Cohort {cohortBuilder}

R6 class representing Cohort object.

Description

R6 class representing Cohort object.

R6 class representing Cohort object.

Details

Cohort object is designed to make operations on source data possible.

Public fields

attributes

List of Cohort attributes defined while creating a new Cohort object.

Methods

Public methods

• Cohort$new()

• Cohort$add_source()

• Cohort$update_source()

• Cohort$get_source()

• Cohort$add_step()

• Cohort$copy_step()

• Cohort$remove_step()

• Cohort$add_filter()

• Cohort$remove_filter()

• Cohort$update_filter()

• Cohort$clear_filter()

• Cohort$clear_step()

• Cohort$sum_up_state()

• Cohort$get_state()

• Cohort$restore()

• Cohort$get_data()

• Cohort$plot_data()

• Cohort$show_attrition()

• Cohort$get_stats()

• Cohort$show_help()

• Cohort$get_code()

• Cohort$run_flow()

• Cohort$run_step()

• Cohort$bind_data()

• Cohort$describe_state()

• Cohort$get_step()

• Cohort$get_filter()

• Cohort$update_cache()

• Cohort$get_cache()

• Cohort$list_active_filters()

• Cohort$last_step_id()

• Cohort$modify()

• Cohort$clone()

Method new()

Create Cohort object.

Usage

Cohort$new(
  source,
  ...,
  run_flow = FALSE,
  hook = list(pre = get_hook("pre_cohort_hook"), post = get_hook("post_cohort_hook"))
)

Arguments

source

Source object created with set_source.

...

Steps definition (optional). Can be also defined as a sequence of filters - the filters will be added to the first step.

run_flow

If 'TRUE', data flow is run after the operation is completed.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Returns

The object of class 'Cohort'.

Method add_source()

Add Source to Cohort object.

Usage

Cohort$add_source(source)

Arguments

source

Source object created with set_source.

Method update_source()

Update Source in the Cohort object.

Usage

Cohort$update_source(
  source,
  keep_steps = !has_steps(source),
  run_flow = FALSE,
  hook = list(pre = get_hook("pre_update_source_hook"), post =
    get_hook("post_update_source_hook"))
)

Arguments

source

Source object created with set_source.

keep_steps

If 'TRUE', steps definition remains unchanged when updating source. If 'FALSE' steps configuration is deleted. If vector of type integer, specified steps will remain.

run_flow

If 'TRUE', data flow is run after the operation is completed.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method get_source()

Return Source object attached to Cohort.

Usage

Cohort$get_source()

Method add_step()

Add filtering step definition

Usage

Cohort$add_step(
  step,
  run_flow = FALSE,
  hook = list(pre = get_hook("pre_add_step_hook"), post = get_hook("post_add_step_hook"))
)

Arguments

step

Step definition created with step.

run_flow

If 'TRUE', data flow is run after the operation is completed.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method copy_step()

Copy selected step.

Usage

Cohort$copy_step(step_id, filters, run_flow = FALSE)

Arguments

step_id

Id of the step to be copied. If missing the last step is taken. The copied step is added as the last one in the Cohort.

filters

List of Source-evaluated filters to copy to new step.

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method remove_step()

Remove filtering step definition

Usage

Cohort$remove_step(
  step_id,
  run_flow = FALSE,
  hook = list(pre = get_hook("pre_rm_step_hook"), post = get_hook("post_rm_step_hook"))
)

Arguments

step_id

Id of the step to remove.

run_flow

If 'TRUE', data flow is run after the operation is completed.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method add_filter()

Add filter definition

Usage

Cohort$add_filter(filter, step_id, run_flow = FALSE)

Arguments

filter

Filter definition created with filter.

step_id

Id of the step to add the filter to. If missing, filter is added to the last step.

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method remove_filter()

Remove filter definition

Usage

Cohort$remove_filter(step_id, filter_id, run_flow = FALSE)

Arguments

step_id

Id of the step from which filter should be removed.

filter_id

Id of the filter to be removed.

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method update_filter()

Update filter definition

Usage

Cohort$update_filter(step_id, filter_id, ..., active, run_flow = FALSE)

Arguments

step_id

Id of the step where filter is defined.

filter_id

Id of the filter to be updated.

...

Filter parameters that should be updated.

active

Mark filter as active ('TRUE') or inactive ('FALSE').

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method clear_filter()

Reset filter to its default values.

Usage

Cohort$clear_filter(step_id, filter_id, run_flow = FALSE)

Arguments

step_id

Id of the step where filter is defined.

filter_id

Id of the filter which should be cleared.

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method clear_step()

Reset all filters included in selected step.

Usage

Cohort$clear_step(step_id, run_flow = FALSE)

Arguments

step_id

Id of the step where filters should be cleared.

run_flow

If 'TRUE', data flow is run after the operation is completed.

Method sum_up_state()

Sum up Cohort configuration - Source, steps definition and evaluated data.

Usage

Cohort$sum_up_state()

Method get_state()

Get Cohort configuration state.

Usage

Cohort$get_state(step_id, json = FALSE, extra_fields = NULL)

Arguments

step_id

If provided, the selected step state is returned.

json

If TRUE, return state in JSON format.

extra_fields

Names of extra fields included in filter to be added to state. Restore Cohort configuration.

Method restore()

Usage

Cohort$restore(
  state,
  modifier = function(prev_state, state) {
     state
 },
  run_flow = FALSE,
  hook = list(pre = get_hook("pre_restore_hook"), post = get_hook("post_restore_hook"))
)

Arguments

state

List or JSON string containing steps and filters configuration.

modifier

Function two parameters combining the previous and provided state. The returned state is then restored.

run_flow

If 'TRUE', data flow is run after the operation is completed.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method get_data()

Get step related data

Usage

Cohort$get_data(step_id, state = "post", collect = TRUE)

Arguments

step_id

Id of the step from which to source data.

state

Return data before ("pre") or after ("post") step filtering?

collect

Return raw data source ('FALSE') object or collected (to R memory) data ('TRUE').

Method plot_data()

Plot filter specific data summary.

Usage

Cohort$plot_data(step_id, filter_id, ..., state = "post")

Arguments

step_id

Id of the step where filter is defined.

filter_id

Id of the filter for which the plot should be returned

...

Another parameters passed to filter specific method.

state

Generate plot on data before ("pre") or after ("post") step filtering?

Method show_attrition()

Show attrition plot.

Usage

Cohort$show_attrition(..., percent = FALSE)

Arguments

...

Source specific parameters required to generate attrition.

percent

Should attrition changes be presented with percentage values.

Method get_stats()

Get Cohort related statistics.

Usage

Cohort$get_stats(step_id, filter_id, ..., state = "post")

Arguments

step_id

When 'filter_id' specified, 'step_id' precises from which step the filter comes from. Otherwise data from specified step is used to calculate required statistics.

filter_id

If not missing, filter related data statistics are returned.

...

Specific parameters passed to filter related method.

state

Should the stats be calculated on data before ("pre") or after ("post") filtering in specified step.

Method show_help()

Show source data or filter description

Usage

Cohort$show_help(
  field,
  step_id,
  filter_id,
  modifier = getOption("cb_help_modifier", default = function(x) x)
)

Arguments

field

Name of the source description field provided as 'description' argument to set_source. If missing, 'step_id' and 'filter_id' are used to return filter description.

step_id

Id of the filter step to return description of.

filter_id

Id of the filter to return description of.

modifier

A function taking the description as argument. The function can be used to modify its argument (convert to html, display in browser etc.).

Method get_code()

Return reproducible data filtering code.

Usage

Cohort$get_code(
  include_source = TRUE,
  include_methods = c(".pre_filtering", ".post_filtering", ".run_binding"),
  include_action = c("pre_filtering", "post_filtering", "run_binding"),
  modifier = .repro_code_tweak,
  mark_step = TRUE,
  ...
)

Arguments

include_source

If 'TRUE' source generating code will be included.

include_methods

Which methods definition should be included in the result.

include_action

Which action should be returned in the result. 'pre_filtering'/'.post_filtering' - to include data transformation before/after filtering. s'run_binding' - data binding transformation.

modifier

A function taking data frame (storing reproducible code metadata) as an argument, and returning data frame with 'expr' column which is then combined into a single expression (final result of 'get_code'). See .repro_code_tweak.

mark_step

Include information which filtering step is performed.

...

Other parameters passed to tidy_source.

Method run_flow()

Trigger data calculations sequentially.

Usage

Cohort$run_flow(
  min_step,
  hook = list(pre = get_hook("pre_run_flow_hook"), post = get_hook("post_run_flow_hook"))
)

Arguments

min_step

Step id starting from the calculation will be started.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method run_step()

Trigger data calculations for selected step.

Usage

Cohort$run_step(
  step_id,
  hook = list(pre = get_hook("pre_run_step_hook"), post = get_hook("post_run_step_hook"))
)

Arguments

step_id

Id of the step for which to run data calculation.

hook

List of hooks describing methods before/after the Cohort is created. See hooks for more details.

Method bind_data()

Run data binding for selected step. See more at binding-keys.

Usage

Cohort$bind_data(step_id)

Arguments

step_id

Id of the step for which to bind the data.

Method describe_state()

Print defined steps configuration.

Usage

Cohort$describe_state()

Method get_step()

Get selected step configuration.

Usage

Cohort$get_step(step_id)

Arguments

step_id

Id of the step to be returned.

Method get_filter()

Get selected filter configuration.

Usage

Cohort$get_filter(step_id, filter_id, method = function(x) x)

Arguments

step_id

Id of the step where filter is defined.

filter_id

If of the filter to be returned.

method

Custom function taking filters list as argument.

Method update_cache()

Update filter or step cache. Caching is saving step and filter attached data statistics such as number of data rows, filter choices or frequencies.

Usage

Cohort$update_cache(step_id, filter_id, state = "post")

Arguments

step_id

Id of the step for which caching should be applied. If 'filter_id' is not missing, the parameter describes id of the step where filter should be found.

filter_id

Id of the filter for which caching should be applied.

state

Should caching be done on data before ("pre") or after ("post") filtering in specified step.

Method get_cache()

Return step of filter specific cache.

Usage

Cohort$get_cache(step_id, filter_id, state = "post")

Arguments

step_id

Id of the step for which cached data should be returned If 'filter_id' is not missing, the parameter describes id of the step where filter should be found.

filter_id

Id of the filter for which cache data should be returned.

state

Should cache be returned on data before ("pre") or after ("post") filtering in specified step.

Method list_active_filters()

List active filters included in selected step.

Usage

Cohort$list_active_filters(step_id)

Arguments

step_id

Id of the step where filters should be found.

Method last_step_id()

Return id of the last existing step in Cohort.

Usage

Cohort$last_step_id()

Method modify()

Helper method enabling to run non-standard operation on Cohort object.

Usage

Cohort$modify(modifier)

Arguments

modifier

Function of two arguments 'self' and 'private'.

Method clone()

The objects of this class are cloneable with this method.

Usage

Cohort$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.