knitr::opts_chunk$set( collapse = TRUE, echo = FALSE, warning = FALSE, message = FALSE, comment = "#>" )
library(multipleITScontrol) library(dplyr) library(ggplot2) library(lubridate) library(stringi) library(rlang) library(purrr) phei_calendar <- function(df, date_column = NULL, factor_column = NULL, colours = NULL, title = "Placeholder: Please supply title or 'element_blank()' to `title` argument", subtitle = "Placeholder: Please supply subtitle or 'element_blank()' to `subtitle` argument", caption = "PH.Intelligence@hertfordshire.gov.uk", ncol, ...) { date_column <- rlang::sym(date_column) factor_column <- rlang::sym(factor_column) df <- df |> dplyr::mutate( mon = lubridate::month(!!date_column, label = T, abbr = F), wkdy = weekdays(!!date_column, abbreviate = T ) |> forcats::fct_relevel("Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun"), day = lubridate::mday(!!date_column), week = stringi::stri_datetime_fields(!!date_column)$WeekOfMonth, year = lubridate::year(!!date_column), year_mon = zoo::as.yearmon(!!date_column, "%Y %m") ) |> dplyr::mutate(across(week, ~ dplyr::case_when(wkdy == "Sun" ~ week - 1, .default = as.numeric(week) ))) df %>% ggplot2::ggplot(., ggplot2::aes(wkdy, week)) + # custom theme stuff below # geom_tile and facet_wrap will do all the heavy lifting ggplot2::geom_tile( alpha = 0.8, ggplot2::aes(fill = !!factor_column), color = "black", ... ) + ggplot2::facet_wrap(~year_mon, scales = "free_x", ncol = ncol) + ggplot2::geom_text(ggplot2::aes(label = day)) + # put your y-axis down, flip it, and reverse it ggplot2::scale_y_reverse(breaks = NULL) + # manually fill scale colors to something you like... ggplot2::scale_fill_manual( values = colours, na.value = "white", na.translate = FALSE ) + ggpubr::theme_pubclean() + ggplot2::theme(legend.position = "bottom") + ggplot2::labs( fill = "", x = "", y = "", title = element_blank(), caption = "PH.Intelligence@hertfordshire.gov.uk" ) }
This is a basic example which shows how to solve a common problem with a two‑stage interrupted time series with a control, for a level (step) change hypothesis.
Background:
\ MetroBike City and RiverCycle District operate bicycle‑sharing networks in neighbouring urban areas. Both systems use similar bicycles, have comparable ridership patterns, and maintain similar maintenance schedules.
In early 2023, MetroBike City implemented two sequential interventions aimed at reducing weekly maintenance incidents (e.g., damaged gears, brake faults, electronic lock failures). RiverCycle District made no fleet-wide changes during the same period and serves as the control.
This example illustrates a scenario where each intervention leads to a significant immediate “step” decrease in the number of maintenance incidents, without slope changes.
Step 1: Baseline Period
Duration: January 1, 2023 – April 2, 2023
Weekly maintenance incident counts collected.
Step 2: Intervention 1 Period
Step 3: Intervention 2 Period
The calendar plot below summarises the timeline of the interventions:
bike_calendar <- its_data_bike_programme |> group_by(group_var) |> arrange(group_var, Date) |> tidyr::complete(Date = seq(min(Date), max(Date), by = "day")) |> tidyr::fill(Period, .direction = "down") plot <- phei_calendar( bike_calendar, date_column = "Date", "Period", colours = c("#3b5163", "#80bb77", "#afd0f0"), ncol = 3 ) + theme(strip.text = element_text(size = rel(0.5)), axis.text = element_text(size = rel(0.5)), plot.caption = element_text(size = rel(0.5)), legend.text = element_text(size = rel(0.5))) plot$layers[[2]]$aes_params$size <- 3 plot
Sample data can be loaded from the package for this scenario through the bundled dataset its_data_bike_programme.
DT::datatable(its_data_bike_programme, options = list(dom = 'tip'), rownames = FALSE)
This sample dataset demonstrates the format your own data should be in.
You can observe that in the Date column, that the dates are of equal distance between each element, and that there are two rows for each date, corresponding to either control or treatment in the group_var variable. control and treatment each have three periods, a Pre-intervention period detailing measurements of the outcome prior to any intervention, the first intervention detailed by Intervention 1) Smart-Lock Upgrade, and the second intervention, detailed by Intervention 2) Predictive Maintenance Algorithm.
The data frame should be passed to multipleITScontrol::tranform_data() with suitable arguments selected, specifying the names of the columns to the required variables and starting intervention time points.
intervention_dates <- c(as.Date("2023-04-03"), as.Date("2023-06-05")) transformed_data <- multipleITScontrol::transform_data(df = its_data_bike_programme, time_var = "Date", group_var = "group_var", outcome_var = "score", intervention_dates = intervention_dates)
Returns the initial data frame with a few transformed variables needed for interrupted time series.
transformed_data
The transformed data is then fit using multipleITScontrol::fit_its_model(). Required arguments are transformed_data, which is simply an unmodified object created from multipleITScontrol::transform_data() in the step above; a defined impact model, with current options being either 'slope', `level, or 'levelslope', and the number of interventions.
fitted_ITS_model <- multipleITScontrol::fit_its_model(transformed_data = transformed_data, impact_model = "level", num_interventions = 2) fitted_ITS_model
Gives a conventional model output from nlme::gls().
fitted_ITS_model
However, the coefficients given do not make intuitive sense to a lay person. We can call the package's internal multipleITScontrol::summary_its() which modifies the summary output by renaming the coefficients, variable names, and other model-related terms to make them easier to interpret in the context of interrupted time series (ITS) analysis.
my_summary_its_model <- multipleITScontrol::summary_its(fitted_ITS_model) my_summary_its_model
my_summary_its_model
summary(my_summary_its_model)
summary(my_summary_its_model)
sjPlot::tab_model( my_summary_its_model, dv.labels = "Weekly Total Maintenance Incidents", show.se = TRUE, collapse.se = TRUE, linebreak = FALSE, string.est = "Estimate (std. error)", string.ci = "95% CI", p.style = "numeric_stars" )
sjPlot::tab_model( my_summary_its_model, dv.labels = "Weekly Total Maintenance Incidents", show.se = TRUE, collapse.se = TRUE, linebreak = FALSE, string.est = "Estimate (std. error)", string.ci = "95% CI", p.style = "numeric_stars" ) a <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "A) Control y-axis intercept")]] |> round(2) # c <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "C) Control pre-intervention slope")]] |> round(2) # d <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "D) Pilot pre-intervention slope difference to control")]] |> round(2) g <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "G) Control intervention 1 level")]] |> round(2) h <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "H) Pilot intervention 1 level difference to control")]] |> round(2) k <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "K) Control intervention 2 level")]] |> round(2) l <- coef(my_summary_its_model)[[which(names(coef(my_summary_its_model)) == "L) Pilot intervention 2 level difference to control")]] |> round(2)
The predictor coefficients elucidate a few things:
G) Control intervention 1 level describes the step change that occurs at the intervention break point in the control group at the start of the first intervention (r g).
H) Pilot intervention 1 level describes the difference in the step change that occurs at the intervention timepoint in the control group for the first intervention compared to the pilot (r h).
To ascertain the level for the pilot data, we add to the control coefficient step of the pilot data, the coefficients G) Control intervention 1 level and H) Pilot intervention 1 level difference to control. G (r g) + H (r h) = r g+h is the step change during the first intervention for the pilot data.
The coefficient H) Pilot intervention 1 level difference to control, in essence acts a t-test of whether there is a statistically significant difference between the step of the pilot data and the control. Mathemetically it is equivalent to a two-sample t-test.
In the regression model results above, We can see there is a statistically significant difference via the p-value for coefficient H.
K) Control intervention 2 level describes the step change that occurs at the intervention break point in the control group at the start of the second intervention (r k).
L) Pilot intervention 2 level difference to control" describes the difference in the step change that occurs at the intervention timepoint in the pilot group for the second intervention compared to the control (r l).
In the regression model results above, We can see there is a statistically significant difference via the p-value for coefficient L.
We can fit predictions with the created model which project the pre-intervention period into the post-intervention period by using the model coefficients using multipleITScontrol::generate_predictions().
transformed_data_with_predictions <- generate_predictions(transformed_data, fitted_ITS_model) transformed_data_with_predictions
DT::datatable(transformed_data_with_predictions, options = list(dom = 'tip', scrollX = TRUE), rownames = FALSE)
We can use the predicted values and map the segmented regression lines which compare whether an intervention had a statistically significant difference.
its_plot(model = my_summary_its_model, data_with_predictions = transformed_data_with_predictions, time_var = "time", intervention_dates = intervention_dates, y_axis = "Weekly Total Maintenance Incidents")
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