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+Log example • whirl
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+ Skip to contents
+
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+
In this example we are going to execute the following script and
+create a log of it’s execution:
+
#> #' Setup
+#> library(dplyr)
+#> library(ggplot2)
+#> #' Prepare data
+#> x <- mtcars |>
+#> as_tibble(rownames = "car")
+#> print(x)
+#> #' Create and save plot
+#> ggplot(data = x)+
+#> geom_point(mapping = aes(x = mpg, y = hp, size = wt, colour = as.factor(am)))
+#> ggsave("plot1.png")
+
We are going to use the run() function to execute the
+script, and since this vignette is created on Linux we can use the
+whirl.track_files option to automatically track the used
+files:
The whirl package provides functionalities for executing scripts in
+batch while simultaneously getting logs from the individual executions.
+In the following sections, we will go through how to use the
+package.
+
+
+
Ways to call the run() function
+
+
+
Single and multiple files, and regular expressions
+
+
The input argument in the run() function
+can in the most simple case point to a single file for which an
+execution and log-generation is required.
The input argument can also point to multiple files in a
+directory using wildcard (or globbing) patterns. In this case, all
+scripts in the directory will be executed in parallel and a log will be
+generated for each script. The number of workers can be specified
+through the n_workers argument (default is set to one). A
+summary log file will also be provided as a fast way to get an overview
+of the execution. The location of the summary file can be controlled
+with the summary_file argument.
+
+# Execution of all R files in a specific directory
+run(
+ input ="path/to/directory/*.(r|R)",
+ n_workers =4,
+ summary_file ="path/to/summary"
+)
+
+# Execution of all R files starting with "mk200" in a specific directory
+run(
+ input ="path/to/directory/mk200*.(r|R)",
+ n_workers =8,
+ summary_file ="path/to/summary"
+)
+
More information on how the wildcards are interpreted see
+utils::glob2rx().
+
It is also possible to provide a character vector of several paths
+(either single files or regular expression) that should be executed.
+Note that whenever the input argument in is supplied with a
+character vector
+(e.g. c("path/to/script1.R", "path/to/script2.R")) it
+assumes that these can be executed independently and in parallel. If the
+elements needs to be executed sequentially this can be achieved by using
+a list() instead (see below).
+
+
+
Using list() as input
+
+
If the scripts have to be executed in a specific order, the
+input argument can be supplied as a list. The scripts will
+then be executed in the order they are listed in the list, with scripts
+listed in the same element being executed in parallel (if
+n_workers > 1).
+
+# In the below example, script1.R and script2.R will be executed in parallel
+run(
+ input =c("path/to/script1.R",
+"path/to/script2.R"),
+ n_workers =2
+)
+
+# In the below example, script1.R and script2.R will be executed in parallel,
+# and all R files in the directory will subsequently be executed in parallel
+run(
+ input =list(
+c("path/to/script1.R", "path/to/script2.R"),
+"path/to/directory/*.R"
+),
+ n_workers =2
+)
+
+# In the below example, script1.R and script2.R will be executed in parallel, and subsequently
+# script3.R and script4.R will be executed in parallel
+run(
+ input =list(
+c("path/to/script1.R", "path/to/script2.R"),
+c("path/to/script3.R", "path/to/script4.R")
+),
+ n_workers =2
+)
+
The list can also be supplied with names list elements. This can be
+useful during execution as some of these ‘name’ will be printed to the
+console.
In this case, the input argument in the
+run() function should point to the config file. Assuming
+the config file is called config.yaml, the execution can be
+initiated as follows:
Each steps in the config file will be executed independently while
+scrips within each step will be executed in parallel using the number of
+workers specified with the n_workers argument.
+
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+Authors and Citation • whirl
+ Skip to contents
+
+
+
