IPDFileCheck v0.5.0

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Basic Functions to Check Readability, Consistency, and Content of an Individual Participant Data File

Basic checks to be carried out with an individual level participant data from randomised controlled trial. This checks files for existence, read access and individual columns for formats. The checks on format is currently implemented for gender and age formats.

Readme

IPDFileCheck

IPDFileCheck is a package that can be used to check the data file from a randomised clinical trial (RCT). The standard checks on data file from RCT will be of the following

  1. To check the file exists and readable
  2. To check if the column exists,
  3. To get the column number if the column name is known,
  4. To test column contents ie do they contain specific items in a given list?
  5. To test column names of a data being different from what specified,
  6. To check the format of column 'age' in data
  7. To check the format of column 'gender' in data
  8. To check the format of column contents -numeric or string
  9. To return the column number if the pattern is contained in the colnames of a data
  10. To return descriptive statistics, sum, no of observations, mean, mode. median, range, standard deviation and standard error
  11. To present the mean and sd of a data set in the form Mean (SD)
  12. To return a subgroup when certain variable equals the given value while omitting those with NA
  13. To find the number and percentages of categories
  14. To calculate age from date of birth and year of birth There are some other helper functions included. Usage
    See the User Guide Vignette for examples on using the package Installation
    Latest release can be installed from www.github.com/sheejamk/ipdfilecheck

Functions in IPDFileCheck

Name Description
getConentdInCols Function to return the unique contents of the column given the column name
representCategoricalData Function to find the number and percentages of categories
testFileExistenceReadability Function to throw error on invalid directory or file or if the file is not readable
testGender Function to check the format of 'gender' column in data
representCategoricalDataText Function to represent categorical data in the form - numbers (percentage)
calculateAgeFromDob Function to calculate age from date of birth
testAge Function to check the format of 'age' in data
testColumnContents Function to check the format of column contents
returnSubgroupOmitNA Function to return a subgroup when certain variable equals the given value while omitting those with NA
getModeForVector Function to return mode
getSEM Function to estimate standard error of the mean
presentMeanSdRemoveNAText Function to present the mean and sd of a data set in the form Mean (SD)
testDataNumeric Function to check the format of a numeric column
testDataNumericNorange Function to check the format of a numeric column when the values are not bounded
testDataColumnNames Function to test column names of a data being different from what specified
testDataString Function to check the format of a string column
testDataStringRestriction Function to check the format of a string column when the string values are given
checkColumnNoForPatternInColumnname Function to return the column number if a given pattern is contained in the column names of a data
cohensD Function to find the effect size Cohen's d
descriptiveStatisticsDataColumn Function to return descriptive statistics, sum, no of observations, mean, mode. median, range, standard deviation and standard error
checkColumnExists Function to check the given column exists
checkLoadPackages Function to check the package is installed, if not install
convertStdDateFormat Helper function to keep date formats in year/month/date
getColumnNoForNames Function to return the column number for column name
getColumnNoForPatternInColumnname Function to return the column number if a given pattern is contained in the column names of a data
calculateAgeFromBirthYear Function to calculate age from year of birth
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Vignettes of IPDFileCheck

Name
User_Guide.Rmd
_gitignore
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Details

Type Package
License CC0
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2019-11-11 16:02:20 UTC; smk543
Repository CRAN
Date/Publication 2019-11-11 16:20:02 UTC

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