Help for package daqapo

Type:

Package

Title:

Data Quality Assessment for Process-Oriented Data

Version:

0.3.2

Date:

2022-07-13

Description:

Provides a variety of methods to identify data quality issues in process-oriented data, which are useful to verify data quality in a process mining context. Builds on the class for activity logs implemented in the package 'bupaR'. Methods to identify data quality issues either consider each activity log entry independently (e.g. missing values, activity duration outliers,...), or focus on the relation amongst several activity log entries (e.g. batch registrations, violations of the expected activity order,...).

License:

MIT + file LICENSE

URL:

https://github.com/bupaverse/daqapo/

BugReports:

https://github.com/bupaverse/daqapo/issues/

LazyData:

true

RoxygenNote:

7.2.0

Encoding:

UTF-8

Depends:

R (≥ 3.5.0)

Imports:

dplyr, lubridate, stringdist, stringr, tidyr, xesreadR, rlang, bupaR (≥ 0.5.0), readr, edeaR, magrittr, purrr, glue, miniUI, shiny, tibble

Suggests:

knitr, rmarkdown

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2022-07-14 08:21:23 UTC; lucp8407

Author:

Niels Martin [aut, cre], Greg Van Houdt [ctb], Gert Janssenswillen [ctb]

Maintainer:

Niels Martin <niels.martin@uhasselt.be>

Repository:

CRAN

Date/Publication:

2022-07-14 09:00:09 UTC

daqapo - Data Quality Assessment for Process-oriented Data

Description

This package is designed to perform data quality assessment on process-oriented data.

Check activity frequencies

Description

Function that detects activity frequency anomalies per case

Usage

detect_activity_frequency_violations(
  activitylog,
  ...,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

...

Named vectors with name of the activity, and value of the threshold.

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of cases for which activities are executed too many times

Examples


data("hospital_actlog")
detect_activity_frequency_violations(activitylog = hospital_actlog,
     "Registration" = 1, "Clinical exam" = 1)

Detect activity order violations

Description

Function detecting violations in activity order. Having additional or less activity types than those specified in activity_order is no violation, but the activity types present should occur in the specified order, and only once.

Usage

detect_activity_order_violations(
  activitylog,
  activity_order,
  timestamp,
  details,
  filter_condition
)

## S3 method for class 'activitylog'
detect_activity_order_violations(
  activitylog,
  activity_order,
  timestamp = c("both", "start", "complete"),
  details = TRUE,
  filter_condition = NULL
)

Arguments

activitylog

The activity log

activity_order

Vector expressing the activity order that needs to be checked (using activity names)

timestamp

Type of timestamp that needs to be taken into account in the analysis (either "start", "complete" or "both)

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of detected activity orders which violate the specified activity order

Methods (by class)

activitylog: Detect activity order_violations in activity log.

Examples


data("hospital_actlog")
detect_activity_order_violations(activitylog = hospital_actlog,
     activity_order = c(
         "Registration",
         "Triage",
         "Clinical exam",
         "Treatment",
         "Treatment evaluation"))

Detect dependency violations between attributes

Description

Function detecting violations of dependencies between attributes (i.e. condition(s) that should hold when (an)other condition(s) hold(s))

Usage

detect_attribute_dependencies(
  activitylog,
  antecedent,
  consequent,
  details = TRUE,
  filter_condition = NULL,
  ...
)

Arguments

activitylog

The activity log

antecedent

(Vector of) condition(s) which serve as an antecedent (if the condition(s) in antecedent hold, then the condition(s) in consequent should also hold)

consequent

(Vector of) condition(s) which serve as a consequent (if the condition(s) in antecedent hold, then the condition(s) in consequent should also hold)

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

...

Named vectors with name of the activity, and value of the threshold.

Value

activitylog containing the rows of the original activity log for which the dependencies between attributes are violated

Examples


data("hospital_actlog")
detect_attribute_dependencies(activitylog = hospital_actlog,
     antecedent = activity == "Registration",
     consequent = startsWith(originator,"Clerk"))

Detect gaps in case_id

Description

Function detecting gaps in the sequence of case identifiers

Usage

detect_case_id_sequence_gaps(activitylog, details, filter_condition)

Arguments

activitylog

The activity log

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

data.frame providing an overview of the case identifiers which are expected, but which are not present in the activity log

Examples


data("hospital_actlog")
detect_case_id_sequence_gaps(activitylog = hospital_actlog)

Detect conditional activity presence violations

Description

Function detecting violations of conditional activity presence (i.e. an activity/activities that should be present when (a) particular condition(s) hold(s))

Usage

detect_conditional_activity_presence(
  activitylog,
  condition,
  activities,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

condition

Condition which serve as an antecedent (if the condition in condition holds, then the activit(y)(ies) in activities should be present.)

activities

Vector of activity/activities which serve as a consequent (if the condition(s) in condition_vector hold, then the activity/activities in activity_vector should be recorded)

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

Numeric vector containing the case identifiers of cases for which the specified conditional activity presence is violated

Examples


data("hospital_actlog")
detect_conditional_activity_presence(activitylog = hospital_actlog,
     condition = specialization == "TRAU",
     activities = "Clinical exam")

Detect activity duration outliers

Description

Function detecting duration outliers for a particular activity

Usage

detect_duration_outliers(activitylog, ..., details, filter_condition)

Arguments

activitylog

The activity log

...

for each activity to be checked, an argument "activity_name" = duration_within(...) to define bounds. See ?duration_within

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log for which activity duration outliers are detected Information on the presence of activity duration outliers

Examples


data("hospital_actlog")
detect_duration_outliers(activitylog = hospital_actlog,
     Treatment = duration_within(bound_sd = 1))

Detect inactive periods

Description

Function detecting inactive periods, i.e. periods of time in which no activity executions/arrivals are recorded in the activity log

Usage

detect_inactive_periods(
  activitylog,
  threshold,
  type,
  timestamp,
  start_activities,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

threshold

Threshold after which a period without activity executions/arrivals is considered as an inactive period (expressed in minutes)

type

Type of inactive periods you want to detect. "arrivals" will look for periods without new cases arriving. "activities" will look for periods where no activities occur.

timestamp

Type of timestamp that needs to be taken into account in the analysis (either "start", "complete" or "both)

start_activities

List of activity labels marking the first activity in the process. When specified, an inactive period only occurs when the time between two consecutive arrivals exceeds the specified threshold (arrival is proxied by the activity/activities specified in this argument).

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of the start and end of the inactive periods that have been detected, together with the length of the inactive period

Examples


data("hospital_actlog")
detect_inactive_periods(activitylog = hospital_actlog,threshold = 30)

Detect incomplete cases

Description

Function detecting incomplete cases in terms of the activities that need to be recorded for a case. The function only checks the presence of activities, not the completeness of the rows describing the activity executions.

Usage

detect_incomplete_cases(activitylog, activities, details, filter_condition)

Arguments

activitylog

The activity log

activities

A vector of activity names which should be present for a case

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of the traces (i.e. the activities executed for a particular case) in which the specified activities are not present, together with its occurrence frequency and cases having this trace

Examples


data("hospital_actlog")
detect_incomplete_cases(activitylog = hospital_actlog,
     activities = c("Registration","Triage","Clinical exam","Treatment","Treatment evaluation"))

Detect incorrect activity names

Description

Function returning the incorrect activity labels in the log as indicated by the user. If details are requested, the entire activity log's rows containing incorrect activities are returned.

Usage

detect_incorrect_activity_names(
  activitylog,
  allowed_activities,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

allowed_activities

Vector with correct activity labels. If NULL, user input will be asked.

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log having incorrect activity labels

Examples


data("hospital_actlog")
detect_incorrect_activity_names(activitylog = hospital_actlog,
     allowed_activities = c(
         "Registration",
         "Triage",
         "Clinical exam",
         "Treatment",
         "Treatment evaluation"))

Detect missing values

Description

Function detecting missing values at different levels of aggregation

overview: presents an overview of the absolute and relative number of missing values for each column
column: presents an overview of the absolute and relative number of missing values for a particular column
activity: presents an overview of the absolute and relative number of missing values for each column, aggregated by activity

Usage

detect_missing_values(
  activitylog,
  level_of_aggregation,
  column,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

level_of_aggregation

Level of aggregation at which missing values are identified (either "overview", "column" or "activity)

column

Column name of the column that needs to be analyzed when the level of aggregation is "column"

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log which contain a missing value

Examples


data("hospital_actlog")
detect_missing_values(activitylog = hospital_actlog)
detect_missing_values(activitylog = hospital_actlog, level_of_aggregation = "activity")
detect_missing_values(activitylog = hospital_actlog, level_of_aggregation = "column",
     column = "triagecode")

Detect multi-registration

Description

Function detecting multi-registration for the same case or by the same resource at the same point in time

Usage

detect_multiregistration(
  activitylog,
  level_of_aggregation,
  timestamp,
  threshold_in_seconds,
  details,
  filter_condition
)

Arguments

activitylog

The activity log (renamed/formatted using functions rename_activity_log and convert_timestamp_format)

level_of_aggregation

Level of aggregation at which multi-registration should be detected (either "resource" or "case")

timestamp

Type of timestamp that needs to be taken into account in the analysis (either "start", "complete" or "both")

threshold_in_seconds

Threshold which is applied to determine whether multi-registration occurs (expressed in seconds) (time gaps smaller than threshold are considered as multi-registration)

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log for which multi-registration is present

Examples


data("hospital_actlog")
detect_multiregistration(activitylog = hospital_actlog, threshold_in_seconds = 10)

Detect overlapping acitivity instances

Description

Detect overlapping acitivity instances

Usage

detect_overlaps(activitylog, details, level_of_aggregation, filter_condition)

Arguments

activitylog

The activity log

details

Boolean indicating wheter details of the results need to be shown

level_of_aggregation

Look for overlapping activity instances within a case or within a resource.

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of activities which are performed in parallel by a resource, together with the occurrence frequency of the overlap and the average time overlap in minutes

Examples


data("hospital_actlog")
detect_overlaps(activitylog = hospital_actlog)

Detect missing related activities

Description

Function detecting missing related activity registration, i.e. detecting activities that should be registered for a case because another activity is registered for that case

Usage

detect_related_activities(
  activitylog,
  antecedent,
  consequent,
  details,
  filter_condition
)

Arguments

activitylog

The activity log

antecedent

Activity name of the activity that acts as a an antecedent (if antecedent occurs, then consequent should also occur)

consequent

Activity name of the activity that acts as a an consequent (if antecedent occurs, then consequent should also occur)

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

Numeric vector containing the case identifiers of cases for which related activities are not present

Examples


data("hospital_actlog")
detect_related_activities(activitylog = hospital_actlog,
     antecedent = "Treatment evaluation",
     consequent = "Treatment")

Search for similar labels in a column

Description

Function that tries to detect spelling mistakes in a given activity log column

Usage

detect_similar_labels(
  activitylog,
  column_labels,
  max_edit_distance,
  show_NA,
  ignore_capitals,
  filter_condition
)

Arguments

activitylog

The activity log

column_labels

The name of the column(s) in which to search for spelling mistakes

max_edit_distance

The maximum number of insertions, deletions and substitutions that are allowed to be executed in order for two strings to be considered similar.

show_NA

A boolean indicating if labels that do not show similarities with others should be shown in the output

ignore_capitals

A boolean indicating if capitalization should be included or excluded when calculating the edit distance between two strings

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

tbl_df providing an overview of similar labels for the indicated column

Examples


data("hospital_actlog")
detect_similar_labels(activitylog = hospital_actlog,
     column_labels = "activity",
     max_edit_distance = 3)

Detect time anomalies

Description

Function detecting time anomalies, which can refer to activities with negative or zero duration

Usage

detect_time_anomalies(
  activitylog,
  anomaly_type = c("both", "negative", "zero"),
  details = TRUE,
  filter_condition = NULL
)

Arguments

activitylog

The activity log

anomaly_type

Type of anomalies that need to be detected (either "negative", "zero" or "both")

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log for which a negative or zero duration is detected, together with the duration value and whether it constitutes a zero or negative duration

Examples


data("hospital_actlog")
detect_time_anomalies(activitylog = hospital_actlog)

Search for unique values / distinct combinations

Description

Function that lists all distinct combinations of the given columns in the activity log

Usage

detect_unique_values(activitylog, column_labels, filter_condition = NULL)

Arguments

activitylog

The activity log

column_labels

The names of columns in the activity log for which you want to show the different combinations found in the log. If only one column is provided, this results in a list of unique values in that column.

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the unique (distinct) values (combinations) in the indicated column(s)

Examples


data("hospital_actlog")
detect_unique_values(activitylog = hospital_actlog,
     column_labels = "activity")
detect_unique_values(activitylog = hospital_actlog,
     column_labels = c("activity", "originator"))

Detect value range violations

Description

Function detecting violations of the value range, i.e. values outside the range of tolerable values

Usage

detect_value_range_violations(activitylog, ..., details, filter_condition)

Arguments

activitylog

The activity log

...

Define domain range using domain_numeric, domain_categorical and/or domain_time for each column

details

Boolean indicating wheter details of the results need to be shown

filter_condition

Condition that is used to extract a subset of the activity log prior to the application of the function

Value

activitylog containing the rows of the original activity log for which the provided value range is violated

Examples


data("hospital_actlog")
detect_value_range_violations(activitylog = hospital_actlog,
     triagecode = domain_numeric(from = 0, to = 5))

Define allowable range of values

Description

Define allowable range of values

Usage

domain_categorical(allowed)

Arguments

allowed

Allowed values of categorical column (character or factor)

Value

No return value, called for side effects

Define allowable range of values

Description

Define allowable range of values

Usage

domain_numeric(from, to)

Arguments

from

Minimum of allowed range

to

Maximum of allowed range

Value

No return value, called for side effects

Define allowable time range

Description

Define allowable time range

Usage

domain_time(from, to, format = ymd_hms)

Arguments

from

Start time interval

to

End time interval

format

Format of to and from (either ymd_hms, dmy_hms, ymd_hm, ymd, dmy, dmy, ...). Both from and to should have the same format.

Value

No return value, called for side effects

Define bounds for activity duration

Description

Funtion to define bounds on the duration of an activity during detection of duration outliers.

Usage

duration_within(bound_sd = 3, lower_bound = NA, upper_bound = NA)

Arguments

bound_sd

Number of standard deviations from the mean duration which is used to define an outlier in the absence of lower_bound and upper_bound (default value of 3 is used)

lower_bound

Lower bound for activity duration used during outlier detection (expressed in minutes). This means disregarding the sd and bound_sd for lower bound

upper_bound

Upper bound for activity duration used during outlier detection (expressed in minutes). This means disregarding the sd and bound_sd for upper bound

Value

No return value, called for side effects

Filter anomalies from the activity log

Description

Function that filters detected anomalies from the activity log

Usage

filter_anomalies(activity_log, anomaly_log)

Arguments

activity_log

The activity log (renamed/formatted using functions rename_activity_log and convert_timestamp_format)

anomaly_log

The anomaly log generated from the different DAQAPO tests

Value

activitylog in which the anomaly rows are filtered out

Fix problems

Description

Fix problems

Usage

fix(detected_problems, ...)

Arguments

detected_problems

Output of a detect_ function. Currently supported: detect_resource_inconsistencies.

...

Additionals parameters, depending on type of anomalies to fix.

Value

No return value, called for side effects

An activity log of 20 patients in a hospital (data frame)

Description

A dataset containing the logged activities in an illustrative hospital process. 20 patients are described in the log. Process activities include Registration, Triage, Clinical exam, Treatment and Treatment evaluation.

Usage

hospital

Format

A data frame with 53 rows and 7 variables:

patient_visit_nr: the patient's identifier
activity: the executed activity
originator: the resource performing the activity execution
start_ts: the timestamp at which the activity was started
complete_ts: the timestamp at which the activity was completed
triagecode: a case attribute describing the triage code
specialization: a case attribute describing the specialization

Source

An illustrative example developed in-house for demonstrational purposes.

An activity log of 20 patients in a hospital (activity log object)

Description

Usage

hospital_actlog

Format

An activity log with 53 rows and 7 variables:

patient_visit_nr: the patient's identifier
activity: the executed activity
originator: the resource performing the activity execution
start: the timestamp at which the activity was started
complete: the timestamp at which the activity was completed
triagecode: a case attribute describing the triage code
specialization: a case attribute describing the specialization

Source

An illustrative example developed in-house for demonstrational purposes.

An event log of 20 patients in a hospital

Description

A dataset containing the logged activities in an illustrative hospital process. 20 patients are described in this log Process activities include Registration, Triage, Clinical exam, Treatment and Treatment evaluation.

Usage

hospital_events

Format

A data frame with 53 rows and 7 variables:

patient_visit_nr: the patient's identifier
activity: the executed activity
originator: the resource performing the activity execution
event_lifecycle_state: the state the activity is in at the given timestamp
timestamp: the moment in time the lifecycle state was reached
triagecode: a case attribute describing the triage code
specialization: a case attribute describing the specialization
event_matching: a specification of which events form a pair in the log

Source

An illustrative example developed in-house for demonstrational purposes.

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

bupaR: activitylog, assign_instance_id, convert_timestamps, detect_resource_inconsistencies, events_to_activitylog, fix_resource_inconsistencies, standardize_lifecycle
dplyr: rename
lubridate: dmy, dmy_h, dmy_hm, dmy_hms, mdy, mdy_h, mdy_hm, mdy_hms, ymd, ymd_h, ymd_hm, ymd_hms
magrittr: %>%
readr: read_csv, read_csv2

daqapo - Data Quality Assessment for Process-oriented Data

Description

Check activity frequencies

Description

Usage

Arguments

Value

Examples

Detect activity order violations

Description

Usage

Arguments

Value

Methods (by class)

Examples

Detect dependency violations between attributes

Description

Usage

Arguments

Value

Examples

Detect gaps in case_id

Description

Usage

Arguments

Value

Examples

Detect conditional activity presence violations

Description

Usage

Arguments

Value

Examples

Detect activity duration outliers

Description

Usage

Arguments

Value

See Also

Examples

Detect inactive periods

Description

Usage

Arguments

Value

Examples

Detect incomplete cases

Description

Usage

Arguments

Value

Examples

Detect incorrect activity names

Description

Usage

Arguments

Value

Examples

Detect missing values

Description

Usage

Arguments

Value

Examples

Detect multi-registration

Description

Usage

Arguments

Value

Examples

Detect overlapping acitivity instances

Description

Usage

Arguments

Value

Examples

Detect missing related activities

Description

Usage

Arguments