This function runs the entire PELFOSS framework from the NORWECOM model output files (biomass in a grid and superindividuals), through surveyPlaner() and StoX to the estimated total stock biomass compared to the corresponding theoretical values:
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dir |
The directory holding the NORWECOM files, the stratum files and the output xml files from the function (temporary stored for insertion into the StoX project). |
run |
The name of the run, which could be used to reflect the input parameters, such as "Run1_parallel" or "Run1_zigzag". |
biomass, superind |
The biomass and superind data read from |
surveyPar |
A list of parameters to be used as input to biomass2tsb (see ?biomass2tsb). |
year, res |
The year and resolution (in km) to run. The NORWECOM files are located in the following folder structure: species / resolution / year, where the resolution folders has names such as "res_4km". |
dateshift |
An integer number of days to shift the survey by, negative values shifting to earlier in the year. |
reversed |
Logical: If TRUE run the survey in the opposite direciton. |
seed |
A single integer, or a list of seeds used in the funciton, including the following seeds: ('transect') for drawing transects using surveyPlanner(), ('trawl') for drawing trawl stations along the transects with probability as a funciton of the NASC (see |
projectName |
The name or full path of the StoX project of the simulated survey. |
nboot |
Number of bootstrap replicates. |
xsd |
A named list of xsd versions of the acoustic and biotic file format. |
format |
The file format of the saved plot, given as a string naming the function to use for saving the plot (such as bmp, jpeg, png, tiff), with |
... |
Additional inputs overriding the defaults returned by pelfossDefaults(). |
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