While calibrating using method CMA-ES, pop size = 12, nbcores = 6, maxgen = 3

• only one simulation is run at a time (no folder >i0 )
• the command for launching simulations is repeated 11 times (with name "_i0") although popsize is 12
• moreover although I limited to 3 generations it launched more and if I get it correctly plannes to realise 36 iterations (pop size x max gen)
• finally the fitness function is said to be flat which is weird (the model was previously calibrated and we know the function is responsive in these domain of values)

while trying to launch calibrar using a different algorithm (CMA-ES), it does not create the ix sub-folders, but just i0 the first one (which is empty).
here is the error message

calib<- calibrate(par=rep(NA,11),fn=objfn, method='cmaes', lower=0,
upper=0.001, control=control)
Error in file(con, "r") : cannot open the connection
Calls: calibrate -> .calibrar -> .cmaes

Hi, Ricardo
I've also run another code and cannot get it run. I'm wondering if you can help me figure out the problem. I think it also has something to do with calibrar.R.
Thanks a lot!
Yi

copy all that is needed for the calibration

YScalib = Calib_YSomose(path = path.dir)

move to the calibration folder

setwd (YScalib$path)
getwd()
[1] "F:/China_YellowSea_Institute/extdata/calib_demo"

run the calibration script

source (YScalib$file)
Creating observed data list for calibration...
Variable: TrachurusTrachurus.biomass

Variable: SardinaPilchardus.biomass

Variable: SardinellaAurita.biomass

Variable: EngraulisEncrasicolus.biomass

Variable: OctopusVulgaris.landings

Variable: MelicertusKerathurus.landings

Variable: MetapenaeusMonoceros.landings

Variable: TrachurusTrachurus.landings

Variable: SardinaPilchardus.landings

Variable: SardinellaAurita.landings

Variable: EngraulisEncrasicolus.landings

Variable: DiplodusAnnularis.landings

Variable: MustelusMustelus.landings

Variable: MerlucciusMerluccius.landings

Variable: PagellusErythrinus.landings

Variable: OctopusVulgaris.thr

Variable: MelicertusKerathurus.thr

Variable: MetapenaeusMonoceros.thr

Variable: TrachurusTrachurus.thr

Variable: SardinaPilchardus.thr

Variable: SardinellaAurita.thr

Variable: EngraulisEncrasicolus.thr

Variable: DiplodusAnnularis.thr

Variable: MustelusMustelus.thr

Variable: MerlucciusMerluccius.thr

Variable: PagellusErythrinus.thr

Optimizing 'popsize' to work with 2 cores.
Error in { : task 1 failed - "cannot open the connection"

Hi,
I am still (succesfully) using calibrar to calibrate the ISIS-Fish with the method AHR-ES. I have a question regarding the criteria used to stop the algo. I am afraid it is not documented. Is control$convergence <- 0.001 the stopping criteria ? what does it mean ? that it stops when the objective function does not change by more than 0.001 from one generation to the other ?

Thank you

Hi, Ricardo
I've got an error when running the demo, I'm wondering if someone has the same problem or just myself?
Error in { : task 1 failed - "The'yield'variable is NULL."
Thanks!
Yi

library(devtools)
install_github("roliveros-ramos/calibrar")
Downloading GitHub repo roliveros-ramos/calibrar@master
√ checking for file 'C:\Users\HP\AppData\Local\Temp\RtmpOcPSpo\remotes6c984f691161\roliveros-ramos-calibrar-4d56e1d/DESCRIPTION' ...

• preparing 'calibrar':
  √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'calibrar_0.2.0.9002.tar.gz'

Installing package into ‘C:/Users/HP/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

• installing source package 'calibrar' ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'calibrar'
  finding HTML links ... done
  SphereN html
  calibrar-package html
  calibrarDemo html
  calibrate html
  createObjectiveFunction html
  getCalibrationInfo html
  getObservedData html
  optimES html
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  *** arch - i386
  *** arch - x64
  ** testing if installed package can be loaded from final location
  *** arch - i386
  *** arch - x64
  ** testing if installed package keeps a record of temporary installation path
• DONE (calibrar)

demo=osmose_calib_demo(path=NULL) #run successfully
setwd(demo$path) #run successfully
source(demo$file) #has the message
Loading required package: calibrar
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Creating observed data list for calibration...
Variable: TrachurusTrachurus.biomass

Variable: SardinaPilchardus.biomass

Variable: SardinellaAurita.biomass

Variable: EngraulisEncrasicolus.biomass

Variable: OctopusVulgaris.landings

Variable: MelicertusKerathurus.landings

Variable: MetapenaeusMonoceros.landings

Variable: TrachurusTrachurus.landings

Variable: SardinaPilchardus.landings

Variable: SardinellaAurita.landings

Variable: EngraulisEncrasicolus.landings

Variable: DiplodusAnnularis.landings

Variable: MustelusMustelus.landings

Variable: MerlucciusMerluccius.landings

Variable: PagellusErythrinus.landings

Variable: OctopusVulgaris.thr

Variable: MelicertusKerathurus.thr

Variable: MetapenaeusMonoceros.thr

Variable: TrachurusTrachurus.thr

Variable: SardinaPilchardus.thr

Variable: SardinellaAurita.thr

Variable: EngraulisEncrasicolus.thr

Variable: DiplodusAnnularis.thr

Variable: MustelusMustelus.thr

Variable: MerlucciusMerluccius.thr

Variable: PagellusErythrinus.thr

Optimizing 'popsize' to work with 2 cores.
Error in { : task 1 failed - "The'yield'variable is NULL."