reproducibleOptions: `reproducible` options

Description

These provide top-level, powerful settings for a comprehensive reproducible workflow. To see defaults, run reproducibleOptions(). See Details below.

Usage

reproducibleOptions()

Arguments

Advanced

The following options are likely not needed by a user.

`cloudChecksumsFilename`	`file.path(dirname(.reproducibleTempCacheDir), "checksums.rds")`	Used in `cloudCache`
`length`	`Inf`	Used in `Cache`, specifically to the internal calls to `CacheDigest`. This is passed to `digest::digest`. Mostly this would be changed from default `Inf` if the digesting is taking too long. Use this with caution, as some objects will have MANY NA values in their first MANY elements
`useragent`	`"http://github.com/PredictiveEcology/reproducible"`	User agent for downloads using this package.

Details

Below are options that can be set with options("reproducible.xxx" = newValue), where xxx is one of the values below, and newValue is a new value to give the option. Sometimes these options can be placed in the user's .Rprofile file so they persist between sessions.

The following options are likely of interest to most users

OPTION	DEFAULT VALUE	DESCRIPTION
`ask`	`TRUE`	Used in `clearCache` and `keepCache`
`cachePath`	`.reproducibleTempCacheDir`	Used in `Cache` and many others. The default path for repositories if not passed as an argument.
`destinationPath`	`NULL`	Used in `prepInputs`, `preProcess`. Can be set globally here.
`futurePlan`	`FALSE`	On Linux OSs, `Cache` and `cloudCache` have some functionality that uses the `future` package. Default is to not use these, as they are experimental. They may, however, be very effective in speeding up some things, specifically, uploading cached elements via googledrive in `cloudCache`
`inputPaths`	`NULL`	Used in `prepInputs`, `preProcess`. If set to a path, this will cause these functions to save their downloaded and preprocessed file to this location, with a hardlink (via `file.link`) to the file created in the `destinationPath`. This can be used so that individual projects that use common data sets can maintain modularity (by placing downloaded objects in their `destinationPath`, but also minimize re-downloading the same (perhaps large) file over and over for each project. Because the files are hardlinks, there is no extra space taken up by the apparently duplicated files
`inputPathsRecursive`	`FALSE`	Used in `prepInputs`, `preProcess`. Should the `reproducible.inputPaths` be searched recursively for existence of a file
`overwrite`	`FALSE`	Used in `prepInputs`, `preProcess`, `downloadFile`, and `postProcess`.
`quick`	`FALSE`	Used in `Cache`. This will cause `Cache` to use `file.size(file)` instead of the `digest::digest(file)`. Less robust to changes, but faster. NOTE: this will only affect objects on disk.
`showSimilar`	Passed to `Cache`. Default `FALSE`.	`useCache`
`TRUE`	Used in `Cache`. If `FALSE`, then the entire `Cache` machinery is skipped and the functions are run as if there was no Cache occurring. Can also take 2 other values: `'overwrite'` and `'devMode'`. `'overwrite'` will cause no recovery of objects from the cache repository, only new ones will be created. If the hash is identical to a previous one, then this will overwrite the previous one. `'devMode'` will function as normally `Cache` except it will use the `userTags` to determine if a previous function has been run. If the `userTags` are identical, but the digest value is different, the old value will be deleted from the cache repository and this new value will be added. This addresses a common situation during the development stage: functions are changing frequently, so any entry in the cache repository will be stale following changes to functions, i.e., they will likely never be relevant again. This will therefore keep the cache repository clean of stale objects. If there is ambiguity in the `userTags`, i.e they do not uniquely identify a single entry in the cacheRepo, then this option will default back to the non devMode behaviour to avoid deleting objects. This, therefore, is most useful if the user is using unique values for `userTags`	`useCloud`
Passed to `Cache`. Default `FALSE`.	`useMemoise`	`TRUE`
Used in `Cache`. If `TRUE`, recovery of cached elements from the cacheRepo will use `memoise::memoise`. This means that the 3rd time running a function will be much faster than the 1st (create cache entry) or 2nd (recover from the SQLite database on dist). NOTE: memoised values are removed when the R session is restarted. This option will use more RAM and so may need to be turned off if RAM is limiting. `clearCache` of any sort will cause all memoising to be 'forgotten' (`memoise::forget`)	`useNewDigestAlgorithm`	`TRUE`
This will mean that previous cache repositories will be defunct. This new algorithm will make `Cache` less sensitive to minor but irrelevant changes (like changing the order of arguments) and will work successfully across operating systems (especially relevant for the new 'cloudCache' function	`verbose`	`FALSE`
If set to `TRUE` then every Cache call will show a summary of the objects being cached, their `object.size` and the time it took to digest them and also the time it took to run the call and save the call to the cache repository or load the cached copy from the repository. This may help diagnosing some problems that may occur.	OPTION	DEFAULT VALUE