convert data.frame to FLStock

[GeoTuxMan]

Hi,

I try to do a stock assement with sca() method.
After I convert my data.frame to FLStock object :
mystock<-as.FLStock(land_t)
the command:
summary(mystock)
give me only values of one (1).

My all code:
`#stock assesment

library(FLCore)
library(ggplotFL)
library(FLa4a)
library(xlsx)
library(plotly)

dat=read.xlsx("Sprot_FLR.xlsx", sheetIndex = 1)

dat<-data.frame(dat$slot,dat$age, dat$year, dat$data, dat$units)
dat2<-na.omit(dat)

select only landings in tone

land_t <- na.omit(subset(dat, dat2$dat.slot=="landings", select=-dat.slot))
colnames(land_t)<- c("age","year","data","units")
landst <- as.FLQuant(land_t)
summary(landst)
plot(landst)

plot1=data.frame(land_t)

#qplot(x=year, y=data, data=plot1, color=factor(age),geom=c("point","line"),ylab="Catch (t)", xlab="")
p1<-ggplot(plot1, aes(x=year, y=data, group = age)) +
geom_line(aes(colour=as.factor(age))) + ylab("Catch (t)") + xlab("") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
ggplotly(p1)

select only landings in numbers

land_n <- na.omit(subset(dat, dat2$dat.slot=="landings.n", select=-dat.slot))
colnames(land_n)<- c("age","year","data","units")
landsn <- as.FLQuant(land_n)
summary(landsn)
plot(landsn)
plot2=data.frame(land_n)

#qplot(x=year, y=data, data=plot2, color=factor(age),geom=c("point","line"),ylab="Catch (1000^3)", xlab="")
p2<-ggplot(plot2, aes(x=year, y=data, group = age)) +
geom_line(aes(colour=as.factor(age))) + ylab("Catch (1000^3)") + xlab("") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
ggplotly(p2)

convert dataframe to FLStock

mystock<-as.FLStock(land_t)
summary(mystock) # empty ?!

add an index of abundance : cpue

#the statistical catch-at-age model
#fit <- sca(mystock, cpue)

update FLStock object

#stk<-mystock+fit
#plot(stk)

plot fitted vs observed catch-at-age

#plot(fit, ple4)

`
Sprot_FLR.xlsx
I look forward to some tips ...
Cheers !

[iagomosqueira]

The table in the XLSX file has data labelled as "landings" and "landings.n". But landings in an FLStock refers to total landings in weight, and not by age. We usually have landings.n, in number, and landings.wt, the mean weight at age in the landings, usually in kg.

From simply the landings.n data, you could create an FLStock using

library(FLCore)
library(xlsx)

dat <- na.omit(read.xlsx("Sprot_FLR.xlsx", sheetIndex = 1, stringsAsFactors=FALSE))
stk <- as(dat[dat$slot == "landings.n",], "FLStock")

If you add other data to the same table, you can add it to the FLStock using the same code.

Maybe take a look at the example dataset for the class, data(ple4) to see what needs to go into each slot

[iagomosqueira]

Also, to use FLa4a::sca() you need to provide at least:

• catch.n, usually a sum of landings.n and discards.n
• catch.wt
• m
• mat
• stock.wt
• harvest.spwn and m.spwn

And one or more indices of abundance, as objects of class FLIndex or FLIndices

[GeoTuxMan]

Dear Iago, Thank you very much for your reply. Now, summary(stk) work fine. If discards is equal with 0, can I use my landings.n like catch.n ? Cheers ! George În vin., 15 feb. 2019 la 11:56, Iago Mosqueira <notifications@github.com> a scris:

…

Also, to use FLa4a::sca() you need to provide at least: - catch.n, usually a sum of landings.n and discards.n - catch.wt - m - mat - stock.wt - harvest.spwn and m.spwn And one or more indices of abundance, as objects of class FLIndex or FLIndices — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMazJQUMI0jRzNsV7Wr1mEP2OB-mybks5vNoQ0gaJpZM4a2YPY> .

[iagomosqueira]

You should do

discards.n(stk) <- 0
discards.wt(stk) <- landings.wt(stk)
catch(stk) <- computeCatch(stk, "all")

or simply load the data into the catch.n slot. And then add all the other biological information.

[GeoTuxMan]

For "index of abundance", I use CPUE; my file look like that: year index 1980 384 1981 2775 ............ How can I load this data into an FLIndex object ? În vin., 15 feb. 2019 la 12:27, Iago Mosqueira <notifications@github.com> a scris:

…

You should do discards.n(stk) <- 0 discards.wt(stk) <- landings.wt(stk) catch(stk) <- computeCatch(stk, "all") or simply load the data into the catch.n slot. And then add all the other biological information. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa10Yq9DAjc-O7V64MxTiVSXlVv0Yks5vNouLgaJpZM4a2YPY> .

[iagomosqueira]

Is this a biomass index? Or is it by age?

Generally, take a look at

http://www.flr-project.org/doc/Loading_your_data_into_FLR.html

for how to load data into FLR.

[GeoTuxMan]

Dear Iago, My CPUE is "kg/fishing day" by year. I try this code:

indices<-read.xlsx("Sprat_Index.xlsx",sheetIndex = 1, stringsAsFactors=FALSE) indices<-as.FLQuant(as.matrix(indices), dimnames=list(year=1981:2007,age=0:4))

The error:

> indices<-as.FLQuant(as.matrix(indices), dimnames=list(year=1981:2007,age=0:4))Error in array(object, dim = dim, dimnames = filldimnames(dimnames, dim = dim)) : length of 'dimnames' [1] not equal to array extent

I use "Loading your data into FLR", pag.8 All the best, George În vin., 15 feb. 2019 la 14:26, Iago Mosqueira <notifications@github.com> a scris:

…

Is this a biomass index? Or is it by age? Generally, take a look at http://www.flr-project.org/doc/Loading_your_data_into_FLR.html for how to load data into FLR. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa1ICtAZ3JxKdEU-fnweAu9I08RjXks5vNqeNgaJpZM4a2YPY> .

[iagomosqueira]

What are the dimensions of the result of as.matrix(indices)?

dim(as.matrix(indices))

should be c(5, 27). First dimension is age, second year.

With regards the data, a biomass index won't have enough information to fit sca(). The method assumes an index at age is available, covering at least some of those ages, like from a survey.

[GeoTuxMan]

Dear Iago,

dim(as.matrix(indices))[1] 27 2

You mean, the file need to be like that ?: year age index 1980 0 123 1980 1 234 1980 2 345 1980 3 456 1980 4 101 1981 0 233 ............................ All the best ! George În lun., 18 feb. 2019 la 18:47, Iago Mosqueira <notifications@github.com> a scris:

…

What are the dimensions of the result of as.matrix(indices)? dim(as.matrix(indices)) should be c(5, 27). First dimension is age, second year. With regards the data, a biomass index won't have enough information to fit sca(). The method assumes an index at age is available, covering at least some of those ages, like from a survey. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa_SUulqUnlWc028yEiVlKLrrRoFRks5vOtkIgaJpZM4a2YPY> .

[iagomosqueira]

It all depends on what information you have. sca() does better when the index of abundance has information on the cohorts' changes in abundance, say from survey at age. If you only have a biomass index, like commercial CPUE, then

• Pass to sca an object of class FLIndexBiomass, created using FLIndexBiomass(index=FLQuant()) where that FLQuant was created as above.
• You might need to set the n1model, the initial abundances at age, as sca will have little information to estimate it.

[GeoTuxMan]

I find some survey indices at age. Now, I have this error:

> fit <- sca(stk, indices)Error in a4aInternal(fmodel = fmodel, qmodel = qmodel, srmodel = srmodel, : only non-zero survey indices allowed.

It's need to replace zero with NA ? În mar., 19 feb. 2019 la 10:38, Iago Mosqueira <notifications@github.com> a scris:

It all depends on what information you have. sca() does better when the index of abundance has information on the cohorts' changes in abundance, say from survey at age. If you only have a biomass index, like commercial CPUE, then - Pass to sca an object of class FLIndexBiomass, created using FLIndexBiomass(index=FLQuant()) where that FLQuant was created as above. - You might need to set the n1model, the initial abundances at age, as sca will have little information to estimate it. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMawfWy50kDuxThbK0oFd4B0nQa278ks5vO7f9gaJpZM4a2YPY> .

0 0 0 0 0 0 0 0 0 0 0 1.999702558 0 0 0 0 0 4.090467626 24.59369527 0 0 0 0 0 0 22.17689243 0 6.942361111 100.8988914 104.6245942 205.4512046 651.3813491 535.2796209 17.89448441 308.6765189 185.2005105 127.3622926 101.0953627 110.1317668 110.082504 12.16489162 6.836087842 12.23692951 0 15.71600719 253.4737303 32.04131227 72.06232687 4.561478599 13.42921914 54.195232 66.31854545 87.92669323 72.97230769 557.7030093 339.1920177 351.7167208 880.7008303 32.96694437 503.5157752 380.0788489 487.0410509 292.2161089 200.9568627 89.00261593 184.9724866 201.8776864 128.8718206 94.79375141 71.34752122 56.13926358 371.0843525 342.0903678 467.09113 331.6038781 127.6290632 74.96146096 80.4232 95.33832727 36.07649402 88.45846154 1258.881481 976.7871397 1012.855114 230.1053491 147.7828541 130.5846987 302.7746763 14.66009852 8.795802609 6.048868778 51.756956 63.24985128 44.4632915 48.08933718 50.28322391 20.11834174 49.58439665 326.7350719 173.1872154 212.8967193 182.2063712 52.48470518 33.91550518 17.454528 52.40465455 9.839043825 47.12615385 488.2793981 729.9068736 756.8587662 53.41731319 7.957538296 7.058632363 15.03136691 4.072249589 2.443278503 1.680241327 0 13.51650803 2.151449589 0.950382158 0 0 0 0 0 0 0 0 0 1.84704 2.665745455 0.156175299 11.13538462

[iagomosqueira]

A4a works in log space, so zeroes are a problem. Try substituting them with a small number, say 1e-6

…

--- Sent from a mobile

On 19 feb 2019 at 12:27 PM, <Gheorghe Sarbu> wrote: I find some survey indices at age. Now, I have this error: > > fit <- sca(stk, indices)Error in a4aInternal(fmodel = fmodel, qmodel = qmodel, srmodel = srmodel, : > > only non-zero survey indices allowed. > > It's need to replace zero with NA ? În mar., 19 feb. 2019 la 10:38, Iago Mosqueira ***@***.***> a scris: > It all depends on what information you have. sca() does better when the > index of abundance has information on the cohorts' changes in abundance, > say from survey at age. If you only have a biomass index, like commercial > CPUE, then > > - Pass to sca an object of class FLIndexBiomass, created using > FLIndexBiomass(index=FLQuant()) where that FLQuant was created as > above. > - You might need to set the n1model, the initial abundances at age, as > sca will have little information to estimate it. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#128 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/APeMawfWy50kDuxThbK0oFd4B0nQa278ks5vO7f9gaJpZM4a2YPY> > . > 0 0 0 0 0 0 0 0 0 0 0 1.999702558 0 0 0 0 0 4.090467626 24.59369527 0 0 0 0 0 0 22.17689243 0 6.942361111 100.8988914 104.6245942 205.4512046 651.3813491 535.2796209 17.89448441 308.6765189 185.2005105 127.3622926 101.0953627 110.1317668 110.082504 12.16489162 6.836087842 12.23692951 0 15.71600719 253.4737303 32.04131227 72.06232687 4.561478599 13.42921914 54.195232 66.31854545 87.92669323 72.97230769 557.7030093 339.1920177 351.7167208 880.7008303 32.96694437 503.5157752 380.0788489 487.0410509 292.2161089 200.9568627 89.00261593 184.9724866 201.8776864 128.8718206 94.79375141 71.34752122 56.13926358 371.0843525 342.0903678 467.09113 331.6038781 127.6290632 74.96146096 80.4232 95.33832727 36.07649402 88.45846154 1258.881481 976.7871397 1012.855114 230.1053491 147.7828541 130.5846987 302.7746763 14.66009852 8.795802609 6.048868778 51.756956 63.24985128 44.4632915 48.08933718 50.28322391 20.11834174 49.58439665 326.7350719 173.1872154 212.8967193 182.2063712 52.48470518 33.91550518 17.454528 52.40465455 9.839043825 47.12615385 488.2793981 729.9068736 756.8587662 53.41731319 7.957538296 7.058632363 15.03136691 4.072249589 2.443278503 1.680241327 0 13.51650803 2.151449589 0.950382158 0 0 0 0 0 0 0 0 0 1.84704 2.665745455 0.156175299 11.13538462 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[GeoTuxMan]

OK, many thanks. Now....

> fit <- sca(stk, indices)Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) : A term has fewer unique covariate combinations than specified maximum degrees of freedom >

În mar., 19 feb. 2019 la 13:58, Iago Mosqueira <notifications@github.com> a scris:

…

A4a works in log space, so zeroes are a problem. Try substituting them with a small number, say 1e-6 --- Sent from a mobile > > On 19 feb 2019 at 12:27 PM, <Gheorghe Sarbu> wrote: > > I find some survey indices at age. Now, I have this error: > > > > fit <- sca(stk, indices)Error in a4aInternal(fmodel = fmodel, qmodel = qmodel, srmodel = srmodel, : > > > > only non-zero survey indices allowed. > > > > > It's need to replace zero with NA ? > > În mar., 19 feb. 2019 la 10:38, Iago Mosqueira ***@***.***> a > scris: > > > It all depends on what information you have. sca() does better when the > > index of abundance has information on the cohorts' changes in abundance, > > say from survey at age. If you only have a biomass index, like commercial > > CPUE, then > > > > - Pass to sca an object of class FLIndexBiomass, created using > > FLIndexBiomass(index=FLQuant()) where that FLQuant was created as > > above. > > - You might need to set the n1model, the initial abundances at age, as > > sca will have little information to estimate it. > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > <#128 (comment)>, or mute > > the thread > > < https://github.com/notifications/unsubscribe-auth/APeMawfWy50kDuxThbK0oFd4B0nQa278ks5vO7f9gaJpZM4a2YPY > > > . > > > > 0 0 0 0 0 0 0 0 0 0 0 1.999702558 0 0 0 0 0 4.090467626 24.59369527 0 0 0 0 0 0 22.17689243 0 > 6.942361111 100.8988914 104.6245942 205.4512046 651.3813491 535.2796209 17.89448441 308.6765189 185.2005105 127.3622926 101.0953627 110.1317668 110.082504 12.16489162 6.836087842 12.23692951 0 15.71600719 253.4737303 32.04131227 72.06232687 4.561478599 13.42921914 54.195232 66.31854545 87.92669323 72.97230769 > 557.7030093 339.1920177 351.7167208 880.7008303 32.96694437 503.5157752 380.0788489 487.0410509 292.2161089 200.9568627 89.00261593 184.9724866 201.8776864 128.8718206 94.79375141 71.34752122 56.13926358 371.0843525 342.0903678 467.09113 331.6038781 127.6290632 74.96146096 80.4232 95.33832727 36.07649402 88.45846154 > 1258.881481 976.7871397 1012.855114 230.1053491 147.7828541 130.5846987 302.7746763 14.66009852 8.795802609 6.048868778 51.756956 63.24985128 44.4632915 48.08933718 50.28322391 20.11834174 49.58439665 326.7350719 173.1872154 212.8967193 182.2063712 52.48470518 33.91550518 17.454528 52.40465455 9.839043825 47.12615385 > 488.2793981 729.9068736 756.8587662 53.41731319 7.957538296 7.058632363 15.03136691 4.072249589 2.443278503 1.680241327 0 13.51650803 2.151449589 0.950382158 0 0 0 0 0 0 0 0 0 1.84704 2.665745455 0.156175299 11.13538462 > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub, or mute the thread. > > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMay8qm3Ih_mtydBhP-vJgNFoU4fPgks5vO-bvgaJpZM4a2YPY> .

[iagomosqueira]

The a4a model is built around a series of submodels, see http://www.flr-project.org/doc/Statistical_catch_at_age_models_in_FLa4a.html foir some explanation and examples.

A call top sca() builds a default model according to the dimensions of the data provided, but it is never fully appropriate. You will need to look at each of the submodels and constrcut those that are right for your data. For example, trhe default srmodel is a factor per year, but you could assume a given SRR, say bevholt.

[GeoTuxMan]

> fit <- sca(stk, indices, fmodel=fmod, qmodel=qmod, srmodel=srmod)This version of C:/Program Files/R/R-3.4.1/library/FLa4a/bin/windows\a4a.exe is not compatible with the version of Windows you're running. Check your computer's system information to see whether you need a x86 (32-bit) or x64 (64-bit) version of the program, and then contact the software publisher.Error in file(file, "r") : cannot open the connectionIn addition: Warning messages:1: running command 'C:\Windows\system32\cmd.exe /c cd /D"C:\Users\User\AppData\Local\Temp\RtmpWIcr3K\file191c6afd982" & a4a > logfile.txt' had status 1 2: In shell(paste0("cd /D", shQuote(wkdir), " & a4a ", args, " > logfile.txt")) : 'cd /D"C:\Users\User\AppData\Local\Temp\RtmpWIcr3K\file191c6afd982" & a4a > logfile.txt' execution failed with error code 13: In file(file, "r") : cannot open file 'C:\Users\User\AppData\Local\Temp\RtmpWIcr3K\file191c6afd982/a4a.par': No such file or directory

I have Windows 7 32-bit, RStudio 1.0.153, R 3.4.1, FLa4a 1.6.4 Where do I find FLa4a for 32 bit ? În mar., 19 feb. 2019 la 14:16, Iago Mosqueira <notifications@github.com> a scris:

…

The a4a model is built around a series of submodels, see http://www.flr-project.org/doc/Statistical_catch_at_age_models_in_FLa4a.html foir some explanation and examples. A call top sca() builds a default model according to the dimensions of the data provided, but it is never fully appropriate. You will need to look at each of the submodels and constrcut those that are right for your data. For example, trhe default srmodel is a factor per year, but you could assume a given SRR, say bevholt. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#128 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APeMa8BCEd61osRlXTn2-GuJLQqAb2pkks5vO-sdgaJpZM4a2YPY> .