Mon, 09 Aug 2010 13:44:41 +0200 FLcore bugs http://flr-project.org/bugs/ Laurie Kell Mon, 09 Aug 2010 13:44:41 +0200
name of data is "missing"
]]> http://flr-project.org/bugs/index.php?do=details&task_id=32 http://flr-project.org/bugs/index.php?do=details&task_id=32 Laurie Kell Sat, 31 Jul 2010 11:08:39 +0200
# class FLGrowth
setClass('FLGrowth', representation('FLModel',
mass='FLArray'))

# constructor
setGeneric('FLGrowth', function(model, ...)
standardGeneric('FLGrowth'))

setMethod('FLGrowth', signature(model='ANY'),
function(model, ...)
return(FLModel(model, ..., class='FLGrowth')))

setMethod('FLGrowth', signature(model='missing'),
function(...)
return(FLModel(formula(NULL), ..., class='FLGrowth')))

# example
data(ple4)

gro ]]> http://flr-project.org/bugs/index.php?do=details&task_id=31 http://flr-project.org/bugs/index.php?do=details&task_id=31 Laurie Kell Fri, 30 Jul 2010 08:33:01 +0200
FLQuant(0:20,dimnames=list(age=0:20,year=1980:2010))

so why not?

FLCohort(0:20,dimnames=list(age=0:20,cohort=1980:2010))

various other things missing from FLCohort]]> http://flr-project.org/bugs/index.php?do=details&task_id=30 http://flr-project.org/bugs/index.php?do=details&task_id=30 Laurie Kell Mon, 26 Jul 2010 19:23:53 +0200
ple4[10]

but this fails

ple4[ac(10)]
]]> http://flr-project.org/bugs/index.php?do=details&task_id=29 http://flr-project.org/bugs/index.php?do=details&task_id=29 Laurie Kell Mon, 26 Jul 2010 15:33:38 +0200
#These dont appear to work but will be required for many applications

FLPar(c(Linf=238.6,K=0.185,t0=-1.404),params=c("Linf","K","t0"),unit=c("male","female"),iter=1)
FLPar(c(Linf=238.6,K=0.185,t0=-1.404),params=c("Linf","K","t0"),season=1:4,iter=1)
FLPar(c(Linf=238.6,K=0.185,t0=-1.404),params=c("Linf","K","t0"),areas=1:2,iter=1)


#This works

params ]]> http://flr-project.org/bugs/index.php?do=details&task_id=28 http://flr-project.org/bugs/index.php?do=details&task_id=28 Laurie Kell Mon, 26 Jul 2010 10:14:42 +0200
mapply(function(x,y) class(y[x]), x=names(t.),y=as.data.frame(m(ple4)))
age year unit season area iter data qname
"numeric" "numeric" "factor" "factor" "factor" "factor" "numeric" "numeric"

mapply(function(x,y) class(y[x]), x=names(t.),y=as.data.frame(FLQuants(m(ple4))))
age year unit season area iter data qname
"factor" "numeric" "factor" "factor" "factor" "factor" "numeric" "character"


If they have to be factors can we also make sure that for ages as years teh order matches the numeric order

Laurie]]> http://flr-project.org/bugs/index.php?do=details&task_id=27 http://flr-project.org/bugs/index.php?do=details&task_id=27 Laurie Kell Sat, 13 Mar 2010 10:02:41 +0100
head(as.data.frame(FLQuants(m=m(ple4))))
age year unit season area iter data qname
m.1 1 1957 unique all unique 1 0.1 m
m.2 2 1957 unique all unique 1 0.1 m
m.3 3 1957 unique all unique 1 0.1 m
m.4 4 1957 unique all unique 1 0.1 m
m.5 5 1957 unique all unique 1 0.1 m
m.6 6 1957 unique all unique 1 0.1 m
> head(as.data.frame(mcf(FLQuants(m=m(ple4)))))
age year unit season area iter data qname
NA.1 1 1957 unique all unique 1 0.1
NA.2 2 1957 unique all unique 1 0.1
NA.3 3 1957 unique all unique 1 0.1
NA.4 4 1957 unique all unique 1 0.1
NA.5 5 1957 unique all unique 1 0.1
NA.6 6 1957 unique all unique 1 0.1 ]]> http://flr-project.org/bugs/index.php?do=details&task_id=26 http://flr-project.org/bugs/index.php?do=details&task_id=26 Laurie Kell Wed, 17 Feb 2010 09:15:57 +0100
#1) There is no creater
flc ]]> http://flr-project.org/bugs/index.php?do=details&task_id=25 http://flr-project.org/bugs/index.php?do=details&task_id=25 Laurie Kell Wed, 23 Dec 2009 09:28:27 +0100
1) Change algorithm for setting initial values in BH
2) Add limits to segreg to ensure breakpoint doesn´t fall outside of the data
3) Calculate sigma from the residuals rather than fitting it as part of the likelihood
4) Add auto parscaling
5) Change all likelihoods to lognormal or at least put a option to choose
6) Ensure residuals are on the log scale if a log normal error model is used.
7) turn sv2ab and ab2sv into methods
8) check that steepness & virgin biomass options work across all classes

1,2,3 and 4 then Beverton and Holt, Ricker and segmented regression SRRs can be fitted to the ICES stock database. Otherwise fits can fail which can cause problems in that
parameters are wrong especially for Monte Carlo simulations.

Problems are due to FLSR simply not being able to find the solution, there are several reasons for this, poor initial values, going off into parameter space with a flat likelihood, different scales for parameters

In some methods normal log likelihood is used while in other the log normal, e.g. in bevholt.ar1() it is the log normal as this is needed to deal with AR1 processes, but you can fixed rho to 0 and you then have a standard normal likelihood but this may differ from bevholt()

Diagnostic plots are on the untransformed scale even when the error model is lognormal, this is because residuals are not on the log scale, this means that the QQ plots are wrong, the residual plots misleading and difficult to interpret and that passing FLSR objects to other methods (e.g. fwd for projection) liable to error.

Most of these suggestions have been coded up and are in FLBocadillio, main task is to check them and add to FLCore]]> http://flr-project.org/bugs/index.php?do=details&task_id=24 http://flr-project.org/bugs/index.php?do=details&task_id=24 Laurie Kell Fri, 30 Oct 2009 17:43:10 +0100 or n, for example having landings.sel with n iters in FLBRP means that
landings.n must also have n iters. I had major problems in fwd() when
working with FLStocks, FLBiols, FLMetiers, FLFleets, FLCatches and FLSRs
and so created some validation code, found in FLCoreVarCon.R. I think it
would be worthwhile either adding this to FLCore or creating some
protocols for use in secondary packages.

I therefore propose we look at FLCoreVarCon.R in FLBRP and add it to FLCore as a generic routine
for use in secondary packages
]]> http://flr-project.org/bugs/index.php?do=details&task_id=23 http://flr-project.org/bugs/index.php?do=details&task_id=23