Cohort {cohortBuilder} | R Documentation |
R6 class representing Cohort object.
R6 class representing Cohort object.
Cohort object is designed to make operations on source data possible.
attributes
List of Cohort attributes defined while creating a new Cohort object.
new()
Create Cohort object.
Cohort$new( source, ..., run_flow = FALSE, hook = list(pre = get_hook("pre_cohort_hook"), post = get_hook("post_cohort_hook")) )
source
Source object created with set_source.
...
Steps definition (optional). Can be also defined as a sequence of filters - the filters will be added to the first step.
run_flow
If 'TRUE', data flow is run after the operation is completed.
hook
List of hooks describing methods before/after the Cohort is created. See hooks for more details.
The object of class 'Cohort'.
add_source()
Add Source to Cohort object.
Cohort$add_source(source)
source
Source object created with set_source.
update_source()
Update Source in the Cohort object.
Cohort$update_source( source, keep_steps = !has_steps(source), run_flow = FALSE, hook = list(pre = get_hook("pre_update_source_hook"), post = get_hook("post_update_source_hook")) )
source
Source object created with set_source.
keep_steps
If 'TRUE', steps definition remains unchanged when updating source. If 'FALSE' steps configuration is deleted. If vector of type integer, specified steps will remain.
run_flow
If 'TRUE', data flow is run after the operation is completed.
hook
List of hooks describing methods before/after the Cohort is created. See hooks for more details.
get_source()
Return Source object attached to Cohort.
Cohort$get_source()
add_step()
Add filtering step definition
Cohort$add_step( step, run_flow = FALSE, hook = list(pre = get_hook("pre_add_step_hook"), post = get_hook("post_add_step_hook")) )
copy_step()
Copy selected step.
Cohort$copy_step(step_id, filters, run_flow = FALSE)
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.
remove_step()
Remove filtering step definition
Cohort$remove_step( step_id, run_flow = FALSE, hook = list(pre = get_hook("pre_rm_step_hook"), post = get_hook("post_rm_step_hook")) )
step_id
Id of the step to remove.
run_flow
If 'TRUE', data flow is run after the operation is completed.
hook
List of hooks describing methods before/after the Cohort is created. See hooks for more details.
add_filter()
Add filter definition
Cohort$add_filter(filter, step_id, run_flow = FALSE)
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.
remove_filter()
Remove filter definition
Cohort$remove_filter(step_id, filter_id, run_flow = FALSE)
step_id
Id of the step from which filter should be removed.
filter_id
Id of the filter to be removed.
run_flow
If 'TRUE', data flow is run after the operation is completed.
update_filter()
Update filter definition
Cohort$update_filter(step_id, filter_id, ..., active, run_flow = FALSE)
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.
clear_filter()
Reset filter to its default values.
Cohort$clear_filter(step_id, filter_id, run_flow = FALSE)
step_id
Id of the step where filter is defined.
filter_id
Id of the filter which should be cleared.
run_flow
If 'TRUE', data flow is run after the operation is completed.
clear_step()
Reset all filters included in selected step.
Cohort$clear_step(step_id, run_flow = FALSE)
step_id
Id of the step where filters should be cleared.
run_flow
If 'TRUE', data flow is run after the operation is completed.
sum_up_state()
Sum up Cohort configuration - Source, steps definition and evaluated data.
Cohort$sum_up_state()
get_state()
Get Cohort configuration state.
Cohort$get_state(step_id, json = FALSE, extra_fields = NULL)
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.
restore()
Cohort$restore( state, modifier = function(prev_state, state) { state }, run_flow = FALSE, hook = list(pre = get_hook("pre_restore_hook"), post = get_hook("post_restore_hook")) )
state
List or JSON string containing steps and filters configuration.
modifier
Function two parameters combining the previous and provided state. The returned state is then restored.
run_flow
If 'TRUE', data flow is run after the operation is completed.
hook
List of hooks describing methods before/after the Cohort is created. See hooks for more details.
get_data()
Get step related data
Cohort$get_data(step_id, state = "post", collect = TRUE)
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').
plot_data()
Plot filter specific data summary.
Cohort$plot_data(step_id, filter_id, ..., state = "post")
step_id
Id of the step where filter is defined.
filter_id
Id of the filter for which the plot should be returned
...
Another parameters passed to filter specific method.
state
Generate plot on data before ("pre") or after ("post") step filtering?
show_attrition()
Show attrition plot.
Cohort$show_attrition(..., percent = FALSE)
...
Source specific parameters required to generate attrition.
percent
Should attrition changes be presented with percentage values.
get_stats()
Get Cohort related statistics.
Cohort$get_stats(step_id, filter_id, ..., state = "post")
step_id
When 'filter_id' specified, 'step_id' precises from which step the filter comes from. Otherwise data from specified step is used to calculate required statistics.
filter_id
If not missing, filter related data statistics are returned.
...
Specific parameters passed to filter related method.
state
Should the stats be calculated on data before ("pre") or after ("post") filtering in specified step.
show_help()
Show source data or filter description
Cohort$show_help( field, step_id, filter_id, modifier = getOption("cb_help_modifier", default = function(x) x) )
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.).
get_code()
Return reproducible data filtering code.
Cohort$get_code( include_source = TRUE, include_methods = c(".pre_filtering", ".post_filtering", ".run_binding"), include_action = c("pre_filtering", "post_filtering", "run_binding"), modifier = .repro_code_tweak, mark_step = TRUE, ... )
include_source
If 'TRUE' source generating code will be included.
include_methods
Which methods definition should be included in the result.
include_action
Which action should be returned in the result. 'pre_filtering'/'.post_filtering' - to include data transformation before/after filtering. s'run_binding' - data binding transformation.
modifier
A function taking data frame (storing reproducible code metadata) as an argument, and returning data frame with 'expr' column which is then combined into a single expression (final result of 'get_code'). See .repro_code_tweak.
mark_step
Include information which filtering step is performed.
...
Other parameters passed to tidy_source.
run_flow()
Trigger data calculations sequentially.
Cohort$run_flow( min_step, hook = list(pre = get_hook("pre_run_flow_hook"), post = get_hook("post_run_flow_hook")) )
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.
run_step()
Trigger data calculations for selected step.
Cohort$run_step( step_id, hook = list(pre = get_hook("pre_run_step_hook"), post = get_hook("post_run_step_hook")) )
step_id
Id of the step for which to run data calculation.
hook
List of hooks describing methods before/after the Cohort is created. See hooks for more details.
bind_data()
Run data binding for selected step. See more at binding-keys.
Cohort$bind_data(step_id)
step_id
Id of the step for which to bind the data.
describe_state()
Print defined steps configuration.
Cohort$describe_state()
get_step()
Get selected step configuration.
Cohort$get_step(step_id)
step_id
Id of the step to be returned.
get_filter()
Get selected filter configuration.
Cohort$get_filter(step_id, filter_id, method = function(x) x)
step_id
Id of the step where filter is defined.
filter_id
If of the filter to be returned.
method
Custom function taking filters list as argument.
update_cache()
Update filter or step cache. Caching is saving step and filter attached data statistics such as number of data rows, filter choices or frequencies.
Cohort$update_cache(step_id, filter_id, state = "post")
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.
get_cache()
Return step of filter specific cache.
Cohort$get_cache(step_id, filter_id, state = "post")
step_id
Id of the step for which cached data should be returned If 'filter_id' is not missing, the parameter describes id of the step where filter should be found.
filter_id
Id of the filter for which cache data should be returned.
state
Should cache be returned on data before ("pre") or after ("post") filtering in specified step.
list_active_filters()
List active filters included in selected step.
Cohort$list_active_filters(step_id)
step_id
Id of the step where filters should be found.
last_step_id()
Return id of the last existing step in Cohort.
Cohort$last_step_id()
modify()
Helper method enabling to run non-standard operation on Cohort object.
Cohort$modify(modifier)
modifier
Function of two arguments 'self' and 'private'.
clone()
The objects of this class are cloneable with this method.
Cohort$clone(deep = FALSE)
deep
Whether to make a deep clone.