rfacts (version 0.2.1)

write_facts: Write modified FACTS files.

Description

Write modified versions of existing FACTS files. This function can be used to tweak properties of a FACTS file such as maximum sample size, number of weeks between interims, allocation ratios, data generation parameters, and analysis priors.

Usage

write_facts(fields, values, default_dir = "_facts")

Value

The function writes FACTS XML files and returns a character vector with the paths to those files.

Arguments

fields

Data frame defining the kind of XML data to be replaced. It must have one row per field definition and the following columns:

1. field: custom name of the field.

2. type: value of the "type" attribute of the <parameterSets> tag.

3. set: value of the "name" attribute of the <parameterSet> tag.

4. property: value of the "name" attribute of the <property> tag.

values

Data frame defining the FACTS files to generate. Must have one row per FACTS file and a column called facts_file with the names of the input FACTS files. An output column with the names of the output FACTS files is recommended but not required. (If output is not specified, the output FACTS files will be written to automatically generated paths inside default_dir.) Other columns must have names corresponding to elements of fields$field and contain values to insert into the FACTS files. These columns could be vectors or lists of vectors. In the former case, each element is a scalar replacement to a property. In the latter case, an XML property receives an entire vector as an item list, and the vector must be the same length as the original item list.

default_dir

Directory to write the output FACTS files if values has no output column.

Details

A FACTS file has a special kind of XML format. Most of the content sits in an overarching <facts> tag, then a <parameterSets> tag, then a <parameterSet> tag, then a <property> tag. For example, here is the part of a FACTS file that controls the weeks between interims.

<facts>
  <parameterSets type="NucleusParameterSet">
    <parameterSet name="nucleus">
      <property name="update_freq_save">4</property>

To use the write_facts() function, you must first identify the parts of the FACTS file you want to modify (the fields argument) then the values that should be substituted in (the values argument). Given the XML above, to create new FACTS files with intervals 5 and 6 instead of 4, you would set

fields <- tibble::tibble(
  field = "my_interval",
  type = "NucleusParameterSet",
  set = "nucleus",
  property = "update_freq_save"
)
values <- tibble::tibble(
  facts_file = "your_facts_file.facts",
  output = "output_file.facts",
  my_interval = c(5, 6)
)

and then call write_facts(fields = fields, values = values).

Examples

# Identify a source FACTS file.
facts_file <- get_facts_file_example("contin.facts")
# Create 4 new FACTS files with different numbers of max patients.
fields <- data.frame(
  field = "my_subjects",
  type = "NucleusParameterSet",
  set = "nucleus",
  property = "max_subjects"
)
values <- data.frame(
  facts_file = facts_file,
  output = c("_facts/out1000.facts", "_facts/out2000.facts"),
  my_subjects = c(1000, 2000)
)
default_dir <- tempfile()
write_facts(fields = fields, values = values, default_dir = default_dir)
list.files("_facts")
unlink("_facts", recursive = TRUE)