Logging with omopgenerics

In omopgenerics: Methods and Classes for the OMOP Common Data Model

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Logging

Logging is a common practice in studies, specially when sharing code. Logging can be useful to check timings or record error messages. There exist multiple packages in R that allow you to record these log messages. For example the logger package is quite useful.

Logging with omopgenerics

omopgenerics does not want to replace any of these packages, we just provide simple functionality to log messages. In the future we might consider building this on top of one of the existing log packages, but for the moment we have these three simple functions:

• createLogFile() It is used to create the log file.
• logMessage() It is used to record the messages that we want in the log file, note those messages will also be displayed in the console. If logFile does not exist the message is only displayed in the console.
• summariseLogFile() It is used to read the log file and format it into a summarised_result object.

Example

Let's see a simple example of logging with omopgenerics:

library(omopgenerics, warn.conflicts = FALSE)

# create the log file
createLogFile(logFile = tempfile(pattern = "log_{date}_{time}"))

# study
logMessage("Generating random numbers")
x <- runif(1e6)

logMessage("Calculating the sum")
result <- sum(x)

# export logger to a `summarised_result`
log <- summariseLogFile()

# content of the log file
readLines(getOption("omopgenerics.logFile")) |>
  cat(sep = "\n")

# `summarised_result` object
log

# `summarised_result` object settings
settings(log)

# tidy version of the `summarised_result`
tidy(log)

options("omopgenerics.logFile" = NULL)

Note that if the logFile is not created the logMessage() function only displays the message in the console.

exportSummarisedResult

The exportSummarisedResult() exports by default the logger if there is one. See example code:

library(dplyr, warn.conflicts = FALSE)
library(tidyr, warn.conflicts = FALSE)

# create the log file
createLogFile(logFile = tempfile(pattern = "log_{date}_{time}"))

# start analysis
logMessage("Deffining toy data")
n <- 1e5
x <- tibble(person_id = seq_len(n), age = rnorm(n = n, mean = 55, sd = 20))

logMessage("Summarise toy data")
res <- x |>
  summarise(
    `number subjects_count` = n(),
    `age_mean` = mean(age),
    `age_sd` = sd(age),
    `age_median` = median(age),
    `age_q25` = quantile(age, 0.25),
    `age_q75` = quantile(age, 0.75)
  ) |>
  pivot_longer(
    cols = everything(), 
    names_to = c("variable_name", "estimate_name"), 
    names_sep = "_",
    values_to = "estimate_value"
  ) |>
  mutate(
    result_id = 1L,
    cdm_name = "mock data",
    variable_level = NA_character_,
    estimate_type = if_else(estimate_name == "count", "integer", "numeric"),
    estimate_value = as.character(estimate_value)
  ) |>
  uniteGroup() |>
  uniteStrata() |>
  uniteAdditional() |>
  newSummarisedResult()

# res is a summarised_result object that we can export using the `exportSummarisedResult`
tempDir <- tempdir()
exportSummarisedResult(res, path = tempDir)

exportSummarisedResult() also exported the log file, let's see it. Let's start importing the exported summarised_result object:

result <- importSummarisedResult(tempDir)

We can see that the log file is exported see result_type = "summarise_log_file":

result |>
  settings() |> 
  glimpse()

The easiest way to explore the log is using the tidy() version:

result |>
  filterSettings(result_type == "summarise_log_file") |>
  tidy()

omopgenerics documentation built on June 8, 2025, 10:40 a.m.