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

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.

R6 class representing Cohort object.

Details

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method add_source()

Usage

Arguments

Method update_source()

Usage

Arguments

Method get_source()

Usage

Method add_step()

Usage

Arguments

Method copy_step()

Usage

Arguments

Method remove_step()

Usage

Arguments

Method add_filter()

Usage

Arguments

Method remove_filter()

Usage

Arguments

Method update_filter()

Usage

Arguments

Method clear_filter()

Usage

Arguments

Method clear_step()

Usage

Arguments

Method sum_up_state()

Usage

Method get_state()

Usage

Arguments

Method restore()

Usage

Arguments

Method get_data()

Usage

Arguments

Method plot_data()

Usage

Arguments

Method show_attrition()

Usage

Arguments

Method get_stats()

Usage

Arguments

Method show_help()

Usage

Arguments

Method get_code()

Usage

Arguments

Method run_flow()

Usage

Arguments

Method run_step()

Usage

Arguments

Method bind_data()

Usage

Arguments

Method describe_state()

Usage

Method get_step()

Usage

Method `new()`

Method `add_source()`

Method `update_source()`

Method `get_source()`

Method `add_step()`

Method `copy_step()`

Method `remove_step()`

Method `add_filter()`

Method `remove_filter()`

Method `update_filter()`

Method `clear_filter()`

Method `clear_step()`

Method `sum_up_state()`

Method `get_state()`

Method `restore()`

Method `get_data()`

Method `plot_data()`

Method `show_attrition()`

Method `get_stats()`

Method `show_help()`

Method `get_code()`

Method `run_flow()`

Method `run_step()`

Method `bind_data()`

Method `describe_state()`

Method `get_step()`

Method `get_filter()`

Method `update_cache()`

Method `get_cache()`

Method `list_active_filters()`

Method `last_step_id()`

Method `modify()`

Method `clone()`