LittleThumb

LittleThumb is an R package providing a lightweight persistence mechanism for R objects, developped mainly to simplify the storage and organization of temporary results produced while programming and testing data analysis scripts or Rmarkdown notebooks. LittleThumb can be used to speed-up repeated executions of a maturing script or notebook by caching intermediate results and skipping the corresponding computations between executions.

Functionalities

• transparent save/load operations to/from RDS files
• global or individual control of storage locations and object updates
• status messages indicating automatically performed operations

Installation

# Package devtools can be installed from CRAN repositories
devtools::install_github("benja0x40/LittleThumb")

Persistent R objects

The MakeObj function serves to define persistent objects and encapsulates the block of code necessary to generate such object from scratch.

Each time a portion of R code including a MakeObj function call is executed, the object defined using this function is automatically generated and saved, or loaded, according to current automation options and depending on the object availability in the current R environment and at its storage location.

Example

The script below shows a minimalistic example defining a single persistent object named xyz.

# MiniScript.R
library(LittleThumb)

# Choose a default location to store RDS files
LittleThumb(rootpath = "AutoSaved")

# Define persistent R object xyz
MakeObj(xyz, {

  # Compute the value of object xyz
  xyz <- 1:10

})

# Do something using object xyz
print(xyz)

When this example is run for the first time, the AutoSaved folder is created and the xyz object is saved to AutoSaved/xyz.rds, as indicated by LittleThumb's status messages.

source("MiniScript.R") # First execution

[LittleThumb] create | AutoSaved
[LittleThumb] save | xyz => AutoSaved/xyz.rds

From the second execution, as long as the xyz object remains available in the R environment and LittleThumb automation options remain unchanged, the MakeObj function call in MiniScript.R bypasses any execution.

source("MiniScript.R") # Second execution

[LittleThumb] bypass | xyz = AutoSaved/xyz.rds

Executing MiniScript.R once again but when the object xyz is no longer available, for instance after restarting the R environment, the MakeObj function call now automatically loads xyz from the AutoSaved/xyz.rds file instead of recomputing this object.

rm(xyz) # Simulate restarting the R environment
source("MiniScript.R")

[LittleThumb] load | xyz <= AutoSaved/xyz.rds

Automation options

The LittleThumb function provides access to automation options controlling storage locations and object updates, either globally or individually for each object defined with MakeObj. The main options are rootpath which specifies the root location of RDS files managed by LittleThumb, as well as reload and rebuild.

The role of the reload and rebuild options is shown hereafter using the MiniScript.R example.

Reloading objects

The reload option allows to force reloading objects from their associated RDS file even when these objects are already available in the current R environment.

# Specify that all persistent objects must be reloaded
LittleThumb(reload = TRUE)

source("MiniScript.R")

[LittleThumb] reload | xyz <= AutoSaved/xyz.rds

Updating objects

The rebuild option controls whether objects should be recomputed and saved even if the associated RDS file already exists at the expected location.

# Specify that all persistent objects must be updated
LittleThumb(rebuild = TRUE)

source("MiniScript.R")

[LittleThumb] update | xyz => AutoSaved/xyz.rds

Selective automation

Both the reload and rebuild options allow to control automation of each persistent object individually.

# To specify that only object xyz must be reloaded
LittleThumb(reload = list(xyz = TRUE)) # option value provided as a named list
LittleThumb(reload = "xyz")            # or as a character vector

# To specify that only object xyz must be updated
LittleThumb(rebuild = list(xyz = TRUE)) # option value provided as a named list
LittleThumb(rebuild = "xyz")            # or as a character vector

These automation options are also accessible as supplementary arguments of the MakeObj function. When used, the value of such argument overrides the corresponding option value set by LittleThumb. For instance, the MiniScript.R example could be modified as follows to make sure that object xyz is always reloaded when the script is executed.

# Object xyz is always reloaded
MakeObj(xyz, reload = TRUE, {
  xyz <- 1:10
})

Author

Benjamin Leblanc | GitHub - ResearchGate