[FLR-list] FLCohort
Laurie
lauriekell at googlemail.com
Tue Oct 18 13:22:07 CEST 2011
On 10/18/2011 01:10 PM, Ernesto Jardim wrote:
>
>
> On Tue, Oct 18, 2011 at 1:03 PM, Laurie <lauriekell at googlemail.com
> <mailto:lauriekell at googlemail.com>> wrote:
>
> On 10/18/2011 12:50 PM, ernesto.jardim at jrc.ec.europa.eu
> <mailto:ernesto.jardim at jrc.ec.europa.eu> wrote:
>> On 10/18/2011 12:02 PM, Laurie wrote:
>>> On 10/18/2011 11:41 AM, ernesto.jardim at jrc.ec.europa.eu
>>> <mailto:ernesto.jardim at jrc.ec.europa.eu> wrote:
>>>> On 10/18/2011 11:26 AM, Laurie wrote:
>>>>> I am working on tagging models, where tags are released for a
>>>>> number of years and then recaptured in subsequent years. This
>>>>> allows M & Z to be estimated along a cohort.
>>>>>
>>>>> The data are in the form of number of fish tagged and
>>>>> recovered each year of a cohort. This means that you can´t use
>>>>> FLCohort which has age & cohort as dims 1&2.
>>>>>
>>>>> However, if you use the 1st dim for cohort then you can model
>>>>> this with an FLQuant, i.e.
>>>>>
>>>>> library(plyr)
>>>>>
>>>>> setGeneric("I", function(object,...)
>>>>> standardGeneric("I"))
>>>>> setGeneric('O', function(object, ...)
>>>>> standardGeneric("O"))
>>>>>
>>>>> setMethod('I', signature(object='FLQuant'),
>>>>> function(object,...){
>>>>> dmns <-dimnames(object)
>>>>> dmns[[1]]
>>>>> <-ac((dims(object)$minyear-dims(object)$max):(dims(object)$maxyear-
>>>>> dims(object)$min))
>>>>> names(dmns)[1]<-"quant"
>>>>> flc <-FLQuant(NA,dimnames=dmns)
>>>>>
>>>>> t. <-as.data.frame(object)
>>>>> t.$cohort <-t.$year-t.$age
>>>>> flc[]
>>>>> <-daply(t.,c("cohort","year","unit","season","area","iter"),function(x)
>>>>> sum(x$data))
>>>>>
>>>>> return(flc)})
>>>>>
>>>>> setMethod('O', signature(object='FLQuant'),
>>>>> function(object,...){
>>>>> dmns <-dimnames(object)
>>>>> dmns[[1]]
>>>>> <-ac((dims(object)$maxyear-dims(object)$max):(dims(object)$minyear-dims(object)$min))
>>>>> names(dmns)[1]<-"age"
>>>>> flc <-FLQuant(NA,dimnames=dmns)
>>>>>
>>>>> t. <-as.data.frame(object)
>>>>> t.$age <-t.$year-t.$quant
>>>>> t. <-t.[!is.na <http://is.na>(t.$data),]
>>>>> flc[]
>>>>> <-daply(t.,c("age","year","unit","season","area","iter"),function(x)
>>>>> sum(x$data))
>>>>>
>>>>> return(flc)})
>>>>>
>>>>> data(ple4)
>>>>>
>>>>> m1=I(m(ple4))
>>>>> m2=O(m1)
>>>>>
>>>>> It is probably best to derive a new class for this object just
>>>>> to break VPAs etc. But what to call it? Also how does it
>>>>> relate to FLCohort.
>>>>> Laurie
>>>>
>>>> You may change the age in FLCohort
>>>>
>>>> library(FLCore)
>>>> data(ple4)
>>>> flc <- FLCohort(catch.n(ple4))
>>>> quant(flc) <- "year"
>>>>
>>>> why not using year in the first dimension ? it should work out
>>>> of the box.
>>>>
>>>> EJ
>>>>
>>>>
>>> But you don´t get what you want.
>>>
>>>
>>>
>>>
>>>
>>>
>>> I(m(ple4))[1:10,1:10]
>>> An object of class "FLQuant"
>>> , , unit = unique, season = all, area = unique
>>>
>>> year
>>> quant 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966
>>> 1947 0.1 NA NA NA NA NA NA NA NA NA
>>> 1948 0.1 0.1 <tel:1948%200.1%20%200.1> NA NA NA NA NA NA NA NA
>>> 1949 0.1 0.1 <tel:1949%200.1%20%200.1> 0.1 NA NA NA NA NA NA NA
>>> 1950 0.1 0.1 0.1 0.1 NA NA NA NA NA NA
>>> 19510.1 0.1 0.1 0.1 0.1 <tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1> NA NA NA NA NA
>>> 1952 0.1 0.1 0.1 0.1 0.1 0.1 NA NA NA NA
>>> 1953 0.1 0.1 0.1 0.1 0.1 0.1 0.1 NA NA NA
>>> 1954 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 NA NA
>>> 1955 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 NA
>>> 1956 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
>>>
>>> units: NA
>>> > FLCohort(m(ple4))[1:10,1:10]
>>> An object of class "FLCohort"
>>> , , unit = unique, season = all, area = unique
>>>
>>> cohort
>>> age 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956
>>> 1 NA NA NA NA NA NA NA NA NA 0.1
>>> 2 NA NA NA NA NA NA NA NA 0.1 0.1
>>> 3 NA NA NA NA NA NA NA 0.1 0.1 0.1
>>> 4 NA NA NA NA NA NA 0.1 0.1 0.1 0.1
>>> 5 NA NA NA NA NA0.1 0.1 0.1 0.1 0.1 <tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1>
>>> 6 NA NA NA NA 0.10.1 0.1 0.1 0.1 0.1 <tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1>
>>> 7 NA NA NA 0.1 0.1 0.1 0.1 0.1 0.1 0.1
>>> 8 NA NA 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
>>> 9 NA 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
>>>
>>> laurie
>>>
>>>
>>>
>>
>> Lost me. What do you want ?
>>
>> EJ
>>
>>
>>
> There are three ways to represent the 1st two dims in an FLQuant.
>
> i) age & year
> ii) age & cohort
> iii) cohort & year
>
> (i) is FLQuant and (ii) is FLCohort; However we do not have (iii)
> which is what I need for my tagging model.
>
> I have created an "FLCohortYear" from an FLQuant by adding I() &
> O() as coercion methods and validity that only allows 1st dim to
> be called cohort.
> But then we have two FLCohort objects which might conflict.
>
> Laurie
>
>
>
> But you can use FLQuant and change the first dimension. You may need a
> method to convert i) or ii) into it but shouldn't create any
> conflicts. If you really need a new data structure and the problem
> only affects tag data, call it FLTag and extend FLQuant.
>
> Best
>
> EJ
>
I would have called in FLCohort but some body got there 1st!
Having 2 versions of FLCohorts with different properties does raise an
issue though.
Laurie
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