Hi Nicole, 

Hm, it seems like the cluster might have a non-standard installation of R. Maybe you can try to load the methods library before running Amelia:

library(methods)

Hope that helps!

Cheers,
Matt

~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Political Science
University of Rochester
url: http://www.mattblackwell.org


On Thu, Jul 18, 2013 at 4:54 AM, Nicole Janz <nicolejanz@gmail.com> wrote:
Can anyone help me with this error when trying to run Amelia:

Error in match.fun(FUN) : object 'is' not found
Calls: amelia -> amelia.default -> sapply -> match.fun
Execution halted
Loading required package: Amelia
Loading required package: foreign
Loading required package: Rcpp
Loading required package: RcppArmadillo

I run the same Amelia code (see copied below) fine on my mac, and on my uni's windows 7 computer (both with Amelia 1.7.2. and R 3.0.1). When I try to run the code for several imputation files on our uni's cluster, I get the above error in the output file. I cannot re-create the error on my own computers. The cluster also uses the same R and Amelia version.

My code is copied below.

Thank you,
Nicole

Nicole Janz, PhD Cand.
Lecturer at Social Sciences Research Methods Centre 2013/14
University of Cambridge
Department of Politics and International Studies
Skype: nicole.janz
Blog: politicalsciencereplication.wordpress.com



Code for imputation (one of 25 for m=1 each):


#######################
# Multiple Imputation
# Darwin - Janz - original FDI - 1 Year Lag
#######################

require(Amelia)

#load data set
load("t1.Rdata")
dim(t1) # 3822   90
colnames(t1)
head(t1)

t <- t1


# remove unnecessary variables (original FDI)
vrm <- c(    
  
  "Mos_labor",   
  
  "CIRI_NEW_EMPINX"  ,
  
  "US_fdi_total",           
  "US_fdi_petrol",          
  "US_fdi_total_manuf",     
  "US_fdi_food",            
  "US_fdi_chemical",        
  "US_fdi_prim_fab_metal",  
  "US_fdi_machinery",       
  "US_fdi_electrical" ,     
  "US_fdi_transport" ,      
  "US_fdi_whole_trade" ,    
  "US_fdi_depository" ,     
  "US_fdi_finance_except",  
  "US_fdi_mining"  ,        
  "polity2"        ,        
  "GDP_const2000"  ,        
  "GDP_curr"        ,       
  "WB_FDI_percentGDP"  ,   
  "WB_FDI_curr"        ,    
  "population"         ,   
  "trade"              ,    
  "confl"             ,     
  "UN_FDI_flow"        ,    
  "UN_FDI_flow_pgdp"   ,    
  "UN_FDI_stock"      ,     
  "UN_FDI_stock_pgdp" ,     
  "l_US_fdi_total"     ,    
  "l_US_fdi_petrol"       , 
  "l_US_fdi_total_manuf"  , 
  "l_US_fdi_food"      ,    
  "l_US_fdi_chemical"   ,   
  "l_US_fdi_prim_fab_metal",
  "l_US_fdi_machinery"     ,
  "l_US_fdi_electrical"    ,
  "l_US_fdi_transport"     ,
  "l_US_fdi_whole_trade"   ,
  "l_US_fdi_depository"    ,
  "l_US_fdi_finance_except",
  "l_US_fdi_mining"        ,
  "l_WB_FDI_percentGDP"    ,
  "l_WB_FDI_curr"          ,
  "l_UN_FDI_flow"          ,
  "l_UN_FDI_flow_pgdp"     ,
  "l_UN_FDI_stock"         ,
  "l_UN_FDI_stock_pgdp"    ,
  "Lag_l_WB_FDI_percentGDP"  ,
  "Lag_l_WB_FDI_curr" ,
  
  "Lag_WB_FDI_percentGDP" ,
  "Lag_WB_FDI_curr"   ,
  "Lag_GDP_const2000",
  
  "Lag_UN_FDI_flow",
  "Lag_UN_FDI_flow_pgdp",
  "Lag_UN_FDI_stock",
  "Lag_UN_FDI_stock_pgdp"      )       

length(vrm)#55

t.new <- t[,!(colnames(t) %in% vrm)]
dim(t)# 3822   
dim(t.new) #3822   37
t <- t.new

colnames(t)

# Declare log variables that have no negative values
vlogs <- c(
  
  "Lag_l_US_fdi_mining", #newly inserted
  
  "Lag_GDP_curr",
  "Lag_population",
  "Lag_trade",
  "Lag_l_US_fdi_total",
  "Lag_l_US_fdi_petrol",
  "Lag_l_US_fdi_total_manuf",   
  "Lag_l_US_fdi_food",
  "Lag_l_US_fdi_chemical",
  "Lag_l_US_fdi_prim_fab_metal",
  "Lag_l_US_fdi_machinery",     
  "Lag_l_US_fdi_electrical",
  "Lag_l_US_fdi_transport",
  "Lag_l_US_fdi_whole_trade",
  "Lag_l_US_fdi_depository",
  "Lag_l_US_fdi_finance_except",
  #"Lag_l_US_fdi_mining",
  "Lag_l_UN_FDI_flow",
  "Lag_l_UN_FDI_flow_pgdp",
  "Lag_l_UN_FDI_stock",
  "Lag_l_UN_FDI_stock_pgdp",
  
  "lifeexp",
  "infmortality" 
)

set.seed(1004)
nmi=1

amelia.out2013.07.10.0004 <- amelia(t, m=nmi, ts="year", cs="country",intercs=TRUE,polytime=1,log=vlogs) 
  
# save file
save(amelia.out2013.07.10.0004, file="amelia.out2013.07.10.0004.Rdata")








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