Function to check setup of package

[dfalster]

Want a function which checks each directory in data and returns TRUE if passes all the tests, checking that all the right parts are there.

Then embed this within getStudyNames --> returns a list of directories that pass all the tests. These dirs are then loaded and built. Make an option to test=FALSE (for getStudyNames, default=FALSE).

Config files

• [ ] When loading dataMashR, check config files exists and have right columns
• [ ] do all files exist? we need to define if methodsDefinitions is among them;
• [ ] does startDataMashR load correctly?

  Variable definitions

• [x] does file exist?
• [x] do all columns exist?
• [x] do all numeric variables contain a valid range of values? if not, throw warning
• [x] are specified ranges valid? (TEST CHECKS IF COLUMNS ARE PURELY NUMERIC)
• [x] are types of variables (e.g. numeric, character) valid modes in R?
• [ ] do variable names contain special characters [/*^, or any nonascii]
• [ ] all numeric vars have methods units specified, i.e. can't be blank
• [ ] check for trailing white spaces after variable names

  Variable conversions

• [x] does file exist?
• [x] can it be empty? What if people are dealing with non-numeric datasets?
• [x] are columns in the right order?
• [x] are conversion functions valid functions?

  For each study

• [ ] modify tests to draw var.def using mashRdetail function

  data.csv

• [x] does file exist?
• [x] no duplicate column names
• [ ] values outside range --> MAYBE THIS SHOULD BE A POST-HOC TEST AFTER PROCESSING THE DATA? OTHERWISE WE'LL HAVE TO PROCESS ALL THE DATA TWICE, WHICH IN TOTAL WOULD TAKE ~30 SEC (IN THE CASE OF BAAD), AND COULD POTENTIALLY CAUSE A MEMORY CRASH DUE TO 'TOO MANY OPEN FILES'
• [ ] contains special characters?
• [ ] file loads without problems

  dataImportOptions

• [ ] does it have the right structure? i.e., colnames
• [ ] are entry values acceptable? (e.g. TRUE or FALSE for header, and a numeric value for skip?)

  dataManipulate

• [ ] is it a valid function?
• [ ] is it a function of 'raw'?
• [ ] does it return 'raw'?

  dataMatchColumns

• [x] order of column names should correspond to data header
• [ ] no NA values in var_in (e.g., was in O'Hara0000)
• [ ] are the listed methods contained within the config table methodsDefinitions?
• [x ] variable names present in var.def
• [x] suitable unit conversion exists, given input units and desired output

  dataNew

• [ ] columns in the right order?
• [ ] if a variable is listed in newVariable only (no case to match, i.e., could be either a new variable to add or a column with unique entry to be completely replaced), but it already exists, then throw a warning that it existed already in data but was completely replaced.
• [ ] do all values listed in lookupVariable exist in the processed data post dataMatchColumns?
• [ ] is the file empty? If so, throw a warning letting the person know that no additions will be made?
• [ ] are the newVariable listed contained within the variableDefinitions table?
• [ ] are new values in accordance with variable type? If so, are they within the correct range?
• [ ] when addNewData adds a new variable conditionally on a lookupValue, it fails when the lookupVariable contains missing values. For example,

lookupVariable,lookupValue,newVariable,newValue,source
species,Cedrela odorata,family,Meliaceae,
species,Tabebuia rosea,family,Bignonaceae,

would fail if species contains NA in the data

studyContact

• [ ] does it contain special characters?
• [ ] does it contain the right columns?

  studyMetadata

• [ ] this should be a relatively free file, is it a true requirement?

  studyRef

• [ ] same as above, should be optional as not all datasets are published..
• [ ] if it exists, does it contain a valid bibtex format/template (check if throws error when loading)

  all files

• [ ] Non-unicode chars, as per #104
• [ ] check for trailing white spaces (before ,)
• [ ] find replace on known strange characters? ’ -> ', – -> -, tabs, other?

[dfalster]

Diego keen to try this, to develop skills writing tests. Suggest that before writing code, scope the problem more, make lists of possible things, review with Rich and Dan, then start coding.

[dfalster]

Hi Diego,

List looks very good. I added one for variable conversions: test each against known result Let's meet tomorrow at 9:30.

DF

[dfalster]

Need to check functionality of functions too. Move to final test coming after others.

• [ ] character data only has allowable values (if these are present)
• [ ] data in specified range