R/prepareMplusData.R
prepareMplusData.RdThe prepareMplusData function converts an R data.frame
(or a list of data frames), into a tab-delimited
file (without header) to be used in an Mplus
input file. The corresponding Mplus syntax, including the
data file definition and variable names,
is printed to the console or optionally to an input file.
prepareMplusData( df, filename = NULL, inpfile = FALSE, keepCols = NULL, dropCols = NULL, dummyCode = NULL, interactive = TRUE, overwrite = TRUE, imputed = FALSE, writeData = c("always", "ifmissing", "never"), hashfilename = FALSE, quiet = TRUE )
| df | The R data.frame to be prepared for Mplus |
|---|---|
| filename | The path and filename for the tab-delimited data file for use with Mplus. Example: "C:/Mplusdata/data1.dat" |
| inpfile | Logical value whether the Mplus syntax should be written
to the console or to an input file. Defaults to |
| keepCols | A character vector specifying the variable names
within |
| dropCols | A character vector specifying the variable names
within |
| dummyCode | An optional character vector of column names indicating
categorical variables in the dataset that should be converted into
dummy codes (using the |
| interactive | Logical value indicating whether file names
should be selected interactively. If |
| overwrite | Logical value indicating whether
data and input (if present) files should be overwritten.
Defaults to |
| imputed | A logical whether data are multiply imputed. Defaults
to |
| writeData | A character vector, one of ‘always’, ‘ifmissing’, ‘never’ indicating whether the data files (*.dat) should be written to disk. Defaults to ‘always’ for consistency with previous behavior. See details for further information. |
| hashfilename | A logical whether or not to add a hash of the raw data to the
data file name. Defaults to |
| quiet | optional. If |
Invisibly returns a character vector of the Mplus input syntax. Primarily called for its side effect of creating Mplus data files and optionally input files.
The writeData argument is new and can be used to reduce overhead
from repeatedly writing the same data from R to the disk. When using the
‘always’ option, prepareMplusData behaves as before, always writing
data from R to the disk. When ‘ifmissing’, R generates an
md5 hash of the data prior to writing it out to the disk. The md5 hash is based on:
(1) the dimensions of the dataset, (2) the variable names,
(3) the class of every variable, and (4) the raw data from the first and last rows.
This combination ensures that under most all circumstances, if the data changes,
the hash will change. The hash is appended to the specified data file name
(which is controlled by the logical hashfilename argument). Next R
checks in the directory where the data would normally be written. If a data file
exists in that directory that matches the hash generated from the data, R will
use that existing data file instead of writing out the data again.
A final option is ‘never’. If this option is used, R will not write
the data out even if no file matching the hash is found.
Michael Hallquist
if (FALSE) { library(foreign) study5 <- read.spss("reanalysis-study-5-mt-fall-08.sav", to.data.frame=TRUE) ASData5 <- subset(study5, select=c("ppnum", paste("as", 1:33, sep=""))) prepareMplusData(ASData5, "study5.dat") # basic example test01 <- prepareMplusData(mtcars, "test01.dat") # see that syntax was stored test01 # example when there is a factor and logical tmpd <- mtcars tmpd$cyl <- factor(tmpd$cyl) tmpd$am <- as.logical(tmpd$am) prepareMplusData(tmpd, "test_type.dat") rm(tmpd) # by default, if re-run, data is re-written, with a note test01b <- prepareMplusData(mtcars, "test01.dat") # if we turn on hashing in the filename the first time, # we can avoid overwriting notes the second time test01c <- prepareMplusData(mtcars, "test01c.dat", hashfilename=TRUE) # now that the filename was hashed in test01c, future calls do not re-write data # as long as the hash matches test01d <- prepareMplusData(mtcars, "test01c.dat", writeData = "ifmissing", hashfilename=TRUE) # now that the filename was hashed in test01c, future calls do not re-write data # as long as the hash matches test01db <- prepareMplusData(mtcars, "test01d.dat", writeData = "ifmissing", hashfilename=TRUE) # however, if the data change, then the file is re-written test01e <- prepareMplusData(iris, "test01c.dat", writeData = "ifmissing", hashfilename=TRUE) # tests for keeping and dropping variables prepareMplusData(mtcars, "test02.dat", keepCols = c("mpg", "hp")) prepareMplusData(mtcars, "test03.dat", keepCols = c(1, 2)) prepareMplusData(mtcars, "test04.dat", keepCols = c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)) prepareMplusData(mtcars, "test05.dat", dropCols = c("mpg", "hp")) prepareMplusData(mtcars, "test06.dat", dropCols = c(1, 2)) prepareMplusData(mtcars, "test07.dat", dropCols = c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)) # interactive (test08.dat) prepareMplusData(mtcars, interactive=TRUE) # write syntax to input file, not stdout prepareMplusData(mtcars, "test09.dat", inpfile=TRUE) # write syntax to alternate input file, not stdout prepareMplusData(mtcars, "test10.dat", inpfile="test10alt.inp") # should be error, no file prepareMplusData(mtcars, interactive=FALSE) # new warnings if it is going to overwrite files # (the default to be consistent with prior behavior) prepareMplusData(mtcars, "test10.dat") # new warnings if it is going to overwrite files # (the default to be consistent with prior behavior) prepareMplusData(mtcars, "test11.dat", inpfile="test10alt.inp") # new errors if files exist and overwrite=FALSE prepareMplusData(mtcars, "test10.dat", inpfile="test10alt.inp", overwrite=FALSE) # can write multiply imputed data too # here are three "imputed" datasets idat <- list( data.frame(mpg = mtcars$mpg, hp = c(100, mtcars$hp[-1])), data.frame(mpg = mtcars$mpg, hp = c(110, mtcars$hp[-1])), data.frame(mpg = mtcars$mpg, hp = c(120, mtcars$hp[-1]))) # if we turn on hashing in the filename the first time, # we can avoid overwriting notes the second time testimp1 <- prepareMplusData(idat, "testi1.dat", writeData = "ifmissing", hashfilename=TRUE, imputed = TRUE) # now that the filename was hashed, future calls do not re-write data # as long as all the hashes match testimp2 <- prepareMplusData(idat, "testi2.dat", writeData = "ifmissing", hashfilename=TRUE, imputed = TRUE) # in fact, the number of imputations can decrease # and they still will not be re-written testimp3 <- prepareMplusData(idat[-3], "testi3.dat", writeData = "ifmissing", hashfilename=TRUE, imputed = TRUE) # however, if the data changes, then all are re-written # note that it warns for the two files that already exist # as these two are overwritten idat2 <- list( data.frame(mpg = mtcars$mpg, hp = c(100, mtcars$hp[-1])), data.frame(mpg = mtcars$mpg, hp = c(109, mtcars$hp[-1])), data.frame(mpg = mtcars$mpg, hp = c(120, mtcars$hp[-1]))) testimp4 <- prepareMplusData(idat2, "testi4.dat", writeData = "ifmissing", hashfilename=TRUE, imputed = TRUE) }