modification of some functions to make gmr compatible with MacOs/Linux and avoid the use of paste() and paste0() for defining file paths to file.path. Some additions have also been made in function documentation (#13).
Versioning has been updated correctly. (change from 0.1.1 to 1.2.0).
createGmacsExe(): Function to get the GMACS executable from TPL file.clean_files(): Function to clean files in a specific folder.clean_root(): Function to clean gmacs compilation-process files in the “root folder”.clean_bat(): Function to clean gmacs output files in a folder.isWindowsOS: Identify if the OS type is windowsDo_GMACS().buildGMACS()write_TPL(): is now exported (#11).(GitHub issue/PR numbers in parentheses)
This new version allows to directly run GMACS within R instead of going through the various windows prompt (#1).
GMACS(), which allows you to compile, run and make comparison of different versions of GMACS for one or several stocks. This is the main function to work with the GMACS model with the gmr package.Do_GMACS(), which is called by the GMACS() function. It allows to build the GMACS executable, run the model and make comparison between multiple versions of GMACS if the user ask for.Do_Comp(), which establishes comparison tables of management quantities between different versions of GMACS..GetGmacsExe(), which allows to update and “release” a new version of GMACS..CallTerm(), which allows to call a R terminal to execute a specific command.read.OUT(), which is designed to read the ‘gmacsall.OUT’ (output of GMACS) to find estimates of specific management/biological quantities.Other functions (called within the ones described above) have also been added to the gmr package but are internal functions.