R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MONETARY failed, using "C"
3: Setting LC_PAPER failed, using "C"
4: Setting LC_MEASUREMENT failed, using "C"
> # Clear objects -------
> rm(list = ls())
> graphics.off()
>
> #Load packages---------
> library (pomp)
> library (plyr)
>
> #setwd("E:/Dropbox/���THESIS!!!/POMP/VS2EI2") #blackhawck
> #setwd("X:/Dropbox/���THESIS!!!/POMP/VS2EI2") #betty
>
> #Load POMP object
> source("pomp_object_VS2EI2_Nov14_Cluster.R")
During startup - Warning messages:
1: Setting LC_TIME failed, using "C"
2: Setting LC_MONETARY failed, using "C"
3: Setting LC_PAPER failed, using "C"
4: Setting LC_MEASUREMENT failed, using "C"
Warning message:
in �^�^�pomp�^�^�: the supplied covariate covariate times �^�^�tcovar�^�^� do not embrace the data times: covariates may be extrapolated
>
> # Cluster input --------------------------------------
> indexCluster <- as.numeric(Sys.getenv("SLURM_ARRAY_TASK_ID"))
> seqP <- seq(from = 1, to = 10000, by = 100)
> now.num <- seqP[indexCluster]
>
> #Define params for POMP ---------------------
> y <- read.csv("mifInput_S1_VS2EI2_Nov13.csv")
> params <- as.numeric(y[now.num,]) #1 se cambia por now.num cuando se manda al cluster.
> param.names <- colnames(y)
> names(params) <- param.names
>
> #MIF -------------------------------------------------------------------------------------------------------
> #Read grid. cont es el contador de la linea.
> #5 cambiar por le tamano de filas que tengo generado por el LatinHC
> for(cont in now.num:(now.num+99)){ #for(cont in now.num:(now.num+99)) cuando se manda al cluster.
+   for(i in 1:3){ #for(i in 1:3) cuando se manda al cluster.
+     param <- as.numeric(y[cont,])
+     names(param) <- param.names
+     cat(cont, i, "\n") ## print look id
+
+     #iterated filtering
+     mif2(
+	po,
+	Nmif = 50, #Change between 50 to 150
+	start = param,
+	rw.sd = rw.sd(sigOBS=0.03, sigPRO=0.03,
+                     muEI1=0.03, muI1I2=0.03, muI1S1=0.03, muS2S1=0.03,
+                     rho=0.03, bT=0.03, q=0.03, c=0.03,
+                     S1_0=0.03, S2_0=0.03, E_0=0.03, I1_0=0.03, I2_0=0.03, K_0=0.03, F_0=0.03),
+	Np = 5000, #change between 1000 to 15000,
+	cooling.type = "hyperbolic",
+	cooling.fraction.50 = 0.6,
+	transform=TRUE
+     ) -> mifout
+
+     #IF para seguir los loops si MIF no cae en el error. Si es cero hay error.
+     if(length(coef(mifout)) > 0){
+	loglik.mif <- replicate(n=5,logLik(pfilter(po,
+                     params=coef(mifout),Np=1000,max.fail=500)))
+	bl <- logmeanexp(loglik.mif,se=TRUE)
+	loglik.mif.est <- bl[1]
+	loglik.mif.se <- bl[2]
+	cat(cont, loglik.mif.est, loglik.mif.se, "\n") #print
+     }
+
+     #Save Output -------
+     if(is.finite(loglik.mif.est)){ #if cuando hay valores que son numeros imprimir MIF
+	par.out <- coef(mifout) #funcion que me da la informacion de los parametros
+	names(par.out) <- param.names
+	if(file.exists("mifOutput_S1_VS2EI2_Nov14_Cluster.csv")){
+         write.table(t(as.matrix(c(cont,par.out,loglik.mif.est,loglik.mif.se))),
+                     "mifOutput_S1_VS2EI2_Nov14_Cluster.csv", append = T,
+                     col.names=F, row.names=F, sep = ",")
+	} else{
+         write.table(t(as.matrix(c(cont,par.out,loglik.mif.est,loglik.mif.se))),
+                     "mifOutput_S1_VS2EI2_Nov14_Cluster.csv", append = T,
+                     col.names=c("run", param.names, "loglik", "loglik.se"), row.names=F, sep = ",")
+	}
+     }
+   }
Error in now.num:(now.num + 99) : NA/NaN argument
Execution halted