Cohort: R6 class representing Cohort object.
In cohortBuilder: Data Source Agnostic Filtering Tools
Cohort R Documentation
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
attributesList of Cohort attributes defined while creating a new Cohort object.
Methods
Public methods
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Method new()
Create Cohort object.
Usage
Cohort$new(
source,
...,
run_flow = FALSE,
hook = list(pre = get_hook("pre_cohort_hook"), post = get_hook("post_cohort_hook"))
)
Arguments
sourceSource object created with set_source.
...Steps definition (optional). Can be also defined as a sequence of
filters - the filters will be added to the first step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Returns
The object of class 'Cohort'.
Method add_source()
Add Source to Cohort object.
Usage
Cohort$add_source(source)
Arguments
sourceSource object created with set_source.
Method update_source()
Update Source in the Cohort object.
Usage
Cohort$update_source(
source,
keep_steps = !has_steps(source),
run_flow = FALSE,
hook = list(pre = get_hook("pre_update_source_hook"), post =
get_hook("post_update_source_hook"))
)
Arguments
sourceSource object created with set_source.
keep_stepsIf 'TRUE', steps definition remains unchanged when updating source.
If 'FALSE' steps configuration is deleted.
If vector of type integer, specified steps will remain.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Method get_source()
Return Source object attached to Cohort.
Usage
Cohort$get_source()
Method add_step()
Add filtering step definition
Usage
Cohort$add_step(
step,
run_flow = FALSE,
hook = list(pre = get_hook("pre_add_step_hook"), post = get_hook("post_add_step_hook"))
)
Arguments
stepStep definition created with step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Method copy_step()
Copy selected step.
Usage
Cohort$copy_step(step_id, filters, run_flow = FALSE)
Arguments
step_idId 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.
filtersList of Source-evaluated filters to copy to new step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method remove_step()
Remove filtering step definition
Usage
Cohort$remove_step(
step_id,
run_flow = FALSE,
hook = list(pre = get_hook("pre_rm_step_hook"), post = get_hook("post_rm_step_hook"))
)
Arguments
step_idId of the step to remove.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Method add_filter()
Add filter definition
Usage
Cohort$add_filter(filter, step_id, run_flow = FALSE)
Arguments
filterFilter definition created with filter.
step_idId of the step to add the filter to.
If missing, filter is added to the last step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method remove_filter()
Remove filter definition
Usage
Cohort$remove_filter(step_id, filter_id, run_flow = FALSE)
Arguments
step_idId of the step from which filter should be removed.
filter_idId of the filter to be removed.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method update_filter()
Update filter definition
Usage
Cohort$update_filter(step_id, filter_id, ..., active, run_flow = FALSE)
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter to be updated.
...Filter parameters that should be updated.
activeMark filter as active ('TRUE') or inactive ('FALSE').
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method clear_filter()
Reset filter to its default values.
Usage
Cohort$clear_filter(step_id, filter_id, run_flow = FALSE)
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter which should be cleared.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method clear_step()
Reset all filters included in selected step.
Usage
Cohort$clear_step(step_id, run_flow = FALSE)
Arguments
step_idId of the step where filters should be cleared.
run_flowIf '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_idIf provided, the selected step state is returned.
jsonIf TRUE, return state in JSON format.
extra_fieldsNames of extra fields included in filter to be added to state.
Restore Cohort configuration.
Method restore()
Usage
Cohort$restore(
state,
modifier = function(prev_state, state) {
state
},
run_flow = FALSE,
hook = list(pre = get_hook("pre_restore_hook"), post = get_hook("post_restore_hook"))
)
Arguments
stateList or JSON string containing steps and filters configuration.
modifierFunction two parameters combining the previous and provided state.
The returned state is then restored.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Method get_data()
Get step related data
Usage
Cohort$get_data(step_id, state = "post", collect = TRUE)
Arguments
step_idId of the step from which to source data.
stateReturn data before ("pre") or after ("post") step filtering?
collectReturn raw data source ('FALSE') object or collected (to R memory) data ('TRUE').
Method plot_data()
Plot filter specific data summary.
Usage
Cohort$plot_data(step_id, filter_id, ..., state = "post")
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter for which the plot should be returned
...Another parameters passed to filter specific method.
stateGenerate plot on data before ("pre") or after ("post") step filtering?
Method show_attrition()
Show attrition plot.
Usage
Cohort$show_attrition(..., percent = FALSE)
Arguments
...Source specific parameters required to generate attrition.
percentShould attrition changes be presented with percentage values.
Method get_stats()
Get Cohort related statistics.
Usage
Cohort$get_stats(step_id, filter_id, ..., state = "post")
Arguments
step_idWhen 'filter_id' specified, 'step_id' precises from which step the filter comes from.
Otherwise data from specified step is used to calculate required statistics.
filter_idIf not missing, filter related data statistics are returned.
...Specific parameters passed to filter related method.
stateShould the stats be calculated on data before ("pre") or after ("post")
filtering in specified step.
Method show_help()
Show source data or filter description
Usage
Cohort$show_help(
field,
step_id,
filter_id,
modifier = getOption("cb_help_modifier", default = function(x) x)
)
Arguments
fieldName 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_idId of the filter step to return description of.
filter_idId of the filter to return description of.
modifierA 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$get_code(
include_source = TRUE,
include_methods = c(".pre_filtering", ".post_filtering", ".run_binding"),
include_action = c("pre_filtering", "post_filtering", "run_binding"),
modifier = .repro_code_tweak,
mark_step = TRUE,
...
)
Arguments
include_sourceIf 'TRUE' source generating code will be included.
include_methodsWhich methods definition should be included in the result.
include_actionWhich action should be returned in the result.
'pre_filtering'/'.post_filtering' - to include data transformation before/after filtering.
s'run_binding' - data binding transformation.
modifierA function taking data frame (storing reproducible code metadata) as
an argument, and returning data frame with 'expr' column which is then
combined into a single expression (final result of 'get_code').
See .repro_code_tweak.
mark_stepInclude information which filtering step is performed.
...Other parameters passed to tidy_source.
Method run_flow()
Trigger data calculations sequentially.
Usage
Cohort$run_flow(
min_step,
hook = list(pre = get_hook("pre_run_flow_hook"), post = get_hook("post_run_flow_hook"))
)
Arguments
min_stepStep id starting from the calculation will be started.
hookList 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$run_step(
step_id,
hook = list(pre = get_hook("pre_run_step_hook"), post = get_hook("post_run_step_hook"))
)
Arguments
step_idId of the step for which to run data calculation.
hookList of hooks describing methods before/after the Cohort is created.
See hooks for more details.
Method bind_data()
Run data binding for selected step.
See more at binding-keys.
Usage
Cohort$bind_data(step_id)
Arguments
step_idId 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_idId of the step to be returned.
Method get_filter()
Get selected filter configuration.
Usage
Cohort$get_filter(step_id, filter_id, method = function(x) x)
Arguments
step_idId of the step where filter is defined.
filter_idIf of the filter to be returned.
methodCustom function taking filters list as argument.
Method update_cache()
Update filter or step cache.
Caching is saving step and filter attached data statistics such as number of
data rows, filter choices or frequencies.
Usage
Cohort$update_cache(step_id, filter_id, state = "post")
Arguments
step_idId 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_idId of the filter for which caching should be applied.
stateShould 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$get_cache(step_id, filter_id, state = "post")
Arguments
step_idId of the step for which cached data should be returned
If 'filter_id' is not missing, the parameter describes id of the step where filter should be found.
filter_idId of the filter for which cache data should be returned.
stateShould cache be returned on data before ("pre") or after ("post")
filtering in specified step.
Method list_active_filters()
List active filters included in selected step.
Usage
Cohort$list_active_filters(step_id)
Arguments
step_idId 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
modifierFunction of two arguments 'self' and 'private'.
Method clone()
The objects of this class are cloneable with this method.
Usage
Cohort$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
cohortBuilder documentation built on Sept. 25, 2024, 5:06 p.m.
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| Cohort | R Documentation |
R6 class representing Cohort object.
Description
R6 class representing Cohort object.
R6 class representing Cohort object.
Details
Cohort object is designed to make operations on source data possible.
Public fields
attributesList of Cohort attributes defined while creating a new Cohort object.
Methods
Public methods
Method new()
Create Cohort object.
Usage
Cohort$new(
source,
...,
run_flow = FALSE,
hook = list(pre = get_hook("pre_cohort_hook"), post = get_hook("post_cohort_hook"))
)Arguments
sourceSource 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_flowIf 'TRUE', data flow is run after the operation is completed.
hookList 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$add_source(source)
Arguments
sourceSource object created with set_source.
Method update_source()
Update Source in the Cohort object.
Usage
Cohort$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
sourceSource object created with set_source.
keep_stepsIf 'TRUE', steps definition remains unchanged when updating source. If 'FALSE' steps configuration is deleted. If vector of type integer, specified steps will remain.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList 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
stepStep definition created with step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created. See hooks for more details.
Method copy_step()
Copy selected step.
Usage
Cohort$copy_step(step_id, filters, run_flow = FALSE)
Arguments
step_idId of the step to be copied. If missing the last step is taken. The copied step is added as the last one in the Cohort.
filtersList of Source-evaluated filters to copy to new step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method remove_step()
Remove filtering step definition
Usage
Cohort$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_idId of the step to remove.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created. See hooks for more details.
Method add_filter()
Add filter definition
Usage
Cohort$add_filter(filter, step_id, run_flow = FALSE)
Arguments
filterFilter definition created with filter.
step_idId of the step to add the filter to. If missing, filter is added to the last step.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method remove_filter()
Remove filter definition
Usage
Cohort$remove_filter(step_id, filter_id, run_flow = FALSE)
Arguments
step_idId of the step from which filter should be removed.
filter_idId of the filter to be removed.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method update_filter()
Update filter definition
Usage
Cohort$update_filter(step_id, filter_id, ..., active, run_flow = FALSE)
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter to be updated.
...Filter parameters that should be updated.
activeMark filter as active ('TRUE') or inactive ('FALSE').
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method clear_filter()
Reset filter to its default values.
Usage
Cohort$clear_filter(step_id, filter_id, run_flow = FALSE)
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter which should be cleared.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method clear_step()
Reset all filters included in selected step.
Usage
Cohort$clear_step(step_id, run_flow = FALSE)
Arguments
step_idId of the step where filters should be cleared.
run_flowIf 'TRUE', data flow is run after the operation is completed.
Method sum_up_state()
Sum up Cohort configuration - Source, steps definition and evaluated data.
Usage
Cohort$sum_up_state()
Method get_state()
Get Cohort configuration state.
Usage
Cohort$get_state(step_id, json = FALSE, extra_fields = NULL)
Arguments
step_idIf provided, the selected step state is returned.
jsonIf TRUE, return state in JSON format.
extra_fieldsNames of extra fields included in filter to be added to state. Restore Cohort configuration.
Method restore()
Usage
Cohort$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
stateList or JSON string containing steps and filters configuration.
modifierFunction two parameters combining the previous and provided state. The returned state is then restored.
run_flowIf 'TRUE', data flow is run after the operation is completed.
hookList of hooks describing methods before/after the Cohort is created. See hooks for more details.
Method get_data()
Get step related data
Usage
Cohort$get_data(step_id, state = "post", collect = TRUE)
Arguments
step_idId of the step from which to source data.
stateReturn data before ("pre") or after ("post") step filtering?
collectReturn raw data source ('FALSE') object or collected (to R memory) data ('TRUE').
Method plot_data()
Plot filter specific data summary.
Usage
Cohort$plot_data(step_id, filter_id, ..., state = "post")
Arguments
step_idId of the step where filter is defined.
filter_idId of the filter for which the plot should be returned
...Another parameters passed to filter specific method.
stateGenerate plot on data before ("pre") or after ("post") step filtering?
Method show_attrition()
Show attrition plot.
Usage
Cohort$show_attrition(..., percent = FALSE)
Arguments
...Source specific parameters required to generate attrition.
percentShould attrition changes be presented with percentage values.
Method get_stats()
Get Cohort related statistics.
Usage
Cohort$get_stats(step_id, filter_id, ..., state = "post")
Arguments
step_idWhen '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_idIf not missing, filter related data statistics are returned.
...Specific parameters passed to filter related method.
stateShould 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$show_help(
field,
step_id,
filter_id,
modifier = getOption("cb_help_modifier", default = function(x) x)
)Arguments
fieldName of the source description field provided as 'description' argument to set_source. If missing, 'step_id' and 'filter_id' are used to return filter description.
step_idId of the filter step to return description of.
filter_idId of the filter to return description of.
modifierA function taking the description as argument. The function can be used to modify its argument (convert to html, display in browser etc.).
Method get_code()
Return reproducible data filtering code.
Usage
Cohort$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_sourceIf 'TRUE' source generating code will be included.
include_methodsWhich methods definition should be included in the result.
include_actionWhich action should be returned in the result. 'pre_filtering'/'.post_filtering' - to include data transformation before/after filtering. s'run_binding' - data binding transformation.
modifierA 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_stepInclude information which filtering step is performed.
...Other parameters passed to tidy_source.
Method run_flow()
Trigger data calculations sequentially.
Usage
Cohort$run_flow(
min_step,
hook = list(pre = get_hook("pre_run_flow_hook"), post = get_hook("post_run_flow_hook"))
)Arguments
min_stepStep id starting from the calculation will be started.
hookList of hooks describing methods before/after the Cohort is created. See hooks for more details.
Method run_step()
Trigger data calculations for selected step.
Usage
Cohort$run_step(
step_id,
hook = list(pre = get_hook("pre_run_step_hook"), post = get_hook("post_run_step_hook"))
)Arguments
step_idId of the step for which to run data calculation.
hookList 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$bind_data(step_id)
Arguments
step_idId of the step for which to bind the data.
Method describe_state()
Print defined steps configuration.
Usage
Cohort$describe_state()
Method get_step()
Get selected step configuration.
Usage
Cohort$get_step(step_id)
Arguments
step_idId of the step to be returned.
Method get_filter()
Get selected filter configuration.
Usage
Cohort$get_filter(step_id, filter_id, method = function(x) x)
Arguments
step_idId of the step where filter is defined.
filter_idIf of the filter to be returned.
methodCustom 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$update_cache(step_id, filter_id, state = "post")
Arguments
step_idId of the step for which caching should be applied. If 'filter_id' is not missing, the parameter describes id of the step where filter should be found.
filter_idId of the filter for which caching should be applied.
stateShould caching be done on data before ("pre") or after ("post") filtering in specified step.
Method get_cache()
Return step of filter specific cache.
Usage
Cohort$get_cache(step_id, filter_id, state = "post")
Arguments
step_idId 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_idId of the filter for which cache data should be returned.
stateShould 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$list_active_filters(step_id)
Arguments
step_idId of the step where filters should be found.
Method last_step_id()
Return id of the last existing step in Cohort.
Usage
Cohort$last_step_id()
Method modify()
Helper method enabling to run non-standard operation on Cohort object.
Usage
Cohort$modify(modifier)
Arguments
modifierFunction of two arguments 'self' and 'private'.
Method clone()
The objects of this class are cloneable with this method.
Usage
Cohort$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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