<br><br><div class="gmail_quote">On Tue, Oct 18, 2011 at 1:03 PM, Laurie <span dir="ltr"><<a href="mailto:lauriekell@googlemail.com">lauriekell@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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On 10/18/2011 12:50 PM, <a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a> wrote:
<blockquote type="cite">
On 10/18/2011 12:02 PM, Laurie wrote:
<blockquote type="cite">
On 10/18/2011 11:41 AM, <a href="mailto:ernesto.jardim@jrc.ec.europa.eu" target="_blank">ernesto.jardim@jrc.ec.europa.eu</a>
wrote:
<blockquote type="cite">On 10/18/2011 11:26 AM, Laurie wrote: <br>
<blockquote type="cite">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. <br>
<br>
The data are in the form of number of fish tagged and
recovered each year of a cohort. This means that you canīt
use FLCohort which has age & cohort as dims 1&2. <br>
<br>
However, if you use the 1st dim for cohort then you can
model this with an FLQuant, i.e. <br>
<br>
library(plyr) <br>
<br>
setGeneric("I", function(object,...) <br>
standardGeneric("I")) <br>
setGeneric('O', function(object, ...) <br>
standardGeneric("O")) <br>
<br>
setMethod('I', signature(object='FLQuant'), <br>
function(object,...){ <br>
dmns <-dimnames(object) <br>
dmns[[1]]
<-ac((dims(object)$minyear-dims(object)$max):(dims(object)$maxyear-
dims(object)$min)) <br>
names(dmns)[1]<-"quant" <br>
flc <-FLQuant(NA,dimnames=dmns) <br>
<br>
t. <-as.data.frame(object) <br>
t.$cohort <-t.$year-t.$age <br>
flc[]
<-daply(t.,c("cohort","year","unit","season","area","iter"),function(x)
sum(x$data)) <br>
<br>
return(flc)}) <br>
<br>
setMethod('O', signature(object='FLQuant'), <br>
function(object,...){ <br>
dmns <-dimnames(object) <br>
dmns[[1]]
<-ac((dims(object)$maxyear-dims(object)$max):(dims(object)$minyear-dims(object)$min))<br>
names(dmns)[1]<-"age" <br>
flc <-FLQuant(NA,dimnames=dmns) <br>
<br>
t. <-as.data.frame(object) <br>
t.$age <-t.$year-t.$quant <br>
t. <-t.[!<a href="http://is.na" target="_blank">is.na</a>(t.$data),] <br>
flc[]
<-daply(t.,c("age","year","unit","season","area","iter"),function(x)
sum(x$data)) <br>
<br>
return(flc)}) <br>
<br>
data(ple4) <br>
<br>
m1=I(m(ple4)) <br>
m2=O(m1) <br>
<br>
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. <br>
Laurie <br>
</blockquote>
<br>
You may change the age in FLCohort <br>
<br>
library(FLCore) <br>
data(ple4) <br>
flc <- FLCohort(catch.n(ple4)) <br>
quant(flc) <- "year" <br>
<br>
why not using year in the first dimension ? it should work out
of the box. <br>
<br>
EJ <br>
<br>
<br>
</blockquote>
But you donīt get what you want.<br>
<br>
<span style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Arial;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><span style="font-family:Monospace;font-size:13px;line-height:17px;white-space:pre-wrap"><br>
<br>
<pre style="font-family:Monospace;font-size:10pt ! important;outline-style:none;border-style:none;white-space:pre-wrap ! important;margin:0px;line-height:1.3"><span style="color:blue">I(m(ple4))[1:10,1:10]
</span>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
<a href="tel:1948%200.1%20%200.1" value="+35319480101" target="_blank">1948 0.1 0.1</a> NA NA NA NA NA NA NA NA
<a href="tel:1949%200.1%20%200.1" value="+35319490101" target="_blank">1949 0.1 0.1</a> 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 <a href="tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1" value="+353101010101" target="_blank">0.1 0.1 0.1 0.1 0.1</a> 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
<span style="white-space:pre-wrap;color:blue">> </span><span style="color:blue">FLCohort(m(ple4))[1:10,1:10]
</span>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 <a href="tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1" value="+353101010101" target="_blank">0.1 0.1 0.1 0.1 0.1</a>
6 NA NA NA NA 0.1 <a href="tel:0.1%20%200.1%20%200.1%20%200.1%20%200.1" value="+353101010101" target="_blank">0.1 0.1 0.1 0.1 0.1</a>
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</pre>
<br>
</span></span></blockquote>
<br>
Lost me. What do you want ?<br>
<br>
EJ<br>
<br>
<br>
<br>
</blockquote></div></div>
There are three ways to represent the 1st two dims in an FLQuant.<br>
<br>
i) age & year<br>
ii) age & cohort<br>
iii) cohort & year<br>
<br>
(i) is FLQuant and (ii) is FLCohort; However we do not have (iii)
which is what I need for my tagging model.<br>
<br>
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.<br>
But then we have two FLCohort objects which might conflict. <br><font color="#888888">
<br>
Laurie <br>
<br><br></font></div></blockquote><div><br>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.<br>
<br>Best<br><br>EJ<br> <br></div></div><br>