bbmFitresiduals class
bbmFitresiduals.RdbbmFitresiduals class is used for storing the residuals for the fitted indices in the bbm function.
This includes residuals for indices in total biomass (indicesB) and as proportions of recruits in biomass (indicesP).
bbmFitresiduals(object, ...)Slots
- residuals.B
Residuals for indices in total biomass (indicesB),
FLQuants.- residuals.P
Residuals for indices as proportions of recruits in biomass (indicesP),
FLQuants.
Accessors
All slots in the class have accessor methods defined that allow retrieving individual slots.
Methods
Methods exist for various calculations based on values stored in the class. these are:
- plot
Method to plot the Pearson residuals.
- qqmath
Method to do a qqplot of the Pearson residuals of survey indices.
Examples
# Load data
data(ane)
# New element of class 'bbmFitresiduals' (empty)
bbmFitresiduals()
#> An object of class "bbmFitresiduals"
#> Slot "residuals.B":
#> An object of class "FLQuants": EMPTY
#>
#> Slot "residuals.P":
#> An object of class "FLQuants": EMPTY
#>
obj <- bbm( catch.ane, indicesB=indicesB.ane, indicesP=indicesP.ane, control=control.ane, inits=inits.ane)
#> outer mgc: 2.991218
#> outer mgc: 2.983554
#> outer mgc: 2.994433
#> outer mgc: 2.980339
#> outer mgc: 2.989589
#> outer mgc: 2.985185
#> outer mgc: 2.990111
#> outer mgc: 2.984663
#> outer mgc: 2.986485
#> outer mgc: 2.988286
#> outer mgc: 2.987929
#> outer mgc: 2.986843
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987382
#> outer mgc: 2.98739
#> outer mgc: 2.987383
#> outer mgc: 2.987388
#> outer mgc: 2.98738
#> outer mgc: 2.987392
#> outer mgc: 2.987369
#> outer mgc: 2.987403
#> outer mgc: 2.987363
#> outer mgc: 2.987409
#> outer mgc: 2.987322
#> outer mgc: 2.98745
#> outer mgc: 2.98723
#> outer mgc: 2.987541
#> outer mgc: 2.987124
#> outer mgc: 2.987647
#> outer mgc: 2.986773
#> outer mgc: 2.987998
#> outer mgc: 2.986082
#> outer mgc: 2.988689
#> outer mgc: 2.986608
#> outer mgc: 2.988164
#> outer mgc: 3.008474
#> outer mgc: 2.96631
#> outer mgc: 2.986905
#> outer mgc: 2.987863
#> outer mgc: 2.986374
#> outer mgc: 2.988397
#> outer mgc: 2.986725
#> outer mgc: 2.988047
#> outer mgc: 2.9823
#> outer mgc: 2.992471
#> outer mgc: 2.985849
#> outer mgc: 2.988921
#> outer mgc: 2.987386
#> outer mgc: 2.991218
#> outer mgc: 2.983554
#> outer mgc: 2.994433
#> outer mgc: 2.980339
#> outer mgc: 2.989589
#> outer mgc: 2.985185
#> outer mgc: 2.990111
#> outer mgc: 2.984663
#> outer mgc: 2.986485
#> outer mgc: 2.988286
#> outer mgc: 2.987929
#> outer mgc: 2.986843
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987386
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987385
#> outer mgc: 2.987387
#> outer mgc: 2.987382
#> outer mgc: 2.98739
#> outer mgc: 2.987383
#> outer mgc: 2.987388
#> outer mgc: 2.98738
#> outer mgc: 2.987392
#> outer mgc: 2.987369
#> outer mgc: 2.987403
#> outer mgc: 2.987363
#> outer mgc: 2.987409
#> outer mgc: 2.987322
#> outer mgc: 2.98745
#> outer mgc: 2.98723
#> outer mgc: 2.987541
#> outer mgc: 2.987124
#> outer mgc: 2.987647
#> outer mgc: 2.986773
#> outer mgc: 2.987998
#> outer mgc: 2.986082
#> outer mgc: 2.988689
#> outer mgc: 2.986608
#> outer mgc: 2.988164
#> outer mgc: 3.008474
#> outer mgc: 2.96631
#> outer mgc: 2.986905
#> outer mgc: 2.987863
#> outer mgc: 2.986374
#> outer mgc: 2.988397
#> outer mgc: 2.986725
#> outer mgc: 2.988047
#> outer mgc: 2.9823
#> outer mgc: 2.992471
#> outer mgc: 2.985849
#> outer mgc: 2.988921
#> outer mgc: 282597.9
#> Warning: NaNs produced
#> Warning: NaNs produced
res <- residuals(obj)
class(res)
#> [1] "bbmFitresiduals"
#> attr(,"package")
#> [1] "bbm"
slotNames(res)
#> [1] "residuals.B" "residuals.P"
# Starndardized residuals plots
plot(res)
qqmath(res)
