Man pages for inspktrgadget/gadgetSim
Create Gadget replicates for use in simulation studies
| add_lengthgroups | Add length groups to Gadget StockStdPrinter output |
| add_survey_fleet | Simple function to add survey fleets to existing fleet |
| as_quoted_ | Convert input to quoted variables |
| call_gadget | Call Gadget executable on the command line |
| check_names | Logical test to see if name(s) are in an object |
| check_stockfile | Check components of a Gadget stockfile that is being read |
| check_stockfile_funs | Check various entries when making a stockfile using... |
| collapse | Collapse objects and vectors so they are ready to be written... |
| def_labs | Some default labels |
| dots2list | Check if '...' is a list or a number of named objects and... |
| fleet_defaults | Fleet Defaults |
| format_printfile | Format printfile component for writing to printfile |
| format_stockfile | Format an object of class 'gadget_stock' to prepare for... |
| f_values | Compute various fishing mortality reference point |
| gadget_defaults | Gadget defaults |
| gadget_likelihood_comps | Create various Gadget likelihood components |
| gadgetSim | gadgetSim: A package for creating simulated datasets from... |
| gadget_sub_dir | Write out a Gadget sub-directory and return the path to it |
| get_index | Get the index of obect(s) in a vector |
| get_pf_type | Format the class of a printfile component to look like that... |
| get_si_data | Strip survey samples for the desired length or age groups to... |
| get_stock_info | Functions to retrieve basic information about Gadget stocks |
| get_stock_std | Make and retrieve output from the StockStdPrinter printfile... |
| gf2list | Convert a Gadget file to a list of components based on a... |
| growth_fun_formulas | Produce growth functions in a gadget readable formula |
| growth_funs | Basic functions for growth curves |
| is_list_element_null | Check to see if elements of a list are null |
| likelihood_helper_funs | Gadget likelihood helper functions |
| makeAggfileHelpers | Functions to make the area, age, length, predator, and prey... |
| make_aggfiles | Make aggregation files for Gadget printfile components that... |
| make_gadget_areafile | Make Gadget areafile |
| make_gadget_fleet | Create a list of class "gadget_fleet" that can be used to... |
| make_gadget_likelihood | Create a Gadget likelihood file |
| make_gadget_mainfile | Create a list of class "gadget_main" |
| make_gadget_model | Assemble an entire Gadget model with a single function |
| make_gadget_optinfofile | Create a Gadget optimization info file |
| make_gadget_printfile | Make Gadget printfile and write out to file |
| make_gadget_spawnfile | Create a list of class "gadget_spawnfile" that can be used to... |
| make_gadget_stockfile | Make Gadget stockfile |
| make_gadget_strayfile | Create a list of class 'gadget_strayfile' to add to a Gadget... |
| make_gadget_timefile | Make Gadget timefile |
| make_list_at_index | Split a vector into a list based on indices |
| make_switches | Turn any character vector into a Gadget switch |
| migration_funs | Helper functions to create and format migration matrices |
| params | Create a data.frame of class "gadget_params" |
| path_dir_funs | Checking path and directory status |
| printfileArgs | Non-optional arguments to Gadget printfile components |
| printfileDefaults | Gadget print file defaults |
| printfile_name_check | Check the names of a printfile component to ensure all... |
| read_gadget_aux_files | Read auxiliary Gadget files (i.e. data files, aggfiles,... |
| read_gadget_fleet | Read Gadget fleet file |
| read_gadget_likelihood | Read Gadget likelihood file |
| read_gadget_main | Read Gadget mainfile |
| read_gadget_model | Read a Gadget model |
| read_gadget_stockfiles | Read Gadget stockfiles |
| read_gadget_stock_std | Read the output from a StockStdPrinter printfile component |
| read_time_area | Read Gadget timefile |
| recruit_formulas | Produce recruitment functions in a Gadget readable formula |
| recruit_funs | Basic functions for recruitment curves |
| rg_class_compatibility | Convert classes of Rgadget and gadgetSim objects to be... |
| sample_gadget | Create length distributions and sample Gadget output |
| selectivity | Selectivity functions |
| simpleCap | Simple function to capitalize all words of a character vector |
| simulate_gadget | Create and get output from Gadget model in one fell swoop |
| split_ | Split and unlist a character vector |
| stock_distribution_funs | Functions to produce initial conditions or renewal... |
| strip_comments | Strip comments from a character vector |
| suit_formulas | Functions to assemble suitability function lines for writing... |
| switches | Switch defaults |
| to_gadget_formula | Turn R expression into Gadget formula string |
| update_model | Update components of an object of class "gadget_model" |
| update_printfile | Access elements of default printfiles and update them |
| update_printfile_dirs | Update path for printfile and aggfiles to include directories... |
| us2dot | Replace an underscore with a period |
| write_aggfiles | Write aggfiles specific to certain Gadget components |
| write_attr | Functions to write attributes of Gadget components to file |
| write_gadget_file | Write Gadget components to file |
| write_gadget_model | Write an object of class 'gadget_model' to the respective... |
| yield_curves | Compute various per-recruit analyses |
