ITSbin

This package takes LENA™ .its (Iterative Time Segments) files, extracts LENA™ automatic annotations, attaches real time, and outputs .csv files of recordings, conversation & pause blocks, segments, centiseconds, seconds and/or minutes.

Installation

This package is not available on CRAN. To install this package from GitHub, you will also need the package devtools. Run the code below to install ITSbin on your computer.

if(!"devtools" %in% installed.packages()[,"Package"]) {
  install.packages("devtools")
  }
devtools::install_github("htanderson/ITSbin", dependencies = TRUE)

If R asks to “install from packages requiring compilation”, type n.

Usage

This package has 4 functions intended to be run in order.

  1. check_multiday Checks whether LENA™ .its files have recordings which start on more than one day and may be too long to process.

    This package cannot handle ITS files in which recordings start on more than one day, due to excessive memory (RAM) requirements (recordings that span multiple days are fine). If an ITS file has recordings which start on more than one day, the ITS_to_seconds script will not process this file and note which files have issues in ITS_file_checks.csv. The file SUBJID_recordings.csv will contain the list, dates, and times of recordings present in the ITS file.

  2. remove_recordings If check_multiday identified .its files with recordings which start on more than one day, use this function to separate those recordings into multiple .its files before running ITS_to_seconds

  3. ITS_to_seconds Takes in a LENA™ .its file and outputs user-specified CSV files of ITS recordings, ITS blocks, ITS segments, centiseconds-since-midnight, & seconds-since-midnight.

  4. bin_seconds Takes files in seconds-since-midnight and flexibly bins them into user-defined minutes. Options include: bin to any integer of minutes, sequential or rolling windows, rows align to midnight or rows align to time recorder was first turned on, & subset data based on one column before binning. Detailed explanation & examples of use: bin_seconds-options

The functions check_multiday, ITS_to_seconds, & bin_seconds run over all relevant files in an entire folder, while the function remove_recordings runs over 1 .its file at a time.

Help Files

Most help files can be accessed within R by typing ?functionname, eg

?ITS_bin::ITS_to_seconds
?bin_seconds

For detailed explanations of the column names of each output file, see below links.

Possible outputs for each input ITS file:

ITS_to_seconds

For each .its file run through ITS_to_seconds, you can choose to output any of the below CSV files. Of these, the Seconds option is necessary to bin to minutes through the bin_seconds function. The default is to output only the Seconds file.

Recordings Explanations of column names and possible values from ITS Recordings level .CSV files from check_multiday and ITS_to_seconds.

Blocks Explanations of column names and possible values from ITS Blocks level .CSV files from ITS_to_seconds.

Segments Explanations of column names and possible values from ITS Segments level .CSV files from ITS_to_seconds. NOTE: Order and number of Segments columns varies within each file, based on when sounds occurred during the recording. Additionally, each segment can contain multiple child utterance, cry, and nonspeech vocalization columns.

Centiseconds Explanations of column names and possible values from Centiseconds .CSV files from ITS_to_seconds function.

Seconds Explanations of column names and possible values from Seconds .CSV files from ITS_to_seconds function.

bin_seconds

Binned Seconds/Minutes Explanations of column names and possible values from binned seconds/minutes .CSV files from bin_seconds function. Detailed explanation & examples of use: bin_seconds-options

Outputs from each ITS_to_seconds function run

For the below outputs, one CSV will be output per folder run through ITS_to_seconds.

ITS_checks ITS_checks.csv output from check_multiday & ITS_to_seconds column name explanations

Validation Column name explanations for ITS_script_validation.csv & ValidationFails.csv output from ITS_to_seconds. These columns indicate whether the ITS_to_seconds function ran as expected. Examples include checking whether each data.table has the expected number of columns and rows, and whether sums of values in the Segments data.table match the same sums of values in the Centiseconds data.table. Possible values for all columns are TRUE or FALSE. If a cell is NA, processing was started but not completed for that file. Levels that have been processed will have validation columns, whether or not they were output as CSV files.

processing_completed Column name explanations for processing_completed.csv output from check_multiday & ITS_to_seconds. The purpose of this CSV is to keep track of what has/has not been completed in a given run of check_multiday or ITS_to_seconds. check_multiday will only have the first 3 fields, while ITS_to_seconds will have all fields listed.