Bayesian age-period-cohort analysis with INLA

[jian iron]

Hello,I'm doing a projection using bayesian age-period-cohort analysis with INLA.

Here's the code:

counts <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/death_counts.csv", header = T)
 pop <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/total_popu.csv", header = T)
 agegroup = c("35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74","75-79", "80-84")
us.APC = APCList(counts, pop, gf=5, agelab=agegroup)

 col <- c("grey20", "grey35", "grey50", "grey65", "grey75", "grey85")
 ratesByAge(us.APC, scale=100000, age=seq(37,82,5), per=1990:2019, col=col)
us.res = BAPC(us.APC, predict=list(npredict=10, retro=TRUE))
sh: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla: Permission denied
Error in inla.inlaprogram.has.crashed() :
  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
  If this does help; please contact the developers at <he...@r-inla.org>.

What's the problem?

Thanks , sincerely looking forward to your reply.

[Helpdesk]

you may try to do, in shell

chmod +x /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla

or 'sudo chmod....'

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Håvard Rue
he...@r-inla.org

[jian iron]

I've tried but more errors arise:

counts <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/death_counts.csv", header = T)

 pop <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/total_popu.csv", header = T)
 agegroup = c("35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74","75-79", "80-84")
us.APC = APCList(counts, pop, gf=5, agelab=agegroup)

 col <- c("grey20", "grey35", "grey50", "grey65", "grey75", "grey85")
 ratesByAge(us.APC, scale=100000, age=seq(37,82,5), per=1990:2019, col=col)

us.res = BAPC(us.APC, predict=list(npredict=10, retro=TRUE))

/Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla: line 11: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla.binary: Permission denied
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla: line 11: exec: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/inla.binary: cannot execute: Undefined error: 0

Error in inla.inlaprogram.has.crashed() :
  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
  If this does help; please contact the developers at <he...@r-inla.org>.

[INLA help]

It’s an error in the installation.    Try to remove the inla package or even R-4.1 itself. And reinstall.  

—

Haavard Rue

HelpDesk 

help@r-inla. org

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/7d254d87-64d7-4285-aaf2-e0c2543d43abn%40googlegroups.com.

[jian iron]

New errors arise after the reinstallation

install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)

library(INLA)

counts <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/death_counts.csv", header = T)
 pop <- read.csv("/Users/ironjian/Downloads/ironjian\ 4/total_popu.csv", header = T)
 agegroup = c("35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74","75-79", "80-84")
us.APC = APCList(counts, pop, gf=5, agelab=agegroup)

 col <- c("grey20", "grey35", "grey50", "grey65", "grey75", "grey85")
 ratesByAge(us.APC, scale=100000, age=seq(37,82,5), per=1990:2019, col=col)
us.res = BAPC(us.APC, predict=list(npredict=10, retro=TRUE))

Error in inla.check.control(control.inla, data) :
  Name `lincomb.derived.only' in control-argument `control.inla', is void.

  Valid ones are:
        adapt.hessian.max.trials
        adapt.hessian.mode
        adapt.hessian.scale
        adaptive.max
        adjust.weights
        b.strategy
        cmin
        constr.marginal.diagonal
        control.vb
        cpo.diff
        cutoff
        diagonal
        diff.logdens
        dz
        fast
        force.diagonal
        global.node.degree
        global.node.factor
        h
        huge
        improved.simplified.laplace
        int.design
        int.strategy
        interpolator
        lincomb.derived.correlation.matrix
        linear.correction
        mode.known
        npoints
        num.gradient
        num.hessian
        numint.abserr
        numint.maxfeval
        numint.relerr
        optimise.strategy
        optimiser
        parallel.linesearch
        print.joint.hyper
        reordering
        restart
        skip.configurations
        stencil
        step.factor
        step.len
        strategy
        stupid.search
        stupid.search.factor
        stupid.search.max.iter
        tolerance
        tolerance.f
        tolerance.g
        tolerance.step
        tolerance.x
        use.directions
        verbose

[INLA help]

Make sure you use R-4.1 and the testing version


The code you’re running is old and that argument that gives the error is not used anymore 

—

Haavard Rue

HelpDesk 

help@r-inla. org

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/22167010-4362-4904-9331-60caf0e429f8n%40googlegroups.com.

[Andrea Riebler]

The BAPC package has been updated so that it should work fine now.