R6 Class for Planning and Executing Analyses

The Plan class organizes and runs multiple analyses on one or more datasets. It enforces a structured approach to analysis in three ways.

Data Management:
- Load data once and reuse it across analyses
- Keep data cleaning separate from analysis
- Track data changes with a hash
Analysis Structure:
- Require all analyses to use the same data sources
- Standardize analysis functions to accept only data and argset parameters
- Organize analyses into clear, maintainable plans
Execution Control:
- Support both single-function and multi-function analysis plans
- Run analyses either in sequence or in parallel
- Supply built-in debugging tools

Details

The framework uses three main concepts:

Argset: A named list that holds 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 analysis holds one argset and one action function.

Methods

`Plan$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. The default is TRUE in interactive mode, or when config$force_verbose is TRUE.
use_foreach: Logical. Whether to use foreach for parallel processing. NULL lets the program decide. FALSE uses a loop. TRUE uses foreach.

Returns

A new Plan instance.

`Plan$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. The name of the dataset.
fn: Optional. A function that returns the dataset.
fn_name: Optional. A character string that names a function that returns the dataset.
direct: Optional. The dataset object itself.

Returns

NULL. The method changes 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()

`Plan$add_argset()`

Add a new argset to the plan.

Usage

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

Arguments

name: Character string. The name of the argset. The default is a UUID.
...: Named arguments that make up the argset.

Returns

NULL. The method changes 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()

`Plan$add_argset_from_df()`

Add multiple argsets from a data frame.

Usage

Plan$add_argset_from_df(df)

Arguments

df: A data frame. Each row is one new argset.

Returns

NULL. The method changes 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()

`Plan$add_argset_from_list()`

Add multiple argsets from a list.

Usage

Plan$add_argset_from_list(l)

Arguments

l: A list of lists. Each inner list is one new argset.

Returns

NULL. The method changes 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()

`Plan$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. The name of the analysis. The default is a UUID.
fn: Optional. The function to use for the analysis.
fn_name: Optional. A character string that names the function to use.
...: Further arguments to add to the argset.

Returns

NULL. The method changes 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")

`Plan$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: Optional. The function to use for all analyses.
fn_name: Optional. A character string that names the function to use.
df: A data frame. Each row is one new analysis.

Returns

NULL. The method changes 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)

`Plan$add_analysis_from_list()`

Add multiple analyses from a list.

Usage

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

Arguments

fn: Optional. The function to use for all analyses.
fn_name: Optional. A character string that names the function to use.
l: A list of lists. Each inner list is one new analysis.

Returns

NULL. The method changes 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")

`Plan$apply_action_fn_to_all_argsets()`

Apply one 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")

`Plan$apply_analysis_fn_to_all()`

Deprecated. Use apply_action_fn_to_all_argsets() instead.

Usage

Plan$apply_analysis_fn_to_all(fn = NULL, fn_name = NULL)

Arguments

fn: Action function.
fn_name: Action function name.

`Plan$x_length()`

Number of analyses in the plan.

Usage

Plan$x_length()

`Plan$x_seq_along()`

Generate a regular sequence from 1 to the number of analyses in the plan.

Usage

Plan$x_seq_along()

`Plan$set_progress()`

Set an internal progress bar.

Usage

Plan$set_progress(pb)

Arguments

pb: Progress bar.

`Plan$set_progressor()`

Set an internal progressor progress bar.

Usage

Plan$set_progressor(pb)

Arguments

pb: progressor progress bar.

`Plan$set_verbose()`

Set the verbose flag.

Usage

Plan$set_verbose(x)

Arguments

x: Boolean.

`Plan$set_use_foreach()`

Set the use_foreach flag.

Usage

Plan$set_use_foreach(x)

Arguments

x: Boolean.

`Plan$get_data()`

Extract the data added with add_data() and return it as a named list.

Usage

Plan$get_data()

Returns

A named list. Most elements come from add_data().

One extra named element is called 'hash'. 'hash' holds the data hashes of particular datasets and variables. digest::digest() calculates them with the 'spookyhash' algorithm.

'hash' holds 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()

`Plan$get_analysis()`

Extract one analysis from the plan.

Usage

Plan$get_analysis(index_analysis)

Arguments

index_analysis: Either an integer in 1:length(analyses), or a character string with 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")

`Plan$get_argset()`

Extract one argset from the plan.

Usage

Plan$get_argset(index_analysis)

Arguments

index_analysis: Either an integer in 1:length(analyses), or a character string with 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")

`Plan$get_argsets_as_dt()`

Get all argsets and return them as a data.table.

Usage

Plan$get_argsets_as_dt()

Returns

A data.table that holds 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()

`Plan$run_one_with_data()`

Run one analysis. You supply the data.

Usage

Plan$run_one_with_data(index_analysis, data, ...)

Arguments

index_analysis: Either an integer in 1:length(analyses), or a character string with the name of the analysis.
data: A named list. You normally get it from p$get_data().
...: Not used.

Returns

The value that the action function returns.

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)

`Plan$run_one()`

Run one analysis. The method gets the data from self$get_data().

Usage

Plan$run_one(index_analysis, ...)

Arguments

index_analysis: Either an integer in 1:length(analyses), or a character string with the name of the analysis.
...: Not used.

Returns

The value that the action function returns.

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")

`Plan$run_all_with_data()`

Run all analyses. You supply the data.

Usage

Plan$run_all_with_data(data, ...)

Arguments

data: A named list. You normally get it from p$get_data().
...: Not used.

Returns

A list. Each element is the value that the action function returns.

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)

`Plan$run_all()`

Run all analyses. The method gets the data from self$get_data().

Usage

Plan$run_all(...)

Arguments

...: Not used.

Returns

A list. Each element is the value that the action function returns.

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()

`Plan$run_all_progress()`

Run all analyses and show a progress bar. The method gets the data from self$get_data().

Usage

Plan$run_all_progress(...)

Arguments

...: Not used.

Returns

A list. Each element is the value that the action function returns.

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()

`Plan$run_all_parallel()`

Run all analyses in parallel. The method gets the data from self$get_data().

This method works only on linux computers. It uses pbmcapply as the parallel backend.

Usage

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

Arguments

mc.cores: The number of cores to use.
...: Not used.

Returns

A list. Each element is the value that the action function returns.

`Plan$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"

R6 Class for Planning and Executing Analyses

Details

See also

Public fields

Methods

Public methods

Plan$new()

Usage

Arguments

Returns

Plan$add_data()

Usage

Arguments

Returns

Examples

Plan$add_argset()

Usage

Arguments

Returns

Examples

Plan$add_argset_from_df()

Usage

Arguments

Returns

Examples

Plan$add_argset_from_list()

Usage

Arguments

Returns

Examples

Plan$add_analysis()

Usage

Arguments

Returns

Examples

Plan$add_analysis_from_df()

Usage

Arguments

Returns

Examples

Plan$add_analysis_from_list()

Usage

Arguments

Returns

Examples

Plan$apply_action_fn_to_all_argsets()

Usage

Arguments

Plan$apply_analysis_fn_to_all()

Usage

Arguments

Plan$x_length()

Usage

Plan$x_seq_along()

Usage

Plan$set_progress()

Usage

Arguments

Plan$set_progressor()

Usage

Arguments

Plan$set_verbose()

Usage

Arguments

Plan$set_use_foreach()

Usage

Arguments

Plan$get_data()

Usage

Returns

Examples

Plan$get_analysis()

Usage

Arguments

Returns

Examples

Plan$get_argset()

Usage

Arguments

Returns

`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()`