Plan: R6 Class representing a Plan
In plnr: A System for Planing Analyses
Plan R Documentation
R6 Class representing a Plan
Description
We work within the mental model where we have one (or more) datasets and we want to run multiple analyses on these datasets.
By demanding that all analyses use the same data sources we can:
Be efficient with requiring the minimal amount of data-pulling (this only happens once at the start).
Better enforce the concept that data-cleaning and analysis should be completely separate.
By demanding that all analysis functions only use two arguments (data and argset) we can:
Reduce mental fatigue by working within the same mental model for each analysis.
Make it easier for analyses to be exchanged with each other and iterated on.
Easily schedule the running of each analysis.
By including all of this in one Plan class, we can easily maintain a good overview of all the analyses (i.e. outputs) that need to be run.
Details
An argset is:
a set of arguments
An analysis is:
one argset
one (action) function
A plan is:
one data pull
a list of analyses
Public fields
analysesList of analyses.
Methods
Public methods
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Method new()
Create a new Plan instance.
Usage
Plan$new(verbose = interactive() | config$force_verbose, use_foreach = FALSE)
Arguments
verboseShould this plan be verbose?
use_foreach???
Method add_data()
Add a new data set.
Usage
Plan$add_data(name, fn = NULL, fn_name = NULL, direct = NULL)
Arguments
nameName of the data set.
fnA function that returns the data set.
fn_nameA character string containing the name of a function that returns the data set.
directA direct data set.
Examples
p <- plnr::Plan$new()
data_fn <- function(){return(plnr::nor_covid19_cases_by_time_location)}
p$add_data("data_1", fn = data_fn)
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)
p$get_data()
Method add_argset()
Add a new argset.
Usage
Plan$add_argset(name = uuid::UUIDgenerate(), ...)
Arguments
nameName of the (eventual) analysis that this argset will be connected to.
...Named arguments that will comprise the argset.
Examples
p <- plnr::Plan$new()
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")
p$get_argsets_as_dt()
Method add_argset_from_df()
Add a batch of argsets from a data.frame.
Usage
Plan$add_argset_from_df(df)
Arguments
dfA data.frame where each row is a new argset, and each column will be a named element in the argset.
Examples
p <- plnr::Plan$new()
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_argset_from_df(batch_argset_df)
p$get_argsets_as_dt()
Method add_argset_from_list()
Add a batch of argsets from a list.
Usage
Plan$add_argset_from_list(l)
Arguments
lA list of lists with named elements where each outermost element is a new argset, and each internal named element named element in the argset.
Examples
p <- plnr::Plan$new()
batch_argset_list <- list(
list(name = "a", var_1 = 1, var_2 = "i"),
list(name = "b", var_1 = 2, var_2 = "j"),
list(name = "c", var_1 = 3, var_2 = "k")
)
p$add_argset_from_list(batch_argset_list)
p$get_argsets_as_dt()
Method add_analysis()
Add a new analysis.
Usage
Plan$add_analysis(name = uuid::UUIDgenerate(), fn = NULL, fn_name = NULL, ...)
Arguments
nameName of the analysis.
fnAction function.
fn_nameAction function name.
...Named arguments to be added to the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_analysis(
name = "analysis_1",
fn_name = "plnr::example_action_fn"
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
Method add_analysis_from_df()
Add a batch of analyses from a data.frame.
Usage
Plan$add_analysis_from_df(fn = NULL, fn_name = NULL, df)
Arguments
fnAction function.
fn_nameAction function name.
dfA data.frame where each row is a new argset, and each column will be a named element in the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_analysis_from_df(
fn_name = "plnr::example_action_fn",
df = batch_argset_df
)
p$get_argsets_as_dt()
p$run_one(1)
Method add_analysis_from_list()
Add a batch of argsets from a list.
Usage
Plan$add_analysis_from_list(fn = NULL, fn_name = NULL, l)
Arguments
fnAction function.
fn_nameAction function name.
lA list of lists with named elements where each outermost element is a new argset, and each internal named element named element in the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
Method apply_action_fn_to_all_argsets()
Applies an action function to all the argsets
Usage
Plan$apply_action_fn_to_all_argsets(fn = NULL, fn_name = NULL)
Arguments
fnAction function.
fn_nameAction function name.
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_argset_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
p$apply_action_fn_to_all_argsets(fn_name = "plnr::example_action_fn")
p$run_one("analysis_1")
Method apply_analysis_fn_to_all()
Deprecated. Use apply_action_fn_to_all_argsets.
Usage
Plan$apply_analysis_fn_to_all(fn = NULL, fn_name = NULL)
Arguments
fnAction function.
fn_nameAction function name.
Method x_length()
Number of analyses in the plan.
Usage
Plan$x_length()
Method x_seq_along()
Generate a regular sequence from 1 to the length of the analyses in the plan.
Usage
Plan$x_seq_along()
Method set_progress()
Set an internal progress bar
Usage
Plan$set_progress(pb)
Arguments
pbProgress bar.
Method set_progressor()
Set an internal progressor progress bar
Usage
Plan$set_progressor(pb)
Arguments
pbprogressor progress bar.
Method set_verbose()
Set verbose flag
Usage
Plan$set_verbose(x)
Arguments
xBoolean.
Method set_use_foreach()
Set use_foreach flag
Usage
Plan$set_use_foreach(x)
Arguments
xBoolean.
Method get_data()
Extracts the data provided via 'add_data' and returns it as a named list.
Usage
Plan$get_data()
Returns
Named list, where most elements have been added via add_data.
One extra named element is called 'hash'. 'hash' contains the data hashes of particular datasets/variables, as calculated using the 'spookyhash' algorithm via digest::digest.
'hash' contains two named elements:
current (the hash of the entire named list)
current_elements (the hash of the named elements within the named list)
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$get_data()
Method get_analysis()
Extracts an analysis from the plan.
Usage
Plan$get_analysis(index_analysis)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
Returns
An analysis.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_analysis("analysis_1")
Method get_argset()
Extracts an argset from the plan.
Usage
Plan$get_argset(index_analysis)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
Returns
An argset
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argset("analysis_1")
Method get_argsets_as_dt()
Gets all argsets and presents them as a data.table.
Usage
Plan$get_argsets_as_dt()
Returns
Data.table that contains all the argsets within a plan.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
Method run_one_with_data()
Run one analysis (data is provided by user).
Usage
Plan$run_one_with_data(index_analysis, data, ...)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
dataNamed list (generally obtained from p$get_data()).
...Not used.
Returns
Returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_one_with_data("analysis_1", data)
Method run_one()
Run one analysis (data is obtained automatically from self$get_data()).
Usage
Plan$run_one(index_analysis, ...)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
...Not used.
Returns
Returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_one("analysis_1")
Method run_all_with_data()
Run all analyses (data is provided by user).
Usage
Plan$run_all_with_data(data, ...)
Arguments
dataNamed list (generally obtained from p$get_data()).
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_all_with_data(data)
Method run_all()
Run all analyses (data is obtained automatically from self$get_data()).
Usage
Plan$run_all(...)
Arguments
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all()
Method run_all_progress()
Run all analyses with a progress bar (data is obtained automatically from self$get_data()).
Usage
Plan$run_all_progress(...)
Arguments
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all_progress()
Method clone()
The objects of this class are cloneable with this method.
Usage
Plan$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Plan$add_data`
## ------------------------------------------------
p <- plnr::Plan$new()
data_fn <- function(){return(plnr::nor_covid19_cases_by_time_location)}
p$add_data("data_1", fn = data_fn)
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)
p$get_data()
## ------------------------------------------------
## Method `Plan$add_argset`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_argset_from_df`
## ------------------------------------------------
p <- plnr::Plan$new()
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_argset_from_df(batch_argset_df)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_argset_from_list`
## ------------------------------------------------
p <- plnr::Plan$new()
batch_argset_list <- list(
list(name = "a", var_1 = 1, var_2 = "i"),
list(name = "b", var_1 = 2, var_2 = "j"),
list(name = "c", var_1 = 3, var_2 = "k")
)
p$add_argset_from_list(batch_argset_list)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_analysis`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_analysis(
name = "analysis_1",
fn_name = "plnr::example_action_fn"
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$add_analysis_from_df`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_analysis_from_df(
fn_name = "plnr::example_action_fn",
df = batch_argset_df
)
p$get_argsets_as_dt()
p$run_one(1)
## ------------------------------------------------
## Method `Plan$add_analysis_from_list`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$get_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$get_data()
## ------------------------------------------------
## Method `Plan$get_analysis`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_analysis("analysis_1")
## ------------------------------------------------
## Method `Plan$get_argset`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argset("analysis_1")
## ------------------------------------------------
## Method `Plan$get_argsets_as_dt`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$run_one_with_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_one_with_data("analysis_1", data)
## ------------------------------------------------
## Method `Plan$run_one`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$run_all_with_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_all_with_data(data)
## ------------------------------------------------
## Method `Plan$run_all`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all()
## ------------------------------------------------
## Method `Plan$run_all_progress`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all_progress()
plnr documentation built on Nov. 23, 2022, 5:06 p.m.
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| Plan | R Documentation |
R6 Class representing a Plan
Description
We work within the mental model where we have one (or more) datasets and we want to run multiple analyses on these datasets.
By demanding that all analyses use the same data sources we can:
Be efficient with requiring the minimal amount of data-pulling (this only happens once at the start).
Better enforce the concept that data-cleaning and analysis should be completely separate.
By demanding that all analysis functions only use two arguments (data and argset) we can:
Reduce mental fatigue by working within the same mental model for each analysis.
Make it easier for analyses to be exchanged with each other and iterated on.
Easily schedule the running of each analysis.
By including all of this in one Plan class, we can easily maintain a good overview of all the analyses (i.e. outputs) that need to be run.
Details
An argset is:
a set of arguments
An analysis is:
one argset
one (action) function
A plan is:
one data pull
a list of analyses
Public fields
analysesList of analyses.
Methods
Public methods
Method new()
Create a new Plan instance.
Usage
Plan$new(verbose = interactive() | config$force_verbose, use_foreach = FALSE)
Arguments
verboseShould this plan be verbose?
use_foreach???
Method add_data()
Add a new data set.
Usage
Plan$add_data(name, fn = NULL, fn_name = NULL, direct = NULL)
Arguments
nameName of the data set.
fnA function that returns the data set.
fn_nameA character string containing the name of a function that returns the data set.
directA direct data set.
Examples
p <- plnr::Plan$new()
data_fn <- function(){return(plnr::nor_covid19_cases_by_time_location)}
p$add_data("data_1", fn = data_fn)
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)
p$get_data()
Method add_argset()
Add a new argset.
Usage
Plan$add_argset(name = uuid::UUIDgenerate(), ...)
Arguments
nameName of the (eventual) analysis that this argset will be connected to.
...Named arguments that will comprise the argset.
Examples
p <- plnr::Plan$new()
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")
p$get_argsets_as_dt()
Method add_argset_from_df()
Add a batch of argsets from a data.frame.
Usage
Plan$add_argset_from_df(df)
Arguments
dfA data.frame where each row is a new argset, and each column will be a named element in the argset.
Examples
p <- plnr::Plan$new()
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_argset_from_df(batch_argset_df)
p$get_argsets_as_dt()
Method add_argset_from_list()
Add a batch of argsets from a list.
Usage
Plan$add_argset_from_list(l)
Arguments
lA list of lists with named elements where each outermost element is a new argset, and each internal named element named element in the argset.
Examples
p <- plnr::Plan$new() batch_argset_list <- list( list(name = "a", var_1 = 1, var_2 = "i"), list(name = "b", var_1 = 2, var_2 = "j"), list(name = "c", var_1 = 3, var_2 = "k") ) p$add_argset_from_list(batch_argset_list) p$get_argsets_as_dt()
Method add_analysis()
Add a new analysis.
Usage
Plan$add_analysis(name = uuid::UUIDgenerate(), fn = NULL, fn_name = NULL, ...)
Arguments
nameName of the analysis.
fnAction function.
fn_nameAction function name.
...Named arguments to be added to the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_analysis(
name = "analysis_1",
fn_name = "plnr::example_action_fn"
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
Method add_analysis_from_df()
Add a batch of analyses from a data.frame.
Usage
Plan$add_analysis_from_df(fn = NULL, fn_name = NULL, df)
Arguments
fnAction function.
fn_nameAction function name.
dfA data.frame where each row is a new argset, and each column will be a named element in the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_analysis_from_df(
fn_name = "plnr::example_action_fn",
df = batch_argset_df
)
p$get_argsets_as_dt()
p$run_one(1)
Method add_analysis_from_list()
Add a batch of argsets from a list.
Usage
Plan$add_analysis_from_list(fn = NULL, fn_name = NULL, l)
Arguments
fnAction function.
fn_nameAction function name.
lA list of lists with named elements where each outermost element is a new argset, and each internal named element named element in the argset.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
Method apply_action_fn_to_all_argsets()
Applies an action function to all the argsets
Usage
Plan$apply_action_fn_to_all_argsets(fn = NULL, fn_name = NULL)
Arguments
fnAction function.
fn_nameAction function name. p <- plnr::Plan$new() p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location") batch_argset_list <- list( list(name = "analysis_1", var_1 = 1, var_2 = "i"), list(name = "analysis_2", var_1 = 2, var_2 = "j"), list(name = "analysis_3", var_1 = 3, var_2 = "k") ) p$add_argset_from_list( fn_name = "plnr::example_action_fn", l = batch_argset_list ) p$get_argsets_as_dt() p$apply_action_fn_to_all_argsets(fn_name = "plnr::example_action_fn") p$run_one("analysis_1")
Method apply_analysis_fn_to_all()
Deprecated. Use apply_action_fn_to_all_argsets.
Usage
Plan$apply_analysis_fn_to_all(fn = NULL, fn_name = NULL)
Arguments
fnAction function.
fn_nameAction function name.
Method x_length()
Number of analyses in the plan.
Usage
Plan$x_length()
Method x_seq_along()
Generate a regular sequence from 1 to the length of the analyses in the plan.
Usage
Plan$x_seq_along()
Method set_progress()
Set an internal progress bar
Usage
Plan$set_progress(pb)
Arguments
pbProgress bar.
Method set_progressor()
Set an internal progressor progress bar
Usage
Plan$set_progressor(pb)
Arguments
pbprogressor progress bar.
Method set_verbose()
Set verbose flag
Usage
Plan$set_verbose(x)
Arguments
xBoolean.
Method set_use_foreach()
Set use_foreach flag
Usage
Plan$set_use_foreach(x)
Arguments
xBoolean.
Method get_data()
Extracts the data provided via 'add_data' and returns it as a named list.
Usage
Plan$get_data()
Returns
Named list, where most elements have been added via add_data.
One extra named element is called 'hash'. 'hash' contains the data hashes of particular datasets/variables, as calculated using the 'spookyhash' algorithm via digest::digest. 'hash' contains two named elements:
current (the hash of the entire named list)
current_elements (the hash of the named elements within the named list)
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$get_data()
Method get_analysis()
Extracts an analysis from the plan.
Usage
Plan$get_analysis(index_analysis)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
Returns
An analysis.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_analysis("analysis_1")
Method get_argset()
Extracts an argset from the plan.
Usage
Plan$get_argset(index_analysis)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
Returns
An argset
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argset("analysis_1")
Method get_argsets_as_dt()
Gets all argsets and presents them as a data.table.
Usage
Plan$get_argsets_as_dt()
Returns
Data.table that contains all the argsets within a plan.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
Method run_one_with_data()
Run one analysis (data is provided by user).
Usage
Plan$run_one_with_data(index_analysis, data, ...)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
dataNamed list (generally obtained from p$get_data()).
...Not used.
Returns
Returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_one_with_data("analysis_1", data)
Method run_one()
Run one analysis (data is obtained automatically from self$get_data()).
Usage
Plan$run_one(index_analysis, ...)
Arguments
index_analysisEither an integer (1:length(analyses)) or a character string representing the name of the analysis.
...Not used.
Returns
Returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_one("analysis_1")
Method run_all_with_data()
Run all analyses (data is provided by user).
Usage
Plan$run_all_with_data(data, ...)
Arguments
dataNamed list (generally obtained from p$get_data()).
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_all_with_data(data)
Method run_all()
Run all analyses (data is obtained automatically from self$get_data()).
Usage
Plan$run_all(...)
Arguments
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all()
Method run_all_progress()
Run all analyses with a progress bar (data is obtained automatically from self$get_data()).
Usage
Plan$run_all_progress(...)
Arguments
...Not used.
Returns
List where each element contains the returned value from the action function.
Examples
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all_progress()
Method clone()
The objects of this class are cloneable with this method.
Usage
Plan$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Plan$add_data`
## ------------------------------------------------
p <- plnr::Plan$new()
data_fn <- function(){return(plnr::nor_covid19_cases_by_time_location)}
p$add_data("data_1", fn = data_fn)
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)
p$get_data()
## ------------------------------------------------
## Method `Plan$add_argset`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_argset_from_df`
## ------------------------------------------------
p <- plnr::Plan$new()
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_argset_from_df(batch_argset_df)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_argset_from_list`
## ------------------------------------------------
p <- plnr::Plan$new()
batch_argset_list <- list(
list(name = "a", var_1 = 1, var_2 = "i"),
list(name = "b", var_1 = 2, var_2 = "j"),
list(name = "c", var_1 = 3, var_2 = "k")
)
p$add_argset_from_list(batch_argset_list)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$add_analysis`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$add_analysis(
name = "analysis_1",
fn_name = "plnr::example_action_fn"
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$add_analysis_from_df`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_df <- data.frame(name = c("a", "b", "c"), var_1 = c(1, 2, 3), var_2 = c("i", "j", "k"))
p$add_analysis_from_df(
fn_name = "plnr::example_action_fn",
df = batch_argset_df
)
p$get_argsets_as_dt()
p$run_one(1)
## ------------------------------------------------
## Method `Plan$add_analysis_from_list`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$get_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
p$get_data()
## ------------------------------------------------
## Method `Plan$get_analysis`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_analysis("analysis_1")
## ------------------------------------------------
## Method `Plan$get_argset`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argset("analysis_1")
## ------------------------------------------------
## Method `Plan$get_argsets_as_dt`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$get_argsets_as_dt()
## ------------------------------------------------
## Method `Plan$run_one_with_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_one_with_data("analysis_1", data)
## ------------------------------------------------
## Method `Plan$run_one`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_one("analysis_1")
## ------------------------------------------------
## Method `Plan$run_all_with_data`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
data <- p$get_data()
p$run_all_with_data(data)
## ------------------------------------------------
## Method `Plan$run_all`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all()
## ------------------------------------------------
## Method `Plan$run_all_progress`
## ------------------------------------------------
p <- plnr::Plan$new()
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")
batch_argset_list <- list(
list(name = "analysis_1", var_1 = 1, var_2 = "i"),
list(name = "analysis_2", var_1 = 2, var_2 = "j"),
list(name = "analysis_3", var_1 = 3, var_2 = "k")
)
p$add_analysis_from_list(
fn_name = "plnr::example_action_fn",
l = batch_argset_list
)
p$run_all_progress()
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