Package 'plnr' reference manual

Title:	A System for Planing Analyses
Description:	A system to plan analyses within the mental model where you have one (or more) datasets and want to run either A) the same function multiple times with different arguments, or B) multiple functions. This is appropriate when you have multiple strata (e.g. locations, age groups) that you want to apply the same function to, or you have multiple variables (e.g. exposures) that you want to apply the same statistical method to, or when you are creating the output for a report and you need multiple different tables or graphs.
Authors:	Richard Aubrey White [aut, cre] , CSIDS [cph]
Maintainer:	Richard Aubrey White <[email protected]>
License:	MIT + file LICENSE
Version:	2022.11.23
Built:	2025-02-12 05:42:42 UTC
Source:	https://github.com/csids/plnr

Create example rmarkdown project

Description

Create example rmarkdown project

Usage

create_rmarkdown(home)
create_rmarkdown(home)

Arguments

home

Location of the 'home' directory

An example action_fn for an analysis

Description

An example action_fn for an analysis

Usage

example_action_fn(data, argset)
example_action_fn(data, argset)

Arguments

`data`	Named list.
`argset`	Named list.

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$run_one("analysis_1")
p <- plnr::Plan$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")

An example data_fn that returns a data set

Description

An example data_fn that returns a data set

Usage

example_data_fn_nor_covid19_cases_by_time_location()
example_data_fn_nor_covid19_cases_by_time_location()

Expand (cross) lists

Description

The same as purrr::cross, but doesn't require an extra list()

Usage

expand_list(...)
expand_list(...)

Arguments

...

Dots

Examples

plnr::expand_list(
  a = 1:2,
  b = c("a", "b")
)
plnr::expand_list(
  a = 1:2,
  b = c("a", "b")
)

Gets anything (including with package scoping)

Description

base::get does not work with package scoping (e.g. get("pkg::var")). plnr::get_anything works with package scoping.

Usage

get_anything(x)
get_anything(x)

Arguments

`x`	the string that we are getting

Examples

plnr::get_anything("plnr::nor_covid19_cases_by_time_location")
plnr::get_anything("plnr::nor_covid19_cases_by_time_location")

Is this code run directly?

Description

This function determines if it is being called from within a function or if it is being run directly

Usage

is_run_directly()
is_run_directly()

Covid-19 data for PCR-confirmed cases in Norway (nation and county)

Description

This data comes from the Norwegian Surveillance System for Communicable Diseases (MSIS). The date corresponds to when the PCR-test was taken.

Usage

nor_covid19_cases_by_time_location
nor_covid19_cases_by_time_location

Format

A csfmt_rts_data_v1 with 11028 rows and 18 variables:

granularity_time: day/isoweek
granularity_geo: nation, county
country_iso3: nor
location_code: norge, 11 counties
border: 2020
age: total
isoyear: Isoyear of event
isoweek: Isoweek of event
isoyearweek: Isoyearweek of event
season: Season of event
seasonweek: Seasonweek of event
calyear: Calyear of event
calmonth: Calmonth of event
calyearmonth: Calyearmonth of event
date: Date of event
covid19_cases_testdate_n: Number of confirmed covid19 cases
covid19_cases_testdate_pr100000: Number of confirmed covid19 cases per 100.000 population

Details

The raw number of cases and cases per 100.000 population are recorded.

This data was extracted on 2022-05-04.

Source

https://github.com/folkehelseinstituttet/surveillance_data/blob/master/covid19/_DOCUMENTATION_data_covid19_msis_by_time_location.txt

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

analyses: List of analyses.

Methods

Public methods

Plan$new()
Plan$add_data()
Plan$add_argset()
Plan$add_argset_from_df()
Plan$add_argset_from_list()
Plan$add_analysis()
Plan$add_analysis_from_df()
Plan$add_analysis_from_list()
Plan$apply_action_fn_to_all_argsets()
Plan$apply_analysis_fn_to_all()
Plan$x_length()
Plan$x_seq_along()
Plan$set_progress()
Plan$set_progressor()
Plan$set_verbose()
Plan$set_use_foreach()
Plan$get_data()
Plan$get_analysis()
Plan$get_argset()
Plan$get_argsets_as_dt()
Plan$run_one_with_data()
Plan$run_one()
Plan$run_all_with_data()
Plan$run_all()
Plan$run_all_progress()
Plan$run_all_parallel()
Plan$clone()

Method `new()`

Create a new Plan instance.

Usage

Plan$new(verbose = interactive() | config$force_verbose, use_foreach = FALSE)

Arguments

verbose: Should 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

name: Name of the data set.
fn: A function that returns the data set.
fn_name: A character string containing the name of a function that returns the data set.
direct: A 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

name: Name 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

df: A 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

l: A 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

name: Name of the analysis.
fn: Action function.
fn_name: Action 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

fn: Action function.
fn_name: Action function name.
df: A 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

fn: Action function.
fn_name: Action function name.
l: A 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

fn: Action function.
fn_name: Action 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

fn: Action function.
fn_name: Action 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

pb: Progress bar.

Method `set_progressor()`

Set an internal progressor progress bar

Usage

Plan$set_progressor(pb)

Arguments

pb: progressor progress bar.

Method `set_verbose()`

Set verbose flag

Usage

Plan$set_verbose(x)

Arguments

x: Boolean.

Method `set_use_foreach()`

Set use_foreach flag

Usage

Plan$set_use_foreach(x)

Arguments

x: Boolean.

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_analysis: Either 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_analysis: Either 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_analysis: Either an integer (1:length(analyses)) or a character string representing the name of the analysis.
data: Named 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_analysis: Either 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

data: Named 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 `run_all_parallel()`

Run all analyses in parallel (data is obtained automatically from self$get_data()).

This function only works on linux computers and uses pbmcapply as the parallel backend.

Usage

Plan$run_all_parallel(mc.cores = getOption("mc.cores", 2L), ...)

Arguments

mc.cores: Number of cores to be used.
...: Not used.

Returns

List where each element contains the returned value from the action function.

Method `clone()`

The objects of this class are cloneable with this method.

Usage

Plan$clone(deep = FALSE)

Arguments

deep: Whether 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()
## ------------------------------------------------
## 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()

set_opts

Description

set_opts

Usage

set_opts(force_verbose = FALSE)
set_opts(force_verbose = FALSE)

Arguments

force_verbose

Force verbose

A test action_fn for an analysis that returns the value 1

Description

A test action_fn for an analysis that returns the value 1

Usage

test_action_fn(data, argset)
test_action_fn(data, argset)

Arguments

`data`	Data
`argset`	argset

Try a code snipped multiple times.

Description

Adapted from function try_again from package testthat.

Usage

try_again(
  x,
  times = 2,
  delay_seconds_min = 5,
  delay_seconds_max = 10,
  verbose = FALSE
)
try_again(
  x,
  times = 2,
  delay_seconds_min = 5,
  delay_seconds_max = 10,
  verbose = FALSE
)

Arguments

`x`	code
`times`	Number of times to try
`delay_seconds_min`	Number of seconds to delay on failure
`delay_seconds_max`	Number of seconds to delay on failure
`verbose`	Boolean. Do you want information?

Package 'plnr'

Help Index

Create example rmarkdown project

Description

Usage

Arguments

An example action_fn for an analysis

Description

Usage

Arguments

Examples

An example data_fn that returns a data set

Description

Usage

Expand (cross) lists

Description

Usage

Arguments

Examples

Gets anything (including with package scoping)

Description

Usage

Arguments

Examples

Is this code run directly?

Description

Usage

Covid-19 data for PCR-confirmed cases in Norway (nation and county)

Description

Usage

Format

Details

Source

R6 Class representing a Plan

Description

Details

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Method add_data()

Usage

Arguments

Examples

Method add_argset()

Usage

Arguments

Examples

Method add_argset_from_df()

Usage

Arguments

Examples

Method add_argset_from_list()

Usage

Arguments

Examples

Method add_analysis()

Usage

Arguments

Examples

Method add_analysis_from_df()

Usage

Arguments

Examples

Method add_analysis_from_list()

Usage

Arguments

Examples

Method apply_action_fn_to_all_argsets()

Usage

Arguments

Method apply_analysis_fn_to_all()

Usage

Arguments

Method x_length()

Usage

Method x_seq_along()

Usage

Method `new()`

Method `add_data()`

Method `add_argset()`

Method `add_argset_from_df()`

Method `add_argset_from_list()`

Method `add_analysis()`

Method `add_analysis_from_df()`

Method `add_analysis_from_list()`

Method `apply_action_fn_to_all_argsets()`

Method `apply_analysis_fn_to_all()`

Method `x_length()`

Method `x_seq_along()`

Method `set_progress()`

Method `set_progressor()`

Method `set_verbose()`

Method `set_use_foreach()`

Method `get_data()`

Method `get_analysis()`

Method `get_argset()`

Method `get_argsets_as_dt()`

Method `run_one_with_data()`

Method `run_one()`

Method `run_all_with_data()`

Method `run_all()`

Method `run_all_progress()`

Method `run_all_parallel()`

Method `clone()`