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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

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Version

Install

install.packages('IPDFileCheck')

Monthly Downloads

140

Version

0.3.0

License

CC0

Maintainer

Sheeja Manchira Krishnan

Last Published

October 7th, 2019

Functions in IPDFileCheck (0.3.0)

testDataNumeric

Function to check the format of a numeric column
testDataColumnNames

Function to test column names of a data being different from what specified
testDataStringRestriction

Function to check the format of a string column when the string values are given
testDataString

Function to check the format of a string column
testColumnContents

Function to check the format of column contents
testFileExistenceReadability

Function to throw error on invalid directory or file or if the file is not readable
presentMeanSdRemoveNAText

Function to present the mean and sd of a data set in the form Mean (SD)
getSEM

Function to estimate standard error of the mean
testGender

Function to check the format of 'gender' column in data
testDataNumericNorange

Function to check the format of a numeric column when the values are not bounded
representCategoricalDataText

Function to represent categorical data in the form - numbers (percentage)
getColumnNoForNames

Function to return the column number for column name
representCategoricalData

Function to find the number and percentages of categories
testAge

Function to check the format of 'age' in data
returnSubgroupOmitNA

Function to return a subgroup when certain variable equals the given value while omitting those with NA
getModeForVector

Function to return mode
checkLoadPackages

Function to check the package is installed, if not install
convertStdDateFormat

Helper function to keep date formats in year/month/date
calculateAgeFromBirthYear

Function to calculate age from year of birth
cohensD

Function to find the effect size Cohen's d
getColumnNoForPatternInColumnname

Function to return the column number if a given attern is contained in the column names of a data
checkColumnExists

Function to check the given column exists
descriptiveStatisticsDataColumn

Function to return descriptive statistics, sum, no of observations, mean, mode. median, range, standard deviation and standard error
calculateAgeFromDob

Function to calculate age from date of birth