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On 10/18/2011 02:34 PM, Laurie wrote:
<blockquote cite="mid:4E9D7254.8080300@gmail.com" type="cite">
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On 10/18/2011 01:34 PM, <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:ernesto.jardim@jrc.ec.europa.eu">ernesto.jardim@jrc.ec.europa.eu</a>
wrote:
<blockquote cite="mid:4E9D6431.9030109@jrc.ec.europa.eu"
type="cite">
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On 10/18/2011 01:22 PM, Laurie wrote:
<blockquote cite="mid:4E9D615F.7030402@gmail.com" type="cite">
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On 10/18/2011 01:10 PM, Ernesto Jardim wrote:
<blockquote
cite="mid:CAC03QWCxARV-RbXfZJNwS8gMLVsgYkRPDrH86LDUkPuyhCmRzg@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Tue, Oct 18, 2011 at 1:03 PM,
Laurie <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:lauriekell@googlemail.com">lauriekell@googlemail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
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<div class="h5"> On 10/18/2011 12:50 PM, <a
moz-do-not-send="true"
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 moz-do-not-send="true"
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 can´t 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.$quant <br>
t. <-t.[!<a moz-do-not-send="true"
href="http://is.na" target="_blank">is.na</a>(t.$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 don´t get what you want.<br>
<br>
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<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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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>
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<br>
Lost me. What do you want ?<br>
<br>
EJ<br>
<br>
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<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>
EJ<br>
<br>
</div>
</div>
</blockquote>
I would have called in FLCohort but some body got there 1st!<br>
<br>
Having 2 versions of FLCohorts with different properties does
raise an issue though.<br>
<br>
Laurie</blockquote>
<br>
Yes, sure ! But you get what you need computing year=cohort+age,
so I don't see the need for a new one.<br>
<br>
Best<br>
<br>
EJ<br>
</blockquote>
<br>
Same argument applies to FLQuant! However, the maths is easier in
my case using sweep & plyr if dims are year & cohort<br>
<br>
Laurie<br>
</blockquote>
<br>
Fine, but we're not changing FLCohort so that you may use plyr. In
that case you should create a new class like you're suggesting and
use it.<br>
<br>
Best<br>
<br>
EJ<br>
<pre class="moz-signature" cols="72">--
Ernesto Jardim <a class="moz-txt-link-rfc2396E" href="mailto:ernesto.jardim@jrc.ec.europa.eu"><ernesto.jardim@jrc.ec.europa.eu></a>
European Commission – Joint Research Center
Institute for the Protection and Security of the Citizen (IPSC)
Maritime Affairs Unit FISHREG – Scientific Support to Fisheries
TP 051, Via Enrico Fermi 2749
I-21027 Ispra (VA), Italy
Office : +39 0332 785311
Fax: +39 0332 789658
<a class="moz-txt-link-freetext" href="http://fishreg.jrc.ec.europa.eu/">http://fishreg.jrc.ec.europa.eu/</a>
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