flr / flasher

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General discussion, documentation and team work

flasher's Issues

Baranov equation to calculate catch is in project_fisheries() and in om::catches() and in om::discards()

Several implementations of Baranov catch equation.
Put into a single method

ADD roxygen documentation

Use templates from https://github.com/flr/FLR-Project/tree/master/templates/roxygen

• fwdElement-class
• fwdControl-class
• fwdControl()
• target, target<-

Evaluating target Catches in OM

When evaluating the target, you may need to get the total catch of a Biol. Should this be calculated using live F and N etc, or just extracted from the FLCatches that catch the biol. The catches in FLCatches may not have been updated to reflect the effort. i.e. the calced catch could be different to the current catches in the objects.

This is also true of the catches in an FLCatch, however when evaluating target catches of an FLCatch we just take it from the object, and not calculate it. This is inconsistent. At the moment the catch of a FLBiol is calculated 'live' whereas catch of a FLCatch is just extracted.

But F is always calculated live. Hmmm.

My feeling is that we just extract from OM and that project_X should always be used to update before doing this. So long as we are clear.

Improve solver performance if some iters fail

Shoule fwdBiol spwn slot have an age structure?

It currently does not. Could easily add it if necessary.

om::landings and om::discards methods may or may not recalculate catch

Calculating total catches, landings or discards on a biol.

In most cases the total catch on a biol is the sum of the catches in the FLCatches that catch that biol.
No recalculation is necessary.
However, if an FLCatch that catches the biol also catches another biol (e.g. a FLCatch catches from two biols), then we cannot use the total catch of the FLCatch (it comes from 2 biols).

Then what?
We can't easily split the the total catch into the constituent parts.
Recalculate the catch using F and N etc?

For now, no recalculation. If the FLCatch catches 2 biols, you cannot get the catch of one of the single biols. At least for now.

Change FLBiol member to FLBiols in operatingModel Cpp class

Lots of other planned changes, like catch_q method, rely on this

fwdControl.get_target_timestep - timing of abundance targets (SSB etc)

In what timestep should abundance targets be set? In an FLBiol abundance is at start of timestep.

Do we keep this pattern in FLasher? i.e. if we have an SSB target we need to know the effort in the previous timestep that gives us that SSB?
Or we solve for the effort in the target timestep (which really affects SSB in next timestep).

I prefer the first option because it is in line with other FLR objects

Add Fspwn calculation

Needed for SSB calculations.
Fspwn comes from 'spwn' member of fwdBiol and some timing slot in the FLCatch (not yet added)

Can we add a 'verbose' argument for Cpp stuff?

Add example of SRR with covariates

Need some kind of Fishery / Catches / Biol map

Need some kind of Fishery / Catches / Biol map to store what Fishery / Catch combinations catch which Biols.
One idea is to use an Rcpp::IntegerMatrix with 3 columns (F, C, B). Each row is a unique Fishery / Catch catching a Biol (although the same C can catch multiple Bs, and the same B can be caught by multiple Cs).
Add this to the fwdControl class.
Need to add Constructor (probably best to build the matrix in R then easy to construct in C++)

Add relFishery and relCatch to control@target@element

Catches can be relative to catches in another fishery, not just to itself.

Test project_biols is doing recruitment OK

Test when calc_rec and hperiod etc are finalised

Compilation error under linux 64 bit and R-mkl

From @poldokim on June 9, 2016 7:40

When I try to compile FLash packages I have this error:

R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

* installing *source* package ‘FLash’ ...
** libs
g++ -I/usr/include/R/ -DNDEBUG -D_FORTIFY_SOURCE=2 -I../inst/include -fpic -O3 -m64 -I/opt/intel/composerxe/linux/mkl/include -c FLCoreClasses.cpp -o FLCoreClasses.o
g++ -I/usr/include/R/ -DNDEBUG -D_FORTIFY_SOURCE=2 -I../inst/include -fpic -O3 -m64 -I/opt/intel/composerxe/linux/mkl/include -c FLashDLL.cpp -o FLashDLL.o
FLashDLL.cpp: In function ‘SEXPREC* fwd_adolc_FLBiol(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:

FLashDLL.cpp:83:14: error: cannot convert ‘bool’ to ‘SEXP {aka SEXPREC*}’ in return
       return false;
              ^~~~~

FLashDLL.cpp: In function ‘SEXPREC* fwd_adolc_FLBiols(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:

FLashDLL.cpp:133:14: error: cannot convert ‘bool’ to ‘SEXP {aka SEXPREC*}’ in return
       return false;
              ^~~~~

FLashDLL.cpp:139:14: error: cannot convert ‘bool’ to ‘SEXP {aka SEXPREC*}’ in return
       return false;
              ^~~~~

/usr/lib64/R/etc/Makeconf:141: recipe for target 'FLashDLL.o' failed
make: *** [FLashDLL.o] Error 1

ERROR: compilation failed for package ‘FLash’

Do you have any suggestion?

Copied from original issue: flr/FLash#3

Finish and test operating_model::f_prop_spwn() when hperiod in FLFishery set

Add srp() methods to operatingModel class

Outline is there. Fill it in.

Things to do for control object

Before dispatch to C++:
Add a 'timestep' column that translates the year / season columns to the timestep.
Check that the timesteps are consecutive
Add 'biol' column for targets that relate to biols
Add a 'target' column (integer, consecutive, starting from 1). 'target' is used to identify which targets are to be processed together, i.e. multiple rows can have the same 'target' value (they are simultaneous targets).
Add the 'FCB' integer matrix as a slot to object@target. This is a map that describes what FLFishery / FLCatch combination catches which FLBiol. It is n x 3 with colnames c('F', 'C', 'B'). The values are integer describing the positions of the FLFishery etc within the lists that are based to the C++ side. See examples for more detail.

It is currently possible for the solver to give negative effort!

Also, better reporting from solver.
What happens if only some iters solve?

FLasher::poly conficts with stats::poly

Flasher hides stats::poly. Could the name be changed?

stats::poly
function (x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE)
{ [...]

FLFishery class in R should only have length 1 in unit dimension for most slots

effort
hperiod
etc

RCpp Flasher plugin might not work in Windows

This line (R/rcpp_plugin.R, line 6) has

FLasher.so_location <- paste(.libPaths()[1], "/FLasher/libs/FLasher.so",sep="")

but this should not work in Windows, it will at least need to use

'FLasher.dll'

We need to find out how to make this cross-platform

Look into implementing SR models with covariates

We currently have one model with covariates in FLCore, rickerCA

rec ~ a * (1 - c * covar) * ssb * exp(-b * ssb)

What would we need to make it work in FLasher? The sr slot in the new FLBiol can accomodate the covariate(s) FLQuant(s), but they would have to be passed via FLBiolCpp to FLasher Rcpp.

Update fwdCtrl class

Changes made at R level need to be made in C++

Add min / max capability to target evaluation

Implement FLQuant %*% operators in Cpp

The %*%, %/%, %+% and %-% operators for FLQuant are able to extend one dimension of length one in one object to the length in the other. They could be very useful in Cpp.

To be done in the near future

Change ssb method for FLBiol to srp

For consistency, the ssb method for FLBiol, both bin FLasher and FLCore, should be called srp, spawning reproductive potential.

ADD warning() if fwdControl sets ssb or biomass target for year 1

Setting ssb or stock targets on the first year of projection can only be done by modifying catch and F in the previous year, so that catch.n, harvest and stock.n are consistent.

Normal practice should be to have ssb/stock targets only from year 2.

A warning will be issued, at both fwdControl() and fwd()

[ and [<- methods to be adapted for wfdControl without fwdElement

New equation for F ~ effort + biomass

The calculation of from effort and biomass should include 3 variables, alpha, beta and epsilon, to account for scaling, and the non-linearity of F and effort and of F and biomass, respectively.

$F = \alpha \cdot E ^\epsilon \cdot sel \cdot B^\beta$

The new parameter, epsilon, should be added to the catch.q slot of FLCatch flr/FLFishery#4

Finish Fbar target

Expose calc catchability function in Cpp to R in helpful way so used by FLOM class

In C++ method om.f_prop_spwn() fix case when hperiod = NA

If hperiod = NA, then no fishing has taken place, all spwn happens before fishing, fprop = 0.0

Need a method for calculating number of timesteps between recruitment and SRP had produces the recruitment

Enhance 1 or n iters performance

Currently fwdControl must have n iters even if target is not varying

Add tests for operating_model::calc_rec method

Need to wait for srp_timelag() to be added and tested

Add dimension checks for objects in operatingModel constructor

Constructor for fwdControl with iters = integer

Can we have a constructorfor fwdControl that looks like:

setMethod('fwdElement', signature(element='data.frame', iters='integer'),
which builds the iter array with appropriate number of iters

minAge and maxAge in fwdControl only refer to ages of target Biol / Catch not relBiol / relCatch

We only have one minAge and maxAge per target line in fwdControl.
These are used to calculate the Fbar when evaluating get_target_value_hat and eval_om.
However, you can have targets relative to another object. e.g. F on one Biol relative to F on another Biol.
At the moment the same age range will be used to calculate Fbar for both Biols.This is not right.

Solution:
include relMinAge and relMaxAge in Control.
include minAge / maxAge information somewhere else.

Why does fwdControl need year / season as indices, and also a timestep column?

Growth and ages better modelled

should we include a relative target type in fwdControl?

Can we have Catch should be relative to Landings etc?
Would need to add relQuant in the fwdControl

How is F calculated?

Remove F member of operatingModel and replace with F() method. F can be:
'partial': F(Fishery, Catch)
'total': F(Biol). (The sum of all partial Fs fishing that Biol)

How is F calculated?
F = Sel. Q. Effort
F = alpha. Sel. Q. Effort^beta (where do alpha and beta come from?)

How is Q calculated? From Biol and Q_params? Is is age-structured?

Fix catch_q operator for FLCatch

All tests have been commented out.
Need better way for getting F = alpha * B ^ beta * sel * effort for each FLC - FLB interaction

Min / Max targets evaluated using CondEx

And add example to FLash vs FLasher as to how this could go wrong

Change name of 'mean' srr model to 'fixed'

Decide time step notation of abundance targets (SSB, biomass, etc.)

Does the target time step refer to abundance at start of year (determined by fishing effort in previous year), or abundance at end of the year (determined by fishing effort in current year)?

Add ability for targets that are relative within the same time step

Biomass calculation should include time of fishing

The calculation for Q is: alpha * B ^-beta

The B should be the biomass at the time of fishing. At the moment the 'biomassb method for a fwdBiol returns the Biomass at the start of the year. If there are more than one FLCatch operating on the stock and they fish at different times, the B will need to be the B at the time of fishing.

Add proper constructor and wrapper for catch_q member of FLCatch in Cpp