ggir.summary: Description of all accelerometer files in the GGIR output

Description Usage Arguments Value

View source: R/part2_summary.pipeline.R

Description

Description of all accelerometer files in the GGIR output and this script was executed when mode=2 in the main call.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
ggir.summary(
  bindir = NULL,
  outputdir,
  studyname,
  numericID = FALSE,
  sortByid = "filename",
  subdir = "summary",
  part5FN = "WW_L50M125V500_T5A5",
  QChours.alpha = 16,
  filename2id = NULL,
  desiredtz = "US/Eastern",
  trace = FALSE
)

Arguments

bindir

character Directory where the accelerometer files are stored or list for the purpose of extracting the bin file list. Default=NULL when it is not available and therefore the bin file list is extracted from the /meta/basic folder of the GGIR output.

outputdir

character Directory where the GGIR output was stored.

studyname

character Specify the study name that used in the output file names

numericID

logical Specify if the ID is numeric when checking ID errors in part2. Default is FALSE.

sortByid

character Specify the name of "ID" for each accelerometer file in the report of part2. The value could be "newID","id" and "filename". Defaut is "filename".

subdir

character Sub-directory where the summary output was stored under the current directory. Defaut is "summary".

part5FN

character Specify which output is used in the GGIR part5 results. Defaut is "WW_L50M125V500_T5A5", which means that part5_daysummary_WW_L50M125V500_T5A5.csv and part5_personsummary_WW_L50M125V500_T5A5.csv are used in the analysis.

QChours.alpha

number Minimum required number of valid hours in day specific analysis as a quality control step in part2. Default is 16 hours.

filename2id

R function User defined function for converting filename to sample IDs. Default is NULL.

desiredtz

charcter desired timezone: see also http://en.wikipedia.org/wiki/Zone.tab. Used in g.inspectfile(). Default is "US/Eastern".

trace

logical Specify if the intermediate results is printed when the function was executed. Default is FALSE.

Value

Four files were written to the specified sub-directory

studyname_ggir_output_summary.xlsx

This excel file includs 9 pages as follows,

page 1

List of files in the GGIR output

page 2

Summary of files

page 3

List of duplicate IDs

page 4

ID errors

page 5

Number of valid days

page 6

Table of number of valid/missing days

page 7

Missing patten

page 8

Frequency of the missing pattern

page 9

Description of all accelerometer files

page 10

Inspects accelerometer file for key information, including: monitor brand, sample frequency and file header

studyname_ggir_output_summary_plot.pdf

Some plots such as the number of valid days, which were included in the part2a_studyname_postGGIR.report.html file as well.

part24daysummary.info.csv

Intermediate results for description of each accelerometer file.

studyname_samples_remove_temp.csv

Create studyname_samples_remove.csv file by filling "remove" in the "duplicate" column in this template. If duplicate="remove", the accelerometer files will not be used in the data analysis of part 5-7.


postGGIR documentation built on July 14, 2021, 5:11 p.m.