[FLR-list] FLa4a release candidate and tech document draft

[Ernesto Jardim]

Hi,

Finally we're about to release the first version of the FLa4a package and a
technical document (
https://github.com/a4a/tech-doc/blob/master/a4aAssessmentMethodology.pdf?raw=true)
which explains how to carry out the analysis.

To run FLa4a you'll need R 3.0.x or higher, and install copula and triangle
from CRAN. The following code should do it:

install.packages(c('copula','triangle'))

and then install the FLCore and FLa4a packages from FLR's repository:

install.packages(c("FLCore","FLa4a"), repos="http://flr-project.org/R"
<http://flr-project.org/R>)

A simple demo using the traditional plaice in area 4 (North Sea) is as
follows

(start R and copy paste the code below)

library(FLa4a)
data(ple4)
data(ple4.indices)
fit <- sca(ple4, ple4.indices, fmodel= ~ s(age, k=4) + s(year, k=20))
res <- residuals(fit, ple4, ple4.indices)
plot(res)
qqmath(res)
plot(fit, ple4)
plot(fit, ple4.indices)
plot(ple4 + fit)

You can try models for fishing mortality, catchability, recruitment, etc,
check the tech doc.

I hope the demo opened your appetite check the pdf for more info. If you're
curious about the models you may jump directly to section 5.

Comments and suggestions are welcome. Feel free to distribute.

Best

EJ

ps: If you'd like to keep up with the development there's a repository in
github https://github.com/flr/FLa4a
ps2: The tech doc code(knitr) is also in github
https://github.com/a4a/tech-doc
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