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R6 Class for Planning and Executing Analyses

Source: R/plan.R
Plan.Rd

The Plan class provides a framework for organizing and executing multiple analyses on one or more datasets. It enforces a structured approach to analysis by:

  1. Data Management:

    • Loading data once and reusing across analyses

    • Separating data cleaning from analysis

    • Providing hash-based tracking of data changes

  2. Analysis Structure:

    • Requiring all analyses to use the same data sources

    • Standardizing analysis functions to accept only data and argset parameters

    • Organizing analyses into clear, maintainable plans

  3. Execution Control:

    • Supporting both single-function and multi-function analysis plans

    • Providing flexible execution options (sequential or parallel)

    • Including built-in debugging tools

Details

The framework uses three main concepts:

  • Argset: A named list containing a set of arguments for an analysis

  • Analysis: A combination of one argset and one action function

  • Plan: A container that holds one data pull and a list of analyses

Public fields

analyses

List of analyses, each containing an argset and action function

Methods

Public methods

Method new()

Create a new Plan instance

Usage

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

Arguments

verbose

Logical, whether to show verbose output. Defaults to TRUE in interactive mode or when config$force_verbose is TRUE

use_foreach

Logical, whether to use foreach for parallel processing. NULL = program decides, FALSE = use loop, TRUE = use foreach

Returns

A new Plan instance

Method add_data()

Add a new dataset to the plan

Usage

Plan$add_data(name, fn = NULL, fn_name = NULL, direct = NULL)

Arguments

name

Character string, name of the dataset

fn

Function that returns the dataset (optional)

fn_name

Character string, name of a function that returns the dataset (optional)

direct

Direct dataset object (optional)

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Add data using a function
data_fn <- function() { return(plnr::nor_covid19_cases_by_time_location) }
p$add_data("data_1", fn = data_fn)

# Add data using a function name
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Add data directly
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)

# View added data
p$get_data()

Method add_argset()

Add a new argset to the plan

Usage

Plan$add_argset(name = uuid::UUIDgenerate(), ...)

Arguments

name

Character string, name of the argset (defaults to a UUID)

...

Named arguments that will comprise the argset

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Add argsets with different arguments
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")

# View added argsets
p$get_argsets_as_dt()

Method add_argset_from_df()

Add multiple argsets from a data frame

Usage

Plan$add_argset_from_df(df)

Arguments

df

Data frame where each row represents a new argset

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Create data frame of argsets
batch_argset_df <- data.frame(
  name = c("a", "b", "c"),
  var_1 = c(1, 2, 3),
  var_2 = c("i", "j", "k")
)

# Add argsets from data frame
p$add_argset_from_df(batch_argset_df)

# View added argsets
p$get_argsets_as_dt()

Method add_argset_from_list()

Add multiple argsets from a list

Usage

Plan$add_argset_from_list(l)

Arguments

l

List of lists, where each inner list represents a new argset

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Create list of argsets
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")
)

# Add argsets from list
p$add_argset_from_list(batch_argset_list)

# View added argsets
p$get_argsets_as_dt()

Method add_analysis()

Add a new analysis to the plan

Usage

Plan$add_analysis(name = uuid::UUIDgenerate(), fn = NULL, fn_name = NULL, ...)

Arguments

name

Character string, name of the analysis (defaults to a UUID)

fn

Function to use for the analysis (optional)

fn_name

Character string, name of the function to use (optional)

...

Additional arguments to be added to the argset

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Add analysis
p$add_analysis(
  name = "analysis_1",
  fn_name = "plnr::example_action_fn"
)

# View argsets and run analysis
p$get_argsets_as_dt()
p$run_one("analysis_1")

Method add_analysis_from_df()

Add multiple analyses from a data frame

Usage

Plan$add_analysis_from_df(fn = NULL, fn_name = NULL, df)

Arguments

fn

Function to use for all analyses (optional)

fn_name

Character string, name of the function to use (optional)

df

Data frame where each row represents a new analysis

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Create data frame of analyses
batch_argset_df <- data.frame(
  name = c("a", "b", "c"),
  var_1 = c(1, 2, 3),
  var_2 = c("i", "j", "k")
)

# Add analyses from data frame
p$add_analysis_from_df(
  fn_name = "plnr::example_action_fn",
  df = batch_argset_df
)

# View argsets and run example
p$get_argsets_as_dt()
p$run_one(1)

Method add_analysis_from_list()

Add multiple analyses from a list

Usage

Plan$add_analysis_from_list(fn = NULL, fn_name = NULL, l)

Arguments

fn

Function to use for all analyses (optional)

fn_name

Character string, name of the function to use (optional)

l

List of lists, where each inner list represents a new analysis

Returns

NULL, modifies the plan in place

Examples

p <- plnr::Plan$new()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Create list of analyses
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")
)

# Add analyses from list
p$add_analysis_from_list(
  fn_name = "plnr::example_action_fn",
  l = batch_argset_list
)

# View argsets and run example
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()

# Add data using a function
data_fn <- function() { return(plnr::nor_covid19_cases_by_time_location) }
p$add_data("data_1", fn = data_fn)

# Add data using a function name
p$add_data("data_2", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Add data directly
p$add_data("data_3", direct = plnr::nor_covid19_cases_by_time_location)

# View added data
p$get_data()
#> $data_1
#>        granularity_time granularity_geo country_iso3 location_code border
#>                  <char>          <char>       <char>        <char>  <int>
#>     1:              day          county          nor  county_nor03   2020
#>     2:              day          county          nor  county_nor03   2020
#>     3:              day          county          nor  county_nor03   2020
#>     4:              day          county          nor  county_nor03   2020
#>     5:              day          county          nor  county_nor03   2020
#>    ---                                                                   
#> 11024:          isoweek          nation          nor    nation_nor   2020
#> 11025:          isoweek          nation          nor    nation_nor   2020
#> 11026:          isoweek          nation          nor    nation_nor   2020
#> 11027:          isoweek          nation          nor    nation_nor   2020
#> 11028:          isoweek          nation          nor    nation_nor   2020
#>           age    sex isoyear isoweek isoyearweek    season seasonweek calyear
#>        <char> <char>   <int>   <int>      <char>    <char>      <num>   <int>
#>     1:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     2:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     3:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     4:  total  total    2020       9     2020-09 2019/2020         32    2020
#>     5:  total  total    2020       9     2020-09 2019/2020         32    2020
#>    ---                                                                       
#> 11024:  total  total    2022      14     2022-14 2021/2022         37      NA
#> 11025:  total  total    2022      15     2022-15 2021/2022         38      NA
#> 11026:  total  total    2022      16     2022-16 2021/2022         39      NA
#> 11027:  total  total    2022      17     2022-17 2021/2022         40      NA
#> 11028:  total  total    2022      18     2022-18 2021/2022         41      NA
#>        calmonth calyearmonth       date covid19_cases_testdate_n
#>           <int>       <char>     <Date>                    <int>
#>     1:        2     2020-M02 2020-02-21                        0
#>     2:        2     2020-M02 2020-02-22                        0
#>     3:        2     2020-M02 2020-02-23                        0
#>     4:        2     2020-M02 2020-02-24                        0
#>     5:        2     2020-M02 2020-02-25                        0
#>    ---                                                          
#> 11024:       NA         <NA> 2022-04-10                     6888
#> 11025:       NA         <NA> 2022-04-17                     3635
#> 11026:       NA         <NA> 2022-04-24                     3764
#> 11027:       NA         <NA> 2022-05-01                     2243
#> 11028:       NA         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>                                  <num>
#>     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
#>                  <char>          <char>       <char>        <char>  <int>
#>     1:              day          county          nor  county_nor03   2020
#>     2:              day          county          nor  county_nor03   2020
#>     3:              day          county          nor  county_nor03   2020
#>     4:              day          county          nor  county_nor03   2020
#>     5:              day          county          nor  county_nor03   2020
#>    ---                                                                   
#> 11024:          isoweek          nation          nor    nation_nor   2020
#> 11025:          isoweek          nation          nor    nation_nor   2020
#> 11026:          isoweek          nation          nor    nation_nor   2020
#> 11027:          isoweek          nation          nor    nation_nor   2020
#> 11028:          isoweek          nation          nor    nation_nor   2020
#>           age    sex isoyear isoweek isoyearweek    season seasonweek calyear
#>        <char> <char>   <int>   <int>      <char>    <char>      <num>   <int>
#>     1:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     2:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     3:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     4:  total  total    2020       9     2020-09 2019/2020         32    2020
#>     5:  total  total    2020       9     2020-09 2019/2020         32    2020
#>    ---                                                                       
#> 11024:  total  total    2022      14     2022-14 2021/2022         37      NA
#> 11025:  total  total    2022      15     2022-15 2021/2022         38      NA
#> 11026:  total  total    2022      16     2022-16 2021/2022         39      NA
#> 11027:  total  total    2022      17     2022-17 2021/2022         40      NA
#> 11028:  total  total    2022      18     2022-18 2021/2022         41      NA
#>        calmonth calyearmonth       date covid19_cases_testdate_n
#>           <int>       <char>     <Date>                    <int>
#>     1:        2     2020-M02 2020-02-21                        0
#>     2:        2     2020-M02 2020-02-22                        0
#>     3:        2     2020-M02 2020-02-23                        0
#>     4:        2     2020-M02 2020-02-24                        0
#>     5:        2     2020-M02 2020-02-25                        0
#>    ---                                                          
#> 11024:       NA         <NA> 2022-04-10                     6888
#> 11025:       NA         <NA> 2022-04-17                     3635
#> 11026:       NA         <NA> 2022-04-24                     3764
#> 11027:       NA         <NA> 2022-05-01                     2243
#> 11028:       NA         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>                                  <num>
#>     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
#>                  <char>          <char>       <char>        <char>  <int>
#>     1:              day          county          nor  county_nor03   2020
#>     2:              day          county          nor  county_nor03   2020
#>     3:              day          county          nor  county_nor03   2020
#>     4:              day          county          nor  county_nor03   2020
#>     5:              day          county          nor  county_nor03   2020
#>    ---                                                                   
#> 11024:          isoweek          nation          nor    nation_nor   2020
#> 11025:          isoweek          nation          nor    nation_nor   2020
#> 11026:          isoweek          nation          nor    nation_nor   2020
#> 11027:          isoweek          nation          nor    nation_nor   2020
#> 11028:          isoweek          nation          nor    nation_nor   2020
#>           age    sex isoyear isoweek isoyearweek    season seasonweek calyear
#>        <char> <char>   <int>   <int>      <char>    <char>      <num>   <int>
#>     1:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     2:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     3:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     4:  total  total    2020       9     2020-09 2019/2020         32    2020
#>     5:  total  total    2020       9     2020-09 2019/2020         32    2020
#>    ---                                                                       
#> 11024:  total  total    2022      14     2022-14 2021/2022         37      NA
#> 11025:  total  total    2022      15     2022-15 2021/2022         38      NA
#> 11026:  total  total    2022      16     2022-16 2021/2022         39      NA
#> 11027:  total  total    2022      17     2022-17 2021/2022         40      NA
#> 11028:  total  total    2022      18     2022-18 2021/2022         41      NA
#>        calmonth calyearmonth       date covid19_cases_testdate_n
#>           <int>       <char>     <Date>                    <int>
#>     1:        2     2020-M02 2020-02-21                        0
#>     2:        2     2020-M02 2020-02-22                        0
#>     3:        2     2020-M02 2020-02-23                        0
#>     4:        2     2020-M02 2020-02-24                        0
#>     5:        2     2020-M02 2020-02-25                        0
#>    ---                                                          
#> 11024:       NA         <NA> 2022-04-10                     6888
#> 11025:       NA         <NA> 2022-04-17                     3635
#> 11026:       NA         <NA> 2022-04-24                     3764
#> 11027:       NA         <NA> 2022-05-01                     2243
#> 11028:       NA         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>                                  <num>
#>     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()

# Add argsets with different arguments
p$add_argset("argset_1", var_1 = 3, var_b = "hello")
p$add_argset("argset_2", var_1 = 8, var_c = "hello2")

# View added argsets
p$get_argsets_as_dt()
#>    name_analysis index_analysis  var_1  var_b  var_c
#>           <char>          <int> <list> <list> <list>
#> 1:      argset_1              1      3  hello [NULL]
#> 2:      argset_2              2      8 [NULL] hello2

## ------------------------------------------------
## Method `Plan$add_argset_from_df`
## ------------------------------------------------

p <- plnr::Plan$new()

# Create data frame of argsets
batch_argset_df <- data.frame(
  name = c("a", "b", "c"),
  var_1 = c(1, 2, 3),
  var_2 = c("i", "j", "k")
)

# Add argsets from data frame
p$add_argset_from_df(batch_argset_df)

# View added argsets
p$get_argsets_as_dt()
#>    name_analysis index_analysis  var_1  var_2
#>           <char>          <int> <list> <list>
#> 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()

# Create list of argsets
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")
)

# Add argsets from list
p$add_argset_from_list(batch_argset_list)

# View added argsets
p$get_argsets_as_dt()
#>    name_analysis index_analysis  var_1  var_2
#>           <char>          <int> <list> <list>
#> 1:             a              1      1      i
#> 2:             b              2      2      j
#> 3:             c              3      3      k

## ------------------------------------------------
## Method `Plan$add_analysis`
## ------------------------------------------------

p <- plnr::Plan$new()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Add analysis
p$add_analysis(
  name = "analysis_1",
  fn_name = "plnr::example_action_fn"
)

# View argsets and run analysis
p$get_argsets_as_dt()
#>    name_analysis index_analysis
#>           <char>          <int>
#> 1:    analysis_1              1
p$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()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Create data frame of analyses
batch_argset_df <- data.frame(
  name = c("a", "b", "c"),
  var_1 = c(1, 2, 3),
  var_2 = c("i", "j", "k")
)

# Add analyses from data frame
p$add_analysis_from_df(
  fn_name = "plnr::example_action_fn",
  df = batch_argset_df
)

# View argsets and run example
p$get_argsets_as_dt()
#>    name_analysis index_analysis  var_1  var_2
#>           <char>          <int> <list> <list>
#> 1:             a              1      1      i
#> 2:             b              2      2      j
#> 3:             c              3      3      k
p$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()

# Add example data
p$add_data("covid_data", fn_name = "plnr::example_data_fn_nor_covid19_cases_by_time_location")

# Create list of analyses
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")
)

# Add analyses from list
p$add_analysis_from_list(
  fn_name = "plnr::example_action_fn",
  l = batch_argset_list
)

# View argsets and run example
p$get_argsets_as_dt()
#>    name_analysis index_analysis  var_1  var_2
#>           <char>          <int> <list> <list>
#> 1:    analysis_1              1      1      i
#> 2:    analysis_2              2      2      j
#> 3:    analysis_3              3      3      k
p$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
#>                  <char>          <char>       <char>        <char>  <int>
#>     1:              day          county          nor  county_nor03   2020
#>     2:              day          county          nor  county_nor03   2020
#>     3:              day          county          nor  county_nor03   2020
#>     4:              day          county          nor  county_nor03   2020
#>     5:              day          county          nor  county_nor03   2020
#>    ---                                                                   
#> 11024:          isoweek          nation          nor    nation_nor   2020
#> 11025:          isoweek          nation          nor    nation_nor   2020
#> 11026:          isoweek          nation          nor    nation_nor   2020
#> 11027:          isoweek          nation          nor    nation_nor   2020
#> 11028:          isoweek          nation          nor    nation_nor   2020
#>           age    sex isoyear isoweek isoyearweek    season seasonweek calyear
#>        <char> <char>   <int>   <int>      <char>    <char>      <num>   <int>
#>     1:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     2:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     3:  total  total    2020       8     2020-08 2019/2020         31    2020
#>     4:  total  total    2020       9     2020-09 2019/2020         32    2020
#>     5:  total  total    2020       9     2020-09 2019/2020         32    2020
#>    ---                                                                       
#> 11024:  total  total    2022      14     2022-14 2021/2022         37      NA
#> 11025:  total  total    2022      15     2022-15 2021/2022         38      NA
#> 11026:  total  total    2022      16     2022-16 2021/2022         39      NA
#> 11027:  total  total    2022      17     2022-17 2021/2022         40      NA
#> 11028:  total  total    2022      18     2022-18 2021/2022         41      NA
#>        calmonth calyearmonth       date covid19_cases_testdate_n
#>           <int>       <char>     <Date>                    <int>
#>     1:        2     2020-M02 2020-02-21                        0
#>     2:        2     2020-M02 2020-02-22                        0
#>     3:        2     2020-M02 2020-02-23                        0
#>     4:        2     2020-M02 2020-02-24                        0
#>     5:        2     2020-M02 2020-02-25                        0
#>    ---                                                          
#> 11024:       NA         <NA> 2022-04-10                     6888
#> 11025:       NA         <NA> 2022-04-17                     3635
#> 11026:       NA         <NA> 2022-04-24                     3764
#> 11027:       NA         <NA> 2022-05-01                     2243
#> 11028:       NA         <NA> 2022-05-08                      502
#>        covid19_cases_testdate_pr100000
#>                                  <num>
#>     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
#>           <char>          <int> <list> <list>
#> 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"