Create executive summary tables from an SS3 Report.sso file
Source:R/SSexecutivesummary.r
SSexecutivesummary.RdTake the output from SS_output() and create executive summary .csv files
as required by the current Terms of Reference for U.S. West Coast
groundfish assessments. Additionally, .csv files of historical catches,
time-series, and numbers-at-age are created.
Usage
SSexecutivesummary(
replist,
plotfolder = "default",
ci_value = 0.95,
es_only = FALSE,
fleetnames = NULL,
add_text = "model area",
so_units = "millions of eggs",
tables = lifecycle::deprecated(),
divide_by_2 = FALSE,
endyr = NULL,
adopted_ofl = NULL,
adopted_abc = NULL,
adopted_acl = NULL,
forecast_ofl = NULL,
forecast_abc = NULL,
format = lifecycle::deprecated(),
match_digits = lifecycle::deprecated(),
verbose = TRUE
)Arguments
- replist
A list object created by
SS_output().- plotfolder
Directory where a new
tablesdirectory will be created, which will be used to store the output from this function. The default is the dir location where the Report.sso file is located.- ci_value
To calculate confidence intervals, the desired interval must be specified. The default is 0.95.
- es_only
A logical that specifies if only the executive summary tables should be produced. The default is
FALSE, which leads to all executive summary and auxiliary tables being produced (see Return).- fleetnames
Optional replacement for fleetnames used in data file.
- add_text
A single character object, where the default is
"model area". The text will be added to some of the table captions to indicate what the results apply to. Besides the default, one could use"base model","sub-area model South of Point Conception.", etc. Just know that the text will be appended to"for the", and thus, the default text leads to"for the model area.". Another thing to note is that a full stop is not needed but can be used because a full stop is appended to the end of the caption if it does not already exist.- so_units
A single character object specifying the unit of measurement that spawning output is reported in. The default is "millions of eggs". This text will be used in the table captions. If fecundity is equal to weight-at-length, then the units are hard-wired to
"mt"regardless of what is used within this argument.- tables
Deprecated as of version 1.49.1 because this function only takes 15 seconds to run and overwriting old tables should not be a problem if users are modifying the .csv files in a programmatic way. The function behavior is the same as the previous default behavior where all tables will be created.
- divide_by_2
A logical allowing the output to be based on single sex values based on the new sex specification (-1) in SS3 for single sex models. Default value is
FALSE.TRUEwill lead to dividing values by 2.- endyr
Optional input to choose a different ending year for tables, which could be useful for catch-only updates. The default is
NULL, which leads to using the ending year defined in Report.sso.- adopted_ofl, adopted_abc, adopted_acl
Vectors of adopted overfishing limits (OFL), acceptable biological catch (ABC), and annual catch limits (ACL) values to be printed in the management performance table. These vectors MUST BE be vectors of length 10. The default of
NULLleads to the table being filled in with notes that the values need to be changed.- forecast_ofl, forecast_abc
Optional input vectors for management adopted OFL and ABC values for table g. These values will overwrite the OFL and ABC values in the projection table, rather than the model estimated OFL values. As an example,
c(1500, 1300)would be viable input.- format
Deprecated as of version 1.49.1 because most users are now using LaTeX instead of microsoft word so formatting can be done inside
sa4ss::es_table_tex()rather than here. From now on, only .csv files will be available. The default wasTRUEbut is now essentiallyFALSE.- match_digits
Deprecated as of version 1.49.1 because this function just returns an unformatted csv file now.
- verbose
A logical value specifying if output should be printed to the screen.