README.md

In jmeydam/countcheck: Detecting Count Anomalies Using Bayesian Hierarchical Models

countcheck

Detecting Count Anomalies Using Bayesian Hierarchical Models

Prototype (R package).

• Dertermines upper control limits for count data
• Reasonable results also in cases with few or no observed events
• HTML reports

Model and code are based on examples in Gelman et al. (2014) and McElreath (2020).

This prototype is related to a previous simulation study.

The distributions and parameters in the simulation study were chosen so that the generated data is comparable to certain data of interest. The prototype is meant to be used for roughly the same kind of data. Please refer to this report for details.

The package documentation can be accessed via the package website.

Installation

Install the following R packages and their dependencies:

• actuar
• extraDistr
• cmdstanr (instructions, also for installing CmdStan)

The prototype can then be installed from GitHub with:

devtools::install_github("https://github.com/jmeydam/countcheck.git", 
                         build_vignettes = FALSE)

Example

We simulate count data for 1000 observational units, assuming a certain known data-generating process.

The data-generating process is free of anomalies, and all counts exceeding their respective upper control limits (UCLs) are false positives. Other things being equal it is desirable to have as few false positives as possible.

Using a Bayesian hierarchical model with partial pooling, 18 new counts exceed their respective upper control limits, vs. 68 when using a no-pooling model. (4 counts exceed the UCLs based on the true value of the parameter theta, which is known in this case.)

> library(countcheck)

> d <- countcheck(random_seed = 200807)

> # Counts exceeding UCLs
> # *********************
> # ucl_true_theta:
> sum(d$y_new - d$ucl_true_theta > 0)
[1] 4
> # ucl_nopool:
> sum(d$y_new - d$ucl_nopool > 0)
[1] 68
> # ucl_complpool:
> sum(d$y_new - d$ucl_complpool > 0)
[1] 74
> # ucl_partpool:
> sum(d$y_new - d$ucl_partpool > 0)
[1] 18

Alternatively:

Using the dataset provided in the package, the same result (here without the true_theta values) can be obtained with:

> e <- simdat
> d1 <- countcheck(unit = e$unit,
+                  n = e$n,
+                  y = e$y,
+                  n_new = e$n_new,
+                  y_new = e$y_new,
+                  random_seed = 200807)

In a realistic scenario it is not possible to assess performance by comparison with "true" values. The true values of theta are generally not known, and the probability distributions assumed for the Bayesian hierarchical model (the no-pooling model) may in fact be inappropriate.

On the other hand, in a realistic scenario it is often possible to assess performance by investigating individual cases.

HTML Report

Select data from data frame d (example above) for the report:

> countcheck_df <- select_for_report(d)

We also need a data frame with unit master data. Here, we just generate some data:

> units_tmp <- sort(unique(countcheck_df$unit))
> unit_df <- data.frame(
+   unit = units_tmp,
+   unit_name = paste("Unit",
+                     units_tmp),
+   unit_url = paste0("http://domain/units/",
+                     units_tmp,
+                     ".html"),
+   unit_group_name = paste("Group",
+                           rep(1:5,
+                               length.out = length(units_tmp)))
+ )

Generate report as R string:

> report <- html_report(
+   countcheck_list = list(
+     list(df = countcheck_df, caption = "KPI 1")
+   ),
+   unit_df = unit_df,
+   title = "Report",
+   table_width_px = 500,
+   column_headers = c(
+     group = "Group",
+     count = "Count",
+     ucl = "UCL",
+     unit = "Unit",
+     name = "Name"),
+   charset = "utf-8",
+   lang = "en",
+   home_url = "https://github.com/jmeydam/countcheck"
+ )

Save HTML report to disk:

> sink("report.html")
> cat(report)
> sink()

View HTML report

jmeydam/countcheck documentation built on Aug. 16, 2024, 11:34 a.m.