The Data List

In metasnf: Meta Clustering with Similarity Network Fusion

knitr::opts_chunk$set(echo = TRUE)

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Download a copy of the vignette to follow along here: data_list.Rmd

The data_list

This vignette outlines the importance, structure, and creation of the data_list object. You can find much of this info by running ?data_list after loading the metasnf package.

The data_list is the main object used in the metasnf package to store data. It is a named and nested list containing input data frames (data), the name of that input data frame (for the user's reference), the 'domain' of that data frame (the broader source of information that the input data frame is capturing, determined by user's domain knowledge), and the type of feature stored in the data frame (continuous, discrete, ordinal, categorical, or mixed).

Some examples of data_list generation and usage are below:

library(metasnf)

# Preparing some mock data
heart_rate_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var1 = c(0.04, 0.1, 0.3),
    var2 = c(30, 2, 0.3)
)

personality_test_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var3 = c(900, 1990, 373),
    var4 = c(509, 2209, 83)
)

survey_response_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var5 = c(1, 3, 3),
    var6 = c(2, 3, 3)
)

city_df <- data.frame(
    patient_id = c("1", "2", "3"),
    var7 = c("toronto", "montreal", "vancouver")
)

# Generating a data_list explicitly (Name each nested list element):
dl <- data_list(
    list(
        data = heart_rate_df,
        name = "heart_rate",
        domain = "clinical",
        type = "continuous"
    ),
    list(
        data = personality_test_df,
        name = "personality_test",
        domain = "surveys",
        type = "continuous"
    ),
    list(
        data = survey_response_df,
        name = "survey_response",
        domain = "surveys",
        type = "ordinal"
    ),
    list(
        data = city_df,
        name = "city",
        domain = "location",
        type = "categorical"
    ),
    uid = "patient_id"
)

# Achieving the same result compactly:
dl <- data_list(
    list(heart_rate_df, "heart_rate", "clinical", "continuous"),
    list(personality_test_df, "personality_test", "surveys", "continuous"),
    list(survey_response_df, "survey_response", "surveys", "ordinal"),
    list(city_df, "city", "location", "categorical"),
    uid = "patient_id"
)

# Printing data_list summaries
summary(dl)

Depending on your data preprocessing, it may be more convenient to you to assemble the components of your data_list in an automated way and then provide that result to data_list.

For example, your code could have generated a list like the one below:

list_of_lists <- list(
    list(heart_rate_df, "data1", "domain1", "continuous"),
    list(personality_test_df, "data2", "domain2", "continuous")
)

If data_list receives only a single list, it'll treat that list as containing all the components required to construct a properly formatted data_list:

dl <- data_list(
    list_of_lists,
    uid = "patient_id"
)

summary(dl)

metasnf documentation built on April 3, 2025, 5:40 p.m.