demographics.to.qdec.table.dat: Convert a dataframe containing demographics data to a...

In dfsp-spirit/fsbrain: Managing and Visualizing Brain Surface Data

Convert a dataframe containing demographics data to a qdec.table.dat file and related files.

Description

This creates the 'qdec.table.dat' and all required related files (the factor level files) in a directory.

Usage

demographics.to.qdec.table.dat(
  df,
  output_path = ".",
  long = FALSE,
  add_fake_level2 = FALSE,
  long_timecolumn = "years",
  qdec_file_name = "qdec.table.dat"
)

Arguments

df	a data.frame containing demographics information. Make sure to have factors encoded as factors (not strings), so that the QDEC level files get created for them. Must contain a column named 'fsid' with the subject IDs as first column. If you want a long table, make sure to use qdec.table.skeleton to generate the timepoint information instead of doing it manually.
output_path	character string, existing directory into which to write the QDEC files. If the last directory level does not exist, it will be created.
long	logical, whether this is for a longitudinal run. If so, the df must contain a column named 'fsid-base' as the second column. It must also contain some column that gives the inter-scan time (from this scan timepoint to the previous one). The time unit (years, days, ...) is up to you, but typically one is interested in yearly change, the unit should be years. The name of the column (e.g., 'years') must be given to 'mris_slopes' later on the command line with the --time <column_name> argument. The requires information can be generated conveniently with the qdec.table.skeleton function.
add_fake_level2	logical, whether to add a 2nd fake level to the level files of factors with only a single level. Such factors make little sense, but QDEC refuses to open the resulting files at all in such a case, which seems a bit overkill. If TRUE, a 2nd level named 'level2' will be added so that one can open the output in QDEC.
long_timecolumn	character string, the name of the column holding the inter-scan time. Ignored unless parameter long is TRUE. See the description for parameter long for details.
qdec_file_name	character string, the filename of the QDEC file to write. Must be only the file name (with extension if you want). See output_path to set the ouput directory where this will be created.

Note

IMPORTANT: If you import the dataframe from a text file with functions like read.table, they will by default replace dashes in column names with dots. So if you have a column named fsid-base in there, after loading it will be named fsid.base. See the check.names parameter for read.table to prevent that.

See Also

The function qdec.table.skeleton to generate the data.frame used as the 'df' argument for this function.

Examples

## Not run: 
   dem = readxl::read_xls("~/data/study1/demographics.xsl");
   # or: dem = read.table("~/demographics.csv", check.names=FALSE);
   # You may want to rearrange/rename/delete some columns here.
   demographics.to.qdec.table.dat(dem, "~/data/study1/qdec/");
   #
   # a second one with real data:
   dem = data.frame("ID"=paste("subject", seq(5), sep=""),
      "age"=sample.int(20, 5)+10L, "isi"=rnorm(5, 2.0, 0.1)); #sample data.
   long_table = qdec.table.skeleton(dem$ID, dem$isi);
   demographics.to.qdec.table.dat(long_table, long=TRUE);

## End(Not run)

dfsp-spirit/fsbrain documentation built on Nov. 28, 2024, 10:29 a.m.