An answer: Leading zeros are the cause. Geographic identifiers cannot begin with a zero, or else digitpull()--a function defined in yourcast--trims them and ends up extracting too many digits--including part of the age into what should be only the country code. For now, a workaround is to add an arbitrary digit to the geographic IDs, keys in G.names, and associated files. Hope that travail helps someone else someday. Ethan |-----Original Message----- |From: yourcast-bounces(a)lists.gking.harvard.edu [mailto:yourcast- |bounces(a)lists.gking.harvard.edu] On Behalf Of Ethan Sharygin |Sent: Wednesday, October 02, 2013 12:22 PM |Cc: &#x27;yourcast(a)lists.gking.harvard.edu&#x27; |Subject: Re: [yourcast] Error in yourcast step after successful yourprep | |An addendum: if it helps, I found the code of the problematic function, |digitpull, at |https://github.com/IQSS/YourCast/blob/master/R/cast.funcs.R |and the YourCast code for the Lee Carter model here |https://github.com/IQSS/YourCast/blob/master/R/lc.funcs.R | |The error is being thrown at this step (from cast.funcs.R): |if (min(abs(v)) < 10^(stopdig-1)) { | stop(message="narrowest element in v not as wide as stopdig in proc |digitpull()") | } | |Here is the code in the Lee Carter model that is calling digitpull, as |well as its arguments. In the comment, I explain what the value was, |according to the debugger, at the time of the crash (plus a question |mark if I can't find it): |who.cntry.digits <- get("who.cntry.digits", envir=ewho) # |who.cntry.digits=3 |who.digit.first <- get("who.digit.first", envir=ewho) # |who.digit.first=0 |digit.cntry.begin <- who.digit.first + 1 # =1 (?) |digit.cntry.end <- who.digit.first + who.cntry.digits # =4 (?) |whoinsampy <- get("whoinsampy", envir= ewho) # see below |for example content |cs.vec <- as.numeric(names(whoinsampy)); cs.cntry.vec <- |digitpull(cs.vec,digit.cntry.begin,digit.cntry.end) | |This is what whoinsampy looks like: |Browse[1]> whoinsampy |$`00400` | depvar |004001970 -1.064245 |004001971 -1.094867 |004001972 -1.125606 |004001973 -1.166485 |... [etc, for each age group up to 004110] | |I feel close to understanding this error, but I can't quite grasp it. | | ||-----Original Message----- ||From: yourcast-bounces(a)lists.gking.harvard.edu [mailto:yourcast- ||bounces(a)lists.gking.harvard.edu] On Behalf Of Ethan Sharygin ||Sent: Wednesday, October 02, 2013 11:42 AM ||Cc: yourcast(a)lists.gking.harvard.edu ||Subject: Re: [yourcast] Error in yourcast step after successful ||yourprep. || ||Thanks, Nicholas, for the tip. That did get past that error! || ||A few new things have happened that are interesting. YourCast seems to ||crash without covariates, which I was able to debug (details below). ||Unfortunately, when I add covariates, I still get a strange error. I'm ||hoping you or someone else might have seen this before too, and got ||past it. || ||I'll document this in reverse order-first, the problem after adding a ||covariate (arbitrarily defined "time", equal to year-30---as in the ||example in the YourCast vignette). Second, for the record, I've ||described the problem I generated when YourCast did not have a ||covariate (might be a bug in the way the lists containing the data are ||named when there is only one covariate). || ||____YourCast returns an error in digitpull().____ || ||I can't tell what is generating this error. I've tried changing the ||number of digits in the age group and country codes, but to no avail so ||far. || ||> dta<-yourprep(dpath=paste(wd,"rawmini",sep=""),# path to text files ||+ year.var=TRUE,# year is a column ||+ tag="mxmale",# file names begin with mxmale index.code="gggaaa",# ||+ 3-digit region and 3-digit age sample.frame=c(1970,2011,2012,2036),# ||+ start,end of model yrs and ||forecast ||+ ) ||Loading cross section files and checking for errors... ||...Finished ||Total number of cross sections: 24 ||> ylc<-yourcast(formula=log(allcause)~index, ||+ dataobj=dta,# name of yourprep data ||+ model="LC",# options:bayes,map,ols,poisson,lc ||+ sample.frame=c(1970,2011,2012,2036),# provide sample frame from ||yourprep step ||+ ) ||Creating formulas for all cross-sections... ||Adding time to the covariate list... ||Applying formulas to data in each cross-section... ||Running model frames for data matrices... ||Building the covariates list... ||Standardizing covariates... ||Constructing the list of dependent variables... ||Creating the in-sample and out-sample periods for covariates... ||Creating lists for dependent variable,in-sample and out-sample... ||Saving preprocessing in the ||file...c:/research/gbdcast/_yourcast/data/yourcast.savetmp ||The size of yourcast.savetmp is = 30434 Using LC model Error in ||digitpull(cs.vec, digit.age.begin, digit.age.end) : || narrowest element in v not as wide as stopdig in proc digitpull() ||Data is inconsistent. ||Error in get("lst.output", envir = ewho) : object 'lst.output' not ||found || ||Some things that might be helpful (?). I can't find cs.vec in any of ||the environments available after debugger(). || ||Browse[1]> digit.first ||digit.first || 0 ||Browse[1]> age.digits ||age.digits || 3 ||Browse[1]> ewho$age.vec || [1] "000" "001" "005" "010" "015" "020" "025" "030" "035" "040" "045" ||"050" ||[13] "055" "060" "065" "070" "075" "080" "085" "090" "095" "100" "105" ||"110" || || || ||____YourCast seems to crash without covariates.____ || ||To my eyes, it appears that yourcast is calling the matrix column with ||the dependent variable, "allcause", but that the matrix is not labeled ||this way when it is the only variable. This happened until I added a ||covariate to the input data (i.e., a new column in the text files read ||by yourprep). || ||> wd<-"c:/research/gbdcast/_yourcast/data/"# update working directory ||> setwd(wd) ||> dta<-yourprep(dpath=paste(wd,"rawmini",sep=""),# path to text files ||+ year.var=TRUE,# year is a column ||+ tag="mxmale",# file names begin with mxmale index.code="gggaaa",# ||+ 3-digit region and 3-digit age G.names="isonames.txt",# file ||+ containing country abbvs sample.frame=c(1970,2011,2012,2036),# ||+ start,end of model yrs and ||forecast ||+ # adjacency="adjacency.txt",# file containing WHO adjacency info ||+ verbose=TRUE,# do not suppress output ||+ ) ||Loading cross section files and checking for errors... ||mxmale004000.txt ||mxmale004001.txt ||.[etc, until] ||mxmale004110.txt ||Loading auxiliary files... ||isonames.txt ||...Finished ||Total number of cross sections: 24 || ||> ylc <- yourcast(formula=log(allcauses)~index, dataobj=dta, ||> model="LC", ||sample.frame=c(1970,2011,2012,2036)) ||Error in mat[, dth] : subscript out of bounds || ||> debugger() ||Message: Error in mat[, dth] : subscript out of bounds Available ||environments had calls: ||1: yourcast(formula = log(allcauses) ~ index, dataobj = dta, model = ||"LC", sam ||2: input.to.model(datamat = dataobj$data, ff = formula, all.pow = ||low.pow, sam ||3: build.covs.depvar.lst(datamat, ff, all.pow, sample.frame, standard, ||verbose ||4: data.after.first.obv(datamat, ff) ||5: lapply(datamat, FUN = "first.obvy", dth, pop) ||6: FUN(X[[1]], ...) ||Enter an environment number, or 0 to exit Selection: 6 Browsing in the ||environment with call: || FUN(X[[1]], ...) ||Called from: debugger.look(ind) || ||Browse[1]> ls() ||[1] "dth" "mat" "pop" "rnm" || ||Browse[1]> dth ||[1] "allcauses" || ||Browse[1]> mat || mat ||0040001970 0.34498817 ||0040001971 0.33458412 ||0040001972 0.32445580 ||0040001973 0.31145978 ||0040001974 0.29705149 ||. [ and so on, until .] ||0040002010 0.07250808 ||0040002011 0.06872911 ||0040002012 NA ||0040002013 NA ||0040002014 NA ||. [ etc, etc, until.] ||0040002035 NA ||0040002036 NA || ||This error was fixed by adding a covariate to the source data, which ||resulting in the appropriate naming of the columns in the matrix "mat", ||e.g.: || ||> dta$data ||$`004000` || allcause time ||1970 0.34498817 1940 ||1971 0.33458412 1941 ||...[etc] || ||And then mat[,dth] pulls from the correct column. || || ||From: Nicholas Martinez [mailto:martinez.nicholas@gmail.com] ||Sent: Tuesday, October 01, 2013 10:24 PM ||To: Ethan Sharygin ||Cc: yourcast(a)lists.gking.harvard.edu ||Subject: Re: [yourcast] Error in yourcast step after successful ||yourprep. || ||Ethan, ||I had the same problem a couple of years ago.  You have to pass the the ||frame you set in your.prep into the your.cast sample.frame. ||Try this. ||ylc <- yourcast(formula=log(allcauses)~index, dataobj=dta, model="LC", ||sample.frame=c(1970,2011,2012,2036)) ||Hope that works. ||Best, ||Nicholas || ||On Tue, Oct 1, 2013 at 8:52 PM, Ethan Sharygin &lt;sharygin(a)uw.edu&gt; wrote: ||Dear yourcast users or moderator, || ||I am unable to get yourcast to run any model with data in yourprep. ||I've formatted my data into text files for each cross-sectional unit, ||following the example in the vignette/documentation for YourCast. || ||Here is a stripped down example for one geographic unit, 24 age groups, ||years 1970-2036 (non-missing data for 1970-2011). No auxiliary files ||are used in this example. || ||(1) The R command and output: ||> dta<-yourprep(dpath=paste(wd,"rawmini",sep=""),# path to text files ||+ year.var=TRUE,# year is a column ||+ tag="mxmale",# file names begin with mxmale index.code="gggaaa",# ||+ 3-digit region and 3-digit age sample.frame=c(1970,2011,2012,2036),# ||+ start,end of model yrs and ||forecast ||+ #G.names="isonames.txt",# file containing country abbvs ||+ #adjacency="mxmale.proxim.txt",# file containing adjacency info ||+ verbose=TRUE,# do not suppress output ||+ ) ||Loading cross section files and checking for errors... ||mxmale004000.txt ||mxmale004001.txt ||mxmale004005.txt ||mxmale004010.txt ||mxmale004015.txt ||mxmale004020.txt ||mxmale004025.txt ||mxmale004030.txt ||mxmale004035.txt ||mxmale004040.txt ||mxmale004045.txt ||mxmale004050.txt ||mxmale004055.txt ||mxmale004060.txt ||mxmale004065.txt ||mxmale004070.txt ||mxmale004075.txt ||mxmale004080.txt ||mxmale004085.txt ||mxmale004090.txt ||mxmale004095.txt ||mxmale004100.txt ||mxmale004105.txt ||mxmale004110.txt ||...Finished ||Total number of cross sections: 24 ||> ylc<-yourcast(formula=log(allcause)~index, ||+ dataobj=dta,# name of yourprep data ||+ model="LC",# options:bayes,map,ols,poisson,lc debug=TRUE,# add debug ||+ info to user space ||+ ) ||Error in seq.default(smpvec[ind], smpvec[ln], by = 1) : ||  wrong sign in 'by' argument || ||(2) an example text file (mxmale004000.txt) for one age category (age ||0) for one country (004) year    allcause ||1970    .3449881673 ||1971    .3345841169 ||1972    .3244557977 ||1973    .3114597797 ||1974    .2970514894 ||[truncated here to save space] ||2010    .0725080818 ||2011    .0687291101 ||2012    NA ||2013    NA ||2014    NA ||[and so on, NA values until 2036] || ||Any insights would be appreciated, as I cannot distinguish how my data, ||after yourprep, are any different from the example in the |documentation. || ||Thanks sincerely, || ||-- ||Ethan Sharygin || ||- ||--- ||yourcast mailing list served by HUIT ||List Address: yourcast(a)lists.gking.harvard.edu ||Subscribe/Unsubscribe: ||http://lists.gking.harvard.edu/mailman/listinfo/yourcast ||Yourcast mailing list ||Yourcast(a)lists.gking.harvard.edu || ||To unsubscribe from this list or get other information: || ||https://lists.gking.harvard.edu/mailman/listinfo/yourcast || ||- ||--- ||yourcast mailing list served by HUIT ||List Address: yourcast(a)lists.gking.harvard.edu ||Subscribe/Unsubscribe: ||http://lists.gking.harvard.edu/mailman/listinfo/yourcast ||Yourcast mailing list ||Yourcast(a)lists.gking.harvard.edu || ||To unsubscribe from this list or get other information: || ||https://lists.gking.harvard.edu/mailman/listinfo/yourcast |- |--- |yourcast mailing list served by HUIT |List Address: yourcast(a)lists.gking.harvard.edu |Subscribe/Unsubscribe: |http://lists.gking.harvard.edu/mailman/listinfo/yourcast |Yourcast mailing list |Yourcast(a)lists.gking.harvard.edu | |To unsubscribe from this list or get other information: | |https://lists.gking.harvard.edu/mailman/listinfo/yourcast