Please disregard all of the issues/questions I raised in my email below, EXCEPT for one: Q:  Does whether or not the input file has a header row (variable names) affect how Amelia works? Matt Blackwell's response to my first issue ( subj: Amelia for R produces no imputed data output files [WAT Issue #1] ) resolved the other  issues in my earlier email below.) I changed the subject line of this message accordingly... DISCUSSION:   It seems that Amelia (and AmeliaView) assume that the input data set has a header row. However I cannot find any discussion in the documentation to confirm this. I have observed the following: -- When I write the data.frame to a csv file to be read by AmeliaView... if the csv file has no header row, then in AmeliaView -> Summarize Data -> "Missing:  x / [total]"... The "total" listed is one less than the rows actually in the data set. -- When I pass the data.frame to Amelia for R directly, it doesn't seem to have this problem. To prevent any problems of this nature, should Amelia and AmeliaView have an input parameter telling it whether or not the input data set has a header row? Wayne Thornton thornton(a)fas.harvard.edu  _____ From: owner-amelia_at_lists_gking_harvard_edu(a)mail.hmdc.harvard.edu [mailto:owner-amelia_at_lists_gking_harvard_edu@mail.hmdc.harvard.edu] On Behalf Of Wayne Thornton Sent: Sunday, June 28, 2009 16:24 To: amelia(a)lists.gking.harvard.edu Subject: [amelia] Amelia output extracted from output[[ ]] looks odd [WAT Issue #2] RE:  Amelia output extracted from output[[ ]] looks odd  [WAT Issue #2] PROBLEM:  After running Amelia to generate 5 imputed files, the output files extracted using output[[ ]]  look odd.... BACKGROUND:  Here is my command line to run Amelia: ******************* CONTROL PANEL ******************* impruns  <- 5 tolX     <- 0.0001 empriX    <- 100 autopriX  <- 0.05 resampleX <- 100 *************************** CONTROL PANEL *******************      imputed <- amelia(DATA8i,                  m  = impruns      ,  p2s = 2      , idvars = c(3,4,5)   ,                  ts = 1         ,  cs  = 2     ,    polytime  = NULL,                                                      startvals = 0   , tolerance = tolX    ,                                                                        noms = nomIV8i      ,                  ords = ordIV8i ,  incheck = T  ,       collect = F     , outname = "DATA8imp",                  write.out = T  ,     archive = T , keep.data = T    ,                  empri = empriX , autopri = autopriX  ,                  bounds = IVlims,                    max.resample = resampleX               ) After a run I am able to extract output info from...      imputed[[ ]] The user guide (p.27, under "Output") says. "...you can refer to any of the datasets by referencing output[[i]], where i is the number of the dataset you wish to reference. These datasets will be returned in the same format which you passed them...." However, the files imputed[[1]], imputed[[2]], etc.......are quite different from the original input file, and different from each other. -- The input file is a data frame (1044 x 487). with no header. -- Output files:  imputed[[ 1]]               1044 x 2435                  numeric; looks like imputed values NOTE:  2435 = 5 * 287...  imputed[[ 2]]                1 x 1                             "5"  imputed[[ 3]]                                                     TRUE / FALSE  imputed[[ 4]]                483 x  2415                   numeric,  does NOT look line imputed values NOTE: 483 = number of IVs minus 4; Data set includes 3 identity variables, 1 time series var, 1 cross-section var  imputed[[ 5]]               483 x 5                           numeric, does NOT look lile imputed values These output files raise the following comments/questions: (1)  Contrary to the info in the user guide, the output files extracted from output[[i]] do not match the format of the input file. (2)  Does whether or not the input file has a header row (variable names) affect how Amelia works? (This question may be an artifact of my lack of understanding about working with data frames... But if you read in the output csv file and compute nrow(file), the result is one less than the number of rows actually  in the csv file. (3)  Is the first output file [[1]] the 5 sets of imputed data? (4) I have no idea what the other files are... Are they for diagnostics? Thanks, Wayne SUBMITTED BY:     Wayne A. Thornton                              Harvard Univ.                        thornton(a)fas.harvard.edu                        781-492-3131 <http://1429236.signature1.mailinfo.com/confirm2.6/0205010E/0202054D/0B034F0 5/13137013.jpg>