[FLR-list] FLCohort

[ernesto.jardim at jrc.ec.europa.eu]

On 10/18/2011 12:02 PM, Laurie wrote:
> On 10/18/2011 11:41 AM, 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.$quant
>>>     t. <-t.[!is.na(t.$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   NA   NA   NA   NA   NA   NA   NA   NA
>    1949 0.1  0.1  0.1   NA   NA   NA   NA   NA   NA   NA
>    1950 0.1  0.1  0.1  0.1   NA   NA   NA   NA   NA   NA
>    1951 0.1  0.1  0.1  0.1  0.1   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   NA  0.1  0.1  0.1  0.1  0.1
>    6   NA   NA   NA   NA  0.1  0.1  0.1  0.1  0.1  0.1
>    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




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