R6 Class representing a Plan

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

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()
#> $data_1
#>        granularity_time granularity_geo country_iso3 location_code border   age
#>     1:              day          county          nor  county_nor03   2020 total
#>     2:              day          county          nor  county_nor03   2020 total
#>     3:              day          county          nor  county_nor03   2020 total
#>     4:              day          county          nor  county_nor03   2020 total
#>     5:              day          county          nor  county_nor03   2020 total
#>    ---                                                                         
#> 11024:          isoweek          nation          nor    nation_nor   2020 total
#> 11025:          isoweek          nation          nor    nation_nor   2020 total
#> 11026:          isoweek          nation          nor    nation_nor   2020 total
#> 11027:          isoweek          nation          nor    nation_nor   2020 total
#> 11028:          isoweek          nation          nor    nation_nor   2020 total
#>          sex isoyear isoweek isoyearweek    season seasonweek calyear calmonth
#>     1: total    2020       8     2020-08 2019/2020         31    2020        2
#>     2: total    2020       8     2020-08 2019/2020         31    2020        2
#>     3: total    2020       8     2020-08 2019/2020         31    2020        2
#>     4: total    2020       9     2020-09 2019/2020         32    2020        2
#>     5: total    2020       9     2020-09 2019/2020         32    2020        2
#>    ---                                                                        
#> 11024: total    2022      14     2022-14 2021/2022         37      NA       NA
#> 11025: total    2022      15     2022-15 2021/2022         38      NA       NA
#> 11026: total    2022      16     2022-16 2021/2022         39      NA       NA
#> 11027: total    2022      17     2022-17 2021/2022         40      NA       NA
#> 11028: total    2022      18     2022-18 2021/2022         41      NA       NA
#>        calyearmonth       date covid19_cases_testdate_n
#>     1:     2020-M02 2020-02-21                        0
#>     2:     2020-M02 2020-02-22                        0
#>     3:     2020-M02 2020-02-23                        0
#>     4:     2020-M02 2020-02-24                        0
#>     5:     2020-M02 2020-02-25                        0
#>    ---                                                 
#> 11024:         <NA> 2022-04-10                     6888
#> 11025:         <NA> 2022-04-17                     3635
#> 11026:         <NA> 2022-04-24                     3764
#> 11027:         <NA> 2022-05-01                     2243
#> 11028:         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>     1:                        0.000000
#>     2:                        0.000000
#>     3:                        0.000000
#>     4:                        0.000000
#>     5:                        0.000000
#>    ---                                
#> 11024:                      126.961423
#> 11025:                       67.001274
#> 11026:                       69.379036
#> 11027:                       41.343564
#> 11028:                        9.252996
#> 
#> $data_2
#>        granularity_time granularity_geo country_iso3 location_code border   age
#>     1:              day          county          nor  county_nor03   2020 total
#>     2:              day          county          nor  county_nor03   2020 total
#>     3:              day          county          nor  county_nor03   2020 total
#>     4:              day          county          nor  county_nor03   2020 total
#>     5:              day          county          nor  county_nor03   2020 total
#>    ---                                                                         
#> 11024:          isoweek          nation          nor    nation_nor   2020 total
#> 11025:          isoweek          nation          nor    nation_nor   2020 total
#> 11026:          isoweek          nation          nor    nation_nor   2020 total
#> 11027:          isoweek          nation          nor    nation_nor   2020 total
#> 11028:          isoweek          nation          nor    nation_nor   2020 total
#>          sex isoyear isoweek isoyearweek    season seasonweek calyear calmonth
#>     1: total    2020       8     2020-08 2019/2020         31    2020        2
#>     2: total    2020       8     2020-08 2019/2020         31    2020        2
#>     3: total    2020       8     2020-08 2019/2020         31    2020        2
#>     4: total    2020       9     2020-09 2019/2020         32    2020        2
#>     5: total    2020       9     2020-09 2019/2020         32    2020        2
#>    ---                                                                        
#> 11024: total    2022      14     2022-14 2021/2022         37      NA       NA
#> 11025: total    2022      15     2022-15 2021/2022         38      NA       NA
#> 11026: total    2022      16     2022-16 2021/2022         39      NA       NA
#> 11027: total    2022      17     2022-17 2021/2022         40      NA       NA
#> 11028: total    2022      18     2022-18 2021/2022         41      NA       NA
#>        calyearmonth       date covid19_cases_testdate_n
#>     1:     2020-M02 2020-02-21                        0
#>     2:     2020-M02 2020-02-22                        0
#>     3:     2020-M02 2020-02-23                        0
#>     4:     2020-M02 2020-02-24                        0
#>     5:     2020-M02 2020-02-25                        0
#>    ---                                                 
#> 11024:         <NA> 2022-04-10                     6888
#> 11025:         <NA> 2022-04-17                     3635
#> 11026:         <NA> 2022-04-24                     3764
#> 11027:         <NA> 2022-05-01                     2243
#> 11028:         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>     1:                        0.000000
#>     2:                        0.000000
#>     3:                        0.000000
#>     4:                        0.000000
#>     5:                        0.000000
#>    ---                                
#> 11024:                      126.961423
#> 11025:                       67.001274
#> 11026:                       69.379036
#> 11027:                       41.343564
#> 11028:                        9.252996
#> 
#> $data_3
#>        granularity_time granularity_geo country_iso3 location_code border   age
#>     1:              day          county          nor  county_nor03   2020 total
#>     2:              day          county          nor  county_nor03   2020 total
#>     3:              day          county          nor  county_nor03   2020 total
#>     4:              day          county          nor  county_nor03   2020 total
#>     5:              day          county          nor  county_nor03   2020 total
#>    ---                                                                         
#> 11024:          isoweek          nation          nor    nation_nor   2020 total
#> 11025:          isoweek          nation          nor    nation_nor   2020 total
#> 11026:          isoweek          nation          nor    nation_nor   2020 total
#> 11027:          isoweek          nation          nor    nation_nor   2020 total
#> 11028:          isoweek          nation          nor    nation_nor   2020 total
#>          sex isoyear isoweek isoyearweek    season seasonweek calyear calmonth
#>     1: total    2020       8     2020-08 2019/2020         31    2020        2
#>     2: total    2020       8     2020-08 2019/2020         31    2020        2
#>     3: total    2020       8     2020-08 2019/2020         31    2020        2
#>     4: total    2020       9     2020-09 2019/2020         32    2020        2
#>     5: total    2020       9     2020-09 2019/2020         32    2020        2
#>    ---                                                                        
#> 11024: total    2022      14     2022-14 2021/2022         37      NA       NA
#> 11025: total    2022      15     2022-15 2021/2022         38      NA       NA
#> 11026: total    2022      16     2022-16 2021/2022         39      NA       NA
#> 11027: total    2022      17     2022-17 2021/2022         40      NA       NA
#> 11028: total    2022      18     2022-18 2021/2022         41      NA       NA
#>        calyearmonth       date covid19_cases_testdate_n
#>     1:     2020-M02 2020-02-21                        0
#>     2:     2020-M02 2020-02-22                        0
#>     3:     2020-M02 2020-02-23                        0
#>     4:     2020-M02 2020-02-24                        0
#>     5:     2020-M02 2020-02-25                        0
#>    ---                                                 
#> 11024:         <NA> 2022-04-10                     6888
#> 11025:         <NA> 2022-04-17                     3635
#> 11026:         <NA> 2022-04-24                     3764
#> 11027:         <NA> 2022-05-01                     2243
#> 11028:         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>     1:                        0.000000
#>     2:                        0.000000
#>     3:                        0.000000
#>     4:                        0.000000
#>     5:                        0.000000
#>    ---                                
#> 11024:                      126.961423
#> 11025:                       67.001274
#> 11026:                       69.379036
#> 11027:                       41.343564
#> 11028:                        9.252996
#> 
#> $hash
#> $hash$current
#> [1] "f94ed40e7cee3cdea8d42ef836fb63cd"
#> 
#> $hash$current_elements
#> $hash$current_elements$data_1
#> [1] "7f1b0a581386e75e907bffd94938a3a7"
#> 
#> $hash$current_elements$data_2
#> [1] "7f1b0a581386e75e907bffd94938a3a7"
#> 
#> $hash$current_elements$data_3
#> [1] "7f1b0a581386e75e907bffd94938a3a7"
#> 
#> 
#> 

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis var_1 var_b  var_c
#> 1:      argset_1              1     3 hello       
#> 2:      argset_2              2     8       hello2

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis var_1 var_2
#> 1:             a              1     1     i
#> 2:             b              2     2     j
#> 3:             c              3     3     k

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis var_1 var_2
#> 1:             a              1     1     i
#> 2:             b              2     2     j
#> 3:             c              3     3     k

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis
#> 1:    analysis_1              1
p$run_one("analysis_1")
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "index_analysis"
#> [1] "index_analysis"

## ------------------------------------------------
## 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$add_analysis_from_df(
  fn_name = "plnr::example_action_fn",
  df = batch_argset_df
 )
#>   name var_1 var_2                 fn_name
#> 1    a     1     i plnr::example_action_fn
#>   name var_1 var_2                 fn_name
#> 2    b     2     j plnr::example_action_fn
#>   name var_1 var_2                 fn_name
#> 3    c     3     k plnr::example_action_fn
p$get_argsets_as_dt()
#>    name_analysis index_analysis var_1 var_2
#> 1:             a              1     1     i
#> 2:             b              2     2     j
#> 3:             c              3     3     k
p$run_one(1)
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis var_1 var_2
#> 1:    analysis_1              1     1     i
#> 2:    analysis_2              2     2     j
#> 3:    analysis_3              3     3     k
p$run_one("analysis_1")
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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()
#> $covid_data
#>        granularity_time granularity_geo country_iso3 location_code border   age
#>     1:              day          county          nor  county_nor03   2020 total
#>     2:              day          county          nor  county_nor03   2020 total
#>     3:              day          county          nor  county_nor03   2020 total
#>     4:              day          county          nor  county_nor03   2020 total
#>     5:              day          county          nor  county_nor03   2020 total
#>    ---                                                                         
#> 11024:          isoweek          nation          nor    nation_nor   2020 total
#> 11025:          isoweek          nation          nor    nation_nor   2020 total
#> 11026:          isoweek          nation          nor    nation_nor   2020 total
#> 11027:          isoweek          nation          nor    nation_nor   2020 total
#> 11028:          isoweek          nation          nor    nation_nor   2020 total
#>          sex isoyear isoweek isoyearweek    season seasonweek calyear calmonth
#>     1: total    2020       8     2020-08 2019/2020         31    2020        2
#>     2: total    2020       8     2020-08 2019/2020         31    2020        2
#>     3: total    2020       8     2020-08 2019/2020         31    2020        2
#>     4: total    2020       9     2020-09 2019/2020         32    2020        2
#>     5: total    2020       9     2020-09 2019/2020         32    2020        2
#>    ---                                                                        
#> 11024: total    2022      14     2022-14 2021/2022         37      NA       NA
#> 11025: total    2022      15     2022-15 2021/2022         38      NA       NA
#> 11026: total    2022      16     2022-16 2021/2022         39      NA       NA
#> 11027: total    2022      17     2022-17 2021/2022         40      NA       NA
#> 11028: total    2022      18     2022-18 2021/2022         41      NA       NA
#>        calyearmonth       date covid19_cases_testdate_n
#>     1:     2020-M02 2020-02-21                        0
#>     2:     2020-M02 2020-02-22                        0
#>     3:     2020-M02 2020-02-23                        0
#>     4:     2020-M02 2020-02-24                        0
#>     5:     2020-M02 2020-02-25                        0
#>    ---                                                 
#> 11024:         <NA> 2022-04-10                     6888
#> 11025:         <NA> 2022-04-17                     3635
#> 11026:         <NA> 2022-04-24                     3764
#> 11027:         <NA> 2022-05-01                     2243
#> 11028:         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>     1:                        0.000000
#>     2:                        0.000000
#>     3:                        0.000000
#>     4:                        0.000000
#>     5:                        0.000000
#>    ---                                
#> 11024:                      126.961423
#> 11025:                       67.001274
#> 11026:                       69.379036
#> 11027:                       41.343564
#> 11028:                        9.252996
#> 
#> $hash
#> $hash$current
#> [1] "18b3aa368375163b3eee188988c8c15c"
#> 
#> $hash$current_elements
#> $hash$current_elements$covid_data
#> [1] "7f1b0a581386e75e907bffd94938a3a7"
#> 
#> 
#> 

## ------------------------------------------------
## 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")
#> $fn
#> NULL
#> 
#> $fn_name
#> [1] "plnr::example_action_fn"
#> 
#> $argset
#> $argset$var_1
#> [1] 1
#> 
#> $argset$var_2
#> [1] "i"
#> 
#> $argset$index_analysis
#> [1] "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")
#> $var_1
#> [1] 1
#> 
#> $var_2
#> [1] "i"
#> 

## ------------------------------------------------
## 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()
#>    name_analysis index_analysis var_1 var_2
#> 1:    analysis_1              1     1     i
#> 2:    analysis_2              2     2     j
#> 3:    analysis_3              3     3     k

## ------------------------------------------------
## 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)
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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")
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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)
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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()
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"

## ------------------------------------------------
## 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()
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"
#> [1] "Data given:"
#> [1] "covid_data" "hash"      
#> [1] "Argset given:"
#> [1] "var_1"          "var_2"          "index_analysis"

R6 Class representing a Plan

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 set_progress()

Usage

Arguments

Method set_progressor()

Usage

Arguments

Method set_verbose()

Usage

Arguments

Method set_use_foreach()

Usage

Arguments

Method get_data()

Usage

Returns

Examples

Method get_analysis()

Usage

Arguments

Returns

Examples

Method get_argset()

Usage

Arguments

Returns

Examples

Method get_argsets_as_dt()

Usage

Returns

Examples

Method run_one_with_data()

Usage

Arguments

Returns

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()`