Unable to replace values in new FLBiol @mat slot

[marchtaylor]

I'm having difficulties trying to replace some NAs in the @mat slot of an FLBiol object (also applies to @fec slot). The error reads "Error in names(lst) <- names(x) : 'names' attribute [1] must be the same length as the vector [0]". As far I can tell, the names of FLQuant objects (original and replacement) are the same, so I don't see where the problem lies.

Here is an example:

library(FLCore)
data(ple4.biol)

# replacement fails
tmp <- replace(ple4.biol@mat$mat, ple4.biol@mat$mat==0, 0.1)
ple4.biol@mat$mat <- tmp

# names are identical
names(ple4.biol@mat$mat)
names(tmp)

# same operation in another slot works
tmp <- replace(ple4.biol@spwn, ple4.biol@spwn==0, 0.1)
ple4.biol@spwn <- tmp

[marchtaylor]

possibly related: window() and trim() do not affect the FLBbiol slots @mat, @fec, and @rec .

[marchtaylor]

I think I have found a solution:

library(FLCore)
data(ple4.biol)

# these work
tmp <- replace(ple4.biol@mat$mat, ple4.biol@mat$mat==0, 0.1)
mat(ple4.biol) <- tmp

mat(ple4.biol)[mat(ple4.biol)==0.1] <- 0.2

mat(ple4.biol) <- replace(mat(ple4.biol), mat(ple4.biol)==0.2, 0.3)

[iagomosqueira]

These methods need redoing for classes like FLBiol, containing predictModel. Do tell us about other methods failing. Will do soon and get back to you.

[iagomosqueira]

Hi. Long delay, but after fixing initially window and trim I got to look at this.

First, you should not use @ and $ unless you can check you are passing to the object a value of the exact class required. To modify an FLQuant inside the mat slot of your FLBiol you can use three calls:

mat(ple4.biol) <- FLQuants(mat=tmp)
mat(ple4.biol) <- tmp
mat(ple4.biol, 'mat') <- tmp

First you can pass an FLQuants with tmp given the default name that matches the formula in @model. You can directly pass the new FLQuant, and it will be plcaed by default under the mat name in the FLQuants object. Or you could specify the element isnide the FLQuants object in the assigment operation.

The first two options have always been there, the third one I have just added, so it will be only available in gihutb until 2.6.5 is released next week.

Note that you cannot do

mat(ple4.biol)$mat <- tmp

as the $ subsetting is applied on the result of mat(ple4biol) which is already and FLQuant.

Do these options cover your needs?

Then, for accessing the contents of mat, we now have

# Returns the calculation
mat(ple4.biol)

# Returns the predictModel object
mat(ple4.biol, compute=FALSE)

# Same as above
mat(ple4.biol, FALSE)

# Returns the "mat" FLQuant inside the predictModel FLQuants
mat(ple4.biol, name="mat")

Again, please do let me know if this is eniught or we need to find better ways of using these slots

@dorleta @ssanchezAZTI

[iagomosqueira]

Changes are available in the latest commit in master, 40273f4

[marchtaylor]

Dear Iago - Thanks for this. This all works and makes sense to me now. Cheers, M