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| r4ss-package | R tools for Stock Synthesis |
| DoProjectPlots | Make plots from Rebuilder program |
| movepars | A function to visual parameterization of movement in Stock Synthesis |
| r4ss | R tools for Stock Synthesis |
| sel.line | a function for drawing selecitivity curves |
| selfit | A function to visual parameterization of double normal and double logistic selectivity in Stock Synthesis |
| SSv3_FishGraph | A function for converting Stock Synthesis output to the format used by FishGraph |
| SSv3_output | A function to create a list object for the output from Stock Synthesis |
| SSv3_plotpars | Plot distributions of priors, posteriors, and estimates. |
| SSv3_plots | function to plot many quantities related to output from Stock Synthesis |
| SS_changepars | Change parameters in the control file. |
| SS_fitbiasramp | Estimate bias adjustment for recruitment deviates |
| SS_parlines | Get parameter lines from Stock Synthesis control file |
| SS_profile | Run a likelihood profile in Stock Synthesis. |
| SS_recdevs | Insert a vector of recruitment deviations into the control file. |
| SS_splitdat | Split apart bootstrap data to make input file. |
| update_r4ss_files | Updates r4ss files to newest versions on web. |