R package with advanced diagnostics to evaluate a Stock Synthesis model. Diagnostics include residual analyses, hindcasting and cross-validation techniques, and retrospective analyses.
The following SSplot Functions arguments itself or its one of its options are either not tested, unused, unimplemented, or has an issue stated in its original code documentation (as of 1/10/2023):
SSplotEnsemble
pdf/use_pdf option for pdf plots (not tested for TRUE)
mcmcVec mcmc vector TODO TODO. Default is FALSE
indexQlabel TRUE/FALSE include labels for indices. Default is TRUE (currently not used)
plot Deprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.
new Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
SSplotModelComp
pdf/use_pdf Not tested for TRUE
indexfleets CHECK IF NEEDED or how to adjust indexfleets
mcmcVec NOT TESTED Vector of TRUE/FALSE values (or single value) indicating
plot Deprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), the option to disable this via FALSE, is unused here.
new Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
SSplotHCXval
subplots optional use of c("cpue","len","age"), yet to be tested for age.
mcmcVec NOT TESTED Vector of TRUE/FALSE values (or single value) indicating
shadealpha Transparancy adjustment used to make default shadecol. (currently not used)
indexfleets CHECK IF NEEDED or how to adjust indexfleets
plot Deprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.
SSplotJABBAres
pdf/use_pdf option for pdf plots (not tested for TRUE)
plot Deprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.
xlim Optional, values for x-axis range of years to display on plot.' Default = "default" displays all years of available data. (currently not used) #67
new Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
SSplotRetro
mcmcVec NOT TESTED Vector of TRUE/FALSE values (or single value) indicating mcmc values are used
plot Option to draw subplots and plot in the interface. Deprecated. Option to disable will be removed in future version.
new Deprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.
pdf/use_pdf option for pdf plots (currently does not work when subplots specified)
indexQlabel TRUE/FALSE, if TRUE add catchability to legend in plot of index fits (currently not used)
shadealpha set the transparency level (alpha) of the area of uncertainty. Defalut to 0.3 (currently not used)
SSplotRunsTest
plot Deprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), the option to disable this via FALSE, is unused here.
The following SSplot Functions arguments itself or its one of its options are either not tested, unused, unimplemented, or has an issue stated in its original code documentation (as of 1/10/2023):
pdf/use_pdfoption for pdf plots (not tested for TRUE)mcmcVecmcmc vector TODO TODO. Default is FALSEindexQlabelTRUE/FALSE include labels for indices. Default is TRUE (currently not used)plotDeprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.newDeprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.pdf/use_pdfNot tested for TRUEindexfleetsCHECK IF NEEDED or how to adjust indexfleetsmcmcVecNOT TESTED Vector of TRUE/FALSE values (or single value) indicatingplotDeprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), the option to disable this via FALSE, is unused here.newDeprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.subplotsoptional use of c("cpue","len","age"), yet to be tested for age.mcmcVecNOT TESTED Vector of TRUE/FALSE values (or single value) indicatingshadealphaTransparancy adjustment used to make default shadecol. (currently not used)indexfleetsCHECK IF NEEDED or how to adjust indexfleetsplotDeprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.pdf/use_pdfoption for pdf plots (not tested for TRUE)plotDeprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), and the option to disable this, via FALSE, is unused.xlimOptional, values for x-axis range of years to display on plot.' Default = "default" displays all years of available data. (currently not used) #67newDeprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.mcmcVecNOT TESTED Vector of TRUE/FALSE values (or single value) indicating mcmc values are usedplotOption to draw subplots and plot in the interface. Deprecated. Option to disable will be removed in future version.newDeprecated. New plot windows are created by default (TRUE), and the option to disable this, via FALSE, is unused.pdf/use_pdfoption for pdf plots (currently does not work when subplots specified)indexQlabelTRUE/FALSE, if TRUE add catchability to legend in plot of index fits (currently not used)shadealphaset the transparency level (alpha) of the area of uncertainty. Defalut to 0.3 (currently not used)plotDeprecated. Plots (and subplots) are drawn to the active plot device by default (TRUE), the option to disable this via FALSE, is unused here.