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: Default: file.path(dirname(.reproducibleTempCacheDir()), "checksums.rds"). Used in cloudCache
length: Default: 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: Default: "https://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:

ask: Default: TRUE. Used in clearCache and keepCache.
cachePath: Default: .reproducibleTempCacheDir. Used in Cache and many others. The default path for repositories if not passed as an argument.
cacheSaveFormat: Default: "rds". What save format to use; currently, "qs" or "rds".
cacheSpeed: Default "slow". One of "slow" or "fast" (1 or 2). "slow" uses digest::digest internally, which is transferable across operating systems, but much slower than fastdigest::fastdigest. So, if all caching is happening on a single machine, "fast" would be a good setting.
conn: Default: NULL. Sets a specific connection to a database, e.g., dbConnect(drv = RSQLite::SQLite()) or dbConnect(drv = RPostgres::Postgres(). For remote database servers, setting one connection may be far faster than using drv which must make a new connection every time.
destinationPath: Default: NULL. Used in prepInputs and preProcess. Can be set globally here.
drv: Default: RSQLite::SQLite(). Sets the default driver for the backend database system. Only tested with RSQLite::SQLite() and RPostgres::Postgres().
futurePlan: Default: FALSE. On Linux OSes, 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: Default: NULL. Used in prepInputs and 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: Default: FALSE. Used in prepInputs and preProcess. Should the reproducible.inputPaths be searched recursively for existence of a file?
nThreads: Default: 1. The number of threads to use for reading/writing cache files.
overwrite: Default: FALSE. Used in prepInputs, preProcess, downloadFile, and postProcess.
quick: Default: 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: Default FALSE. Passed to Cache.
useCache: Default: 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-dev-mode behaviour to avoid deleting objects. This, therefore, is most useful if the user is using unique values for userTags.
useCloud: Default FALSE. Passed to Cache.
useDBI: Default: TRUE. As of version 0.3, the backend is now DBI instead of archivist.
useGDAL: Default TRUE. Passed to useGDAL in projectInputs.Raster.
useMemoise: Default: FALSE. 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 first (create cache entry) or second (recover from the SQLite database on disk). 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: Default: 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: Default: 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.