inst/doc/jmvReadWrite.R

In jmvReadWrite: Read and Write 'jamovi' Files ('.omv')

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(echo = TRUE,
                      comment = "#>",
                      collapse = TRUE,
                      message = FALSE,
                      warning = FALSE,
                      fig.height = 5,
                      fig.width = 7,
                      fig.align = "center",
                      out.width = "100%")

## ----eval=FALSE---------------------------------------------------------------
# install.packages("jmvReadWrite")

## ----eval=FALSE---------------------------------------------------------------
# if (!require(devtools)) install.packages("devtools")
# devtools::install_github("sjentsch/jmvReadWrite")

## ----echo=TRUE----------------------------------------------------------------
fleOMV <- system.file("extdata", "ToothGrowth.omv", package = "jmvReadWrite")
data <- jmvReadWrite::read_omv(fleOMV)
# if the "jmv"-package is installed, we can run a test analysis with the data
if ("jmv" %in% rownames(installed.packages())) {
    jmv::ANOVA(
        formula = len ~ supp + dose + supp:dose,
        data = data,
        effectSize = c("omega"),
        modelTest = TRUE,
        homo = TRUE,
        norm = TRUE)
    }

## ----echo=TRUE----------------------------------------------------------------
fleOMV <- system.file("extdata", "ToothGrowth.omv", package = "jmvReadWrite")
data <- jmvReadWrite::read_omv(fleOMV, getSyn = TRUE)
# shows the syntax of the analyses from the .omv-file
# please note that syntax extraction may not work on all systems
# if the syntax couldn't be extracted, an empty list (length = 0) is returned,
# otherwise, the syntax of the analyses from the .omv-file is shown and
# the commands of the first and the second analysis are run, with the
# output of the second analysis assigned to the variable result
if (length(attr(data, "syntax")) >= 2) {
    attr(data, "syntax")
    # if the "jmv"-package is installed, we can run the analyses in "syntax"
    if ("jmv" %in% rownames(installed.packages())) {
        eval(parse(text = attr(data, "syntax")[[1]]))
        eval(parse(text = paste0("result = ", attr(data, "syntax")[[2]])))
        names(result)
        # -> "main"      "assump"    "contrasts" "postHoc"   "emm"
        # (the names of the five output tables)
    }
}

## ----echo=TRUE----------------------------------------------------------------
# use the data set "ToothGrowth" and, if it exists, write it as jamovi-file
# using write_omv()
data("ToothGrowth", package = "jmvReadWrite")
# "retDbg" has to be set in order to return debug information to wrtDta
wrtDta <- jmvReadWrite::write_omv(ToothGrowth, "Trial.omv", retDbg = TRUE)
names(wrtDta)
# -> "mtaDta" "xtdDta" "dtaFrm"
# this debug information contains a list with the metadata ("mtaDta", e.g.,
# column and data type), the extended data ("xtdDta", e.g., variable lables),
# and the data frame (dtaFrm) for checking (understanding the file format) and
# debugging

# check whether the file was written to the disk, get the file information (size, etc.)
# and delete the file afterwards
list.files(".", "Trial.omv")
file.info("Trial.omv")
unlink("Trial.omv")

## ----echo=TRUE----------------------------------------------------------------
# reading and writing a file with the "sveAtt"-parameter permits you to keep
# essential meta-data to ensure that the written file looks and works like the
# original file (plus you modifications)
fleOMV <- system.file("extdata", "ToothGrowth.omv", package = "jmvReadWrite")
data <- jmvReadWrite::read_omv(fleOMV, sveAtt = TRUE)
# shows the names of the attributes for the whole data set (e.g., number of
# rows and columns) and the names of the attributes of the first column
names(attributes(data))
names(attributes(data[[1]]))
#
# perhaps do some modifications to the file here and write it back afterwards
jmvReadWrite::write_omv(data, "Trial.omv")
unlink("Trial.omv")