[R] R Crash -- R Gui crashes during MCMC iteration
Hi I am posting to seek some advice regarding the R Gui 2.12.0 that keeps
freezing on my pc.
I have been trying to run MCMC ordinal factanal code on my PC but the window
freezes everytime after 7001 iterations (total of 25 iterations). My
operating system is window vista 64-bit with 4.0 gb of memory.
Here is the code that I was trying to run under MCMCpack.
## installing packages
install.packages("MCMCpack")
install.packages("foreign")
## calling libraries
library(MCMCpack)
library(foreign)
## opening a data set on the desktop
setwd("C:/Users/haillie/Desktop")
UN2009<- read.csv("UN2009.csv")
#calling libraries
library(reshape)
library(car)
colname <- names(UN2009)
## these are thevariables I want to recode
UN2009[colname] <-
lapply(UN2009[colname],
function(x) recode(x, recodes = "8=NA",
as.factor.result = TRUE, as.numeric.result = FALSE))
## this applies the recode functionto all the variable I wantto recode
## Ordinalfactanal Code
un2009<-MCMCordfactanal(~R.64.6+R.64.10+R.64.16+R.64.17+R.64.18+R.64.19+R.64.20+R.64.21+R.64.23+R.64.28+R.64.31+R.64.34+R.64.37+R.64.39+R.64.42+R.64.44+R.64.47+R.64.48+R.64.50+R.64.52+R.64.53+R.64.54+R.64.55+R.64.56+R.64.57+R.64.59+R.64.66+R.64.69+R.64.27+R.64.71+R.64.89+R.64.90+R.64.91+R.64.93+R.64.94+R.64.98+R.64.99+R.64.105+R.64.88+R.64.106+R.64.87+R.64.92+R.64.95+R.64.97+R.64.147+R.64.160+R.64.170+R.64.172+R.64.173+R.64.174+R.64.175+R.64.176+R.64.148+R.64.150+R.64.151+R.64.152+R.64.156+R.64.157+R.64.195+R.64.185+R.64.188+R.64.209+R.64.197+R.64.189+R.64.238+R.64.254+R.64.282+R.64.292+R.64.296,
data=UN2009,lambda.constraints=list(R.64.18=list(2,"+")), factors=1,
burnin=5000, mcmc=20, thin=40, verbose=1000, L0=0.05, store.lambda=TRUE,
store.scores=TRUE, tune=1.2)
The system is fine until I try to run the ordinalfactanal iterations I
am also using the most recent version of Tinn R with R gui. not at the same
time but they share the same window space. Could this be a problem?
I do not think the data set I am using is too big ( dimension 193, 27).
If anyone could help me gain some insight into this problem, I would greatly
appreciate it. Thank you very much and I hope to hear from you soon.
Sincerely,
Haillie
--
View this message in context:
http://r.789695.n4.nabble.com/R-Crash-R-Gui-crashes-during-MCMC-iteration-tp3308047p3308047.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Setting Lambda constraints for MCMC ordinal model
post47 <- MCMCordfactanal(~a1+a2+a3+a4+a5+a6+a7+a8+a9+a10+a11+a12+a13+a14+a15+a16+a17+a18+a19+a20+a21+a22+a23+a24+a25+a26+a27+a28+a29+a30+a31+a32+a33+a34+a35+a36+a37+a38, data=un47,lambda.constraints=list(a8=list(2,"+")), factors=1, burnin=5000, mcmc=20, thin=40, verbose=1000, L0=0.05, store.lambda=TRUE, store.scores=TRUE, tune=1.2) I have a question regarding setting lambda.constraints in the code above. What is the criteria one should use for setting lambda constraint? For example, why would you chose to set the 2nd factor loading of a8 as + instead of choosing a different variables and factor loadings and setting it to negative? Above is a code for ordinal MCMC factanal model. Thank you very much in advance and I hope to hear from you soon! -- View this message in context: http://r.789695.n4.nabble.com/Setting-Lambda-constraints-for-MCMC-ordinal-model-tp3313777p3313777.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Saving summary outputs in a table form
Dear R help, Is there a way to extract a variable ( one column) from my summary statistics to save it in a table form? My post-factor analysis summary statistics gave me the output below. Is there anyway to just save the mean of all the phi? The filename of this summary output is postun2010sum. Also is there a way to just save phi(,2) or phi(,3) in a table form on my desktop? Any help would be deeply appreciated. Thank you very much and I would be grateful for any comments. Mean SD Naive SE Time-series SE LambdaR.64.6.1 -2.441402 0.37438 0.0118390 0.0099447 LambdaR.64.6.20.918276 0.34265 0.0108355 0.0101326 LambdaR.64.6.30.216445 0.32877 0.0103965 0.0108384 LambdaR.64.10.1 -0.269011 0.16282 0.0051488 0.0078555 LambdaR.64.10.2 1.379486 0.20658 0.0065327 0.0070898 LambdaR.64.10.3 0.235941 0.15448 0.0048851 0.0063958 phi.1.2 1.095283 0.11438 0.0036170 0.0060156 phi.1.3 -0.141687 0.16288 0.0051507 0.0101297 phi.2.2 0.890038 0.11511 0.0036401 0.0057195 phi.2.3 0.104225 0.15570 0.0049238 0.0090702 phi.3.2 -0.379830 0.21483 0.0067936 0.0078231 phi.3.3 -0.266584 0.32148 0.0101661 0.0102912 phi.4.2 -1.056815 0.37530 0.0118682 0.0149568 phi.4.3 -1.193200 0.31209 0.0098691 0.0129749 phi.5.2 0.364988 0.16384 0.0051812 0.0084784 phi.5.3 -1.324649 0.18231 0.0057652 0.0063309 phi.6.2 -1.078973 0.41542 0.0131368 0.0154569 phi.6.3 0.275169 0.44999 0.0142300 0.0157746 phi.7.2 -1.055651 0.36960 0.0116879 0.0132779 phi.7.3 0.664266 0.47810 0.0151190 0.0169993 phi.8.2 -0.869908 0.34998 0.0110672 0.0111003 phi.8.3 0.276252 0.42348 0.0133915 0.0124475 phi.9.2 -0.587335 0.26497 0.0083792 0.0090293 phi.9.3 0.085117 0.37280 0.0117891 0.0134057 phi.10.2 -0.996298 0.39233 0.0124066 0.0128439 phi.10.3 -0.392418 0.38979 0.0123263 0.0138242 -- View this message in context: http://r.789695.n4.nabble.com/Saving-summary-outputs-in-a-table-form-tp3381959p3381959.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Saving summary outputs in a table form
Thank you very much! I will check out help page for extraction operator. Many thanks, Haillie -- View this message in context: http://r.789695.n4.nabble.com/Saving-summary-outputs-in-a-table-form-tp3381959p3383316.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] converting data.frame into a numeric ( integer) form
Hi Everyone, I am relatively new to R and would appreciate your help on this problem that I encontered this morning. When running an ordinal IRT model using Ratings package on R, I keep getting this error message. ord.out<-ordrating(UNORD, burnin = 1000, mcmc = 40,000, thin = 400, tune = 1, verbose = 1000, seed = NA) Error in as.vector(as.integer(Y)) : (list) object cannot be coerced to type 'integer' UNORD is my data.frame and it is in the form of delimited CSV file without either row or column name. According to the help page on Ordinal ratings, Y should be "a Matrix of data to be analyzed. Entries must be integers from 1; : : : ;C or NA where C is the number of ordinal categories. Items are on the rows and subjects are on the columns." I am confused because my data.frame only contains numerica values of 1,2,3, and NA. I checked and my NAs were all numeric. Any help or advice you could provide on this issue would be greatly appreciated. Thank you very much. I would like to thank all the R experts navigating this forum in advance. Sincerely, Haillie -- View this message in context: http://r.789695.n4.nabble.com/converting-data-frame-into-a-numeric-integer-form-tp3455811p3455811.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error message while running IRT model
I have been struggling with the same problem for the past few hours and am
desperately in need of some help. The code I am running is as follows:
## opening a data set on the desktop
setwd("C:/Users/haillie/Desktop")
UN2010<- read.csv("UN2010.csv",header=TRUE)
##calling libraries
library(reshape)
library(car)
## these are the variables I want to recode
colname <- names(UN2010)
## this applies the recode functionto all the variable I want to recode
UN2010[colname] <-
lapply(UN2010[colname],
function(x) recode(x, recodes = "8=NA",
as.factor.result = FALSE, as.numeric.result = TRUE))
UN2010frame<-data.matrix(lapply(UN2010,as.numeric))
ord.out1<-ordrating(UN2010, beta.constraint=1, tune=.035,
ma=1, mb=-5, vinva=1, vinvb=0.05,
gamma.start=c(-300, 0, 1.5, 3.0, 4.5, 300),
thin=20, burnin=2, mcmc=10, verbose=1000)
##
However, when i try to run the above ordrating code, an error message comes
up " NA/NaN/Inf in foreign function call (arg 24)." Because I interpreted
this as that this model has no ability to perform na.omit, I did na.omit
myself using the code UN2010<-na.omit(UN2010). However, I encoutered another
problem then.
I recieved the below error messages this time..
Error in dimnames(x) <- dn :
length of 'dimnames' [1] not equal to array extent
In addition: Warning messages:
1: In min(Y, na.rm = TRUE) :
no non-missing arguments to min; returning Inf
2: In max(Y, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
3: In max(Y, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
>
##
I have tried everything I could but nothing has worked so far. Any advice or
help would be deeply appreciated. Thank you very much.
Haillie
--
View this message in context:
http://r.789695.n4.nabble.com/error-message-while-running-IRT-model-tp3456603p3456603.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Unlist command drops all my column names in the first row and adopts NAs
Hi Everyone, I am having trouble turning my data.frame into a matrix format. Because I wanted to change my data.frame with mostly factor variables into a numeric matrix, I used the following code --> UN2010frame<-data.matrix(lapply(UN2010,as.numeric)) However when i checked the mode of the UN2010frame, it still showed up as a list. Because the code I want to run (Ordrating) does not accept data in a list format, I used UN2010matrix <- unlist(UN2010frame) to unlist my matrix. When I did this, my first row ( which was formerly a row with column names) turned into NAs. This was a problem for me because when I tried to run an ordinal IRT model using this data set, I got the following error message. Error in 1:nrow(Y) : argument of length 0 I think it is because all the values in my first row are now gone If you could help me on any front, It would be deeply appreciated. Thank you very much! Haillie -- View this message in context: http://r.789695.n4.nabble.com/Unlist-command-drops-all-my-column-names-in-the-first-row-and-adopts-NAs-tp3463294p3463294.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] MCMCfactanal inquiries
Dear list,
Hi, I am emailing to see if it would be possible to get some help on
running MCMCfactanal on R. I am trying to derive a single score measuring a
likelihood to recieve IMF loans from 8 different variables related to IMF
representation but for reason, my codes do not seem to take me to where I
want to be. For some reason my code drops certain rows ( countries)
automatically, making it impossible for me to acquires factor scores for
those observations. It would also be great if you could let me know if
MCMCfactanal is the program to use for my purposes and recommend me better
functions or codes if possible.
Thank you very much in advance and I look forward to any help.
Sincerely,
Haillie
I am pasting the codes I have used below.
# installing packages
install.packages("MCMCpack")
install.packages("foreign")
install.packages("reshape")
install.packages("car")
## calling libraries
library(MCMCpack)
library(foreign)
### this loads TeachingDemos pkg and allows me to save txts
library(TeachingDemos)
txtStart("imfproject7.txt",commands = TRUE, results = TRUE, append = FALSE)
## calling libraries
library(MCMCpack)
library(foreign)
## opening a data set on the desktop
setwd("C:/Users/haillie/Desktop")
imfdata<- read.csv("imfdata.csv")
##calling libraries
library(reshape)
library(car)
## factanal Code ( 1 dimension with continuous variable)
postimfdata<-MCMCfactanal(~shstaff+shquota+frusanew+trshusnew+frdfgnew+trsheunew+usbanksh+eubanksh,
factors=1, data=imfdata, burnin=2, mcmc=20, thin=100, verbose=1000,
seed = NA, lambda.start = NA, psi.start = NA, l0 = 0, L0 = 0, a0 = 0.001,
b0 = 0.001, store.lambda = FALSE, store.scores = TRUE, std.var = TRUE)
Sincerely,
Haillie
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
