Preparing runs and reading input filesThe following functions allow (i) read the various input files and (ii) create folders (and clean them) needed for the runs. |
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Functions to read input files |
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Read all the GMACS input files |
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Read the gmacs.dat file |
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Read the GMACS data file |
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readGMACSctl |
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readGMACSprj |
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Function to extract the Version number of GMACS |
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Functions to create specific folders and clean output files from GMACS |
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Create the needed folders to run GMACS |
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Clean gmacs output files in a folder |
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Clean files in a folder |
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Clean gmacs compilation-process files in the "root folder" |
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Clean the output files of the Gmacs simulation module |
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Functions to (re)write the input/output files |
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Write the gmacs.dat file |
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Write data file |
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Write the control file |
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Write the projection file |
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Write the gmacs.par file |
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Conducting a stock assessment using GMACSSet of functions for working with GMACS while realizing specific tasks (building the gmacs executable, running a stock assessment for one or several stocks, making comparisons between model versions). |
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GMACS |
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Do_GMACS |
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Do_Comp |
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.GetGmacsExe |
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Create the Gmacs executable from the tpl file |
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.buildGMACS |
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write_TPL |
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Copy specific GMACS input files |
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Updating a version of GMACS for a new releaseSet of functions for implementing and releasing a new version (including making comparison) |
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Do_Comp |
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UpdateGMACS |
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Realizing a simulation-estimation analysisSet of functions to generate simulated data and realize estimations in the context of a simulation-estimation approach. |
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Get the original input files for the simulation approach |
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Generate the input files to get the simulated data for each simulation |
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Generate the simulated data |
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Save the outputs of each simulation-estimation run |
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Generates the simulated data for a set of simulation |
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Run the GMACS simulation-estimation |
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Manipulating outputs from the GMACS functionThe following functions allow to read GMACS outputs and manipulate the results. These functions are called in the graphical functions. |
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Read GMACS outputs |
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readGMACSpar |
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Read GmacsAll.out |
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Read Gmacs.rep |
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readGMACSsimdat |
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Read ADMB output files |
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Read ADMB .par, .std, and .cor file and return an R object of type 'list' of estimates and correlations |
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Read ADMB .rep file |
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Read ADMB .psv file |
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Read ADMB .ctl file |
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read.OUT |
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Manipulate GMACS results |
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Get cpue or other indices |
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Get observed and predicted catch values |
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Get growth increment data |
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Get F parameters |
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Extract spawning stock biomass (ssb) from gmacs run |
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Get length-weight data |
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Get maturity data |
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Get observed and predicted mean lengths |
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Get molting probability data |
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Get natural mortality data |
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Get numbers at length data |
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Get recruitment data |
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Get recruitment size distribution data |
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Get the selectivity data |
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Get observed and predicted size composition values |
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Extract spawning stock biomass (ssb) from gmacs run |
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Making results tablesThe following functions can be used to create tables of catches, likelihoods and reference points |
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Create a table of catches |
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Create a table of likelihoods |
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Create a table of penalties |
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Create a table of priors |
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Create a table of SPR reference points |
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Creating plotsThe following functions are awesome for creating plots of data and model fits, model outputs estimates (biological, fisheries and, demographic parameters), model residuals and, stock status. |
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Do all plots from gmr |
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Do all gmr plots |
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Plotting the basic outputs of GMACS |
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Plot Gmacs on shiny app |
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Plotting data used and model fits |
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Plot data range by fleet and year |
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Plot cpue or other indices |
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Plot observed and predicted catch values |
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Plot fits to size composition data |
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Plot fits to size composition data |
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Plotting Biological parameters |
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Plot growth from arbitrary start age |
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Plot growth from arbitrary start age |
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Plot length-weight relationship |
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Plot length-maturity relationship |
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Plot molting probability relationship |
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Plot growth transition |
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Plot size transition |
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Plotting Fisheries parameters |
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Plot fishing mortality |
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Plot fishing mortality (F) |
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Plot selectivity |
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Plot selectivity 3D |
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Plotting Demographic parameters |
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Plot predicted spawning stock biomass (ssb) |
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Plot natural mortality |
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Plot numbers at length |
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Plot predicted recruitment and approximate asymptotic error-bars |
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Plot recruitment size distribution |
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Plot predicted recruitment across model runs |
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Plot predicted spawning stock biomass (ssb) |
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Plotting Model residuals |
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Plot residuals of cpue or other indices |
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Plot fits to size composition data |
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Plotting Stock Status |
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Plot predicted spawning stock biomass (ssb) |
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TerminalsThese functions allow the user to launch a scpecific command in a R Terminal. |
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.CallTerm |
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Plotting options and ggplot utilitiesSet of functions for settings the type of plot, the rezolution, the size and disposition of the graphics as well as the colors. |
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GMR plotting options |
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Base theme for plotting with gmr |
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The color-blind friendly palette with grey |
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The color-blind friendly palette with black |
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Set plotting theme for ggplot2 via gmr |
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Specify the type of plot you would like to create |
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Multi-Plot utility for ggplot2 ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects) - cols: Number of columns in layout - layout: A matrix specifying the layout. If present, 'cols' is ignored. |
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Plot multiple figures on a page |