combine_biomarkers

Combines specified biomarker measurements across a list of data frames and
returns a unified long-format data set restricted to subjects with at least
one recorded measurement for EVERY requested biomarker.
The function searches each provided data frame for the biomarker names listed
in <code>biomarkers</code>, extracts the matching measurement rows, and standardizes
the output into a common structure. Subjects are retained only if they have
at least one non-missing measurement for every requested biomarker across the
supplied data frames. It is intended for settings where biomarker measurements 
may be distributed across multiple data frames, and where each data frame may 
contain one or more of the requested biomarkers. The returned data are in long 
format so that repeated measurements per subject and per biomarker are preserved. 
No collapsing, averaging, or other within-subject summarization is performed.

Implements scalable joint models for large-scale competing risks time-to-event data with one or multiple longitudinal biomarkers using the efficient algorithms developed by Li et al. (2022) <doi:10.1155/2022/1362913> and <doi:10.48550/arXiv.2506.12741>.
The time-to-event process is modeled using a cause-specific Cox proportional hazards model
with time-fixed covariates, while longitudinal biomarkers are modeled
using linear mixed-effects models. The association between the longitudinal
and survival processes is captured through shared random effects. The
package enables analysis of large-scale biomedical data to model biomarker
trajectories, estimate their effects on event risks, and perform dynamic
prediction of future events based on patients' longitudinal histories.
Functions for simulating survival and longitudinal data for multiple
biomarkers are included, along with built-in example datasets. The package
also supports modeling a single biomarker with heterogeneous within-subject
variability via functionality adapted from the 'JMH' package.

Shanpeng Li

FastJM

Semi-Parametric Joint Modeling of Longitudinal and Survival Data

Ace Mejia-Sanchez

Emily Ouyang

Gang Li

combine_biomarkers function

<dl><dt>data_list</dt>
<dd>A non-empty list of data frames containing subject-level
biomarker measurements.</dd>
<dt>biomarkers</dt>
<dd>A character vector of biomarker column names to search for
across the supplied data frames.</dd>
<dt>id_col</dt>
<dd>A character string giving the subject ID column name. This
column must be present in every data frame in <code>data_list</code>.</dd>
<dt>time_col</dt>
<dd>An optional character string giving the time variable column
name, such as days from baseline. If supplied, this column must be present
in every data frame in <code>data_list</code>, and it is standardized to
<code>"time"</code> in the returned long-format output.</dd>
<dt>dataset_names</dt>
<dd>An optional character vector of names for the supplied
data frames. If omitted, the function uses <code>names(data_list)</code> when
available; otherwise it creates default names of the form
<code>"dataset_1"</code>, <code>"dataset_2"</code>, and so on.</dd></dl>

Arguments

Shanpeng Li <a href="/link/lishanpeng0913%40ucla.edu?package=FastJM&version=1.7.0" data-mini-rdoc="FastJM::lishanpeng0913@ucla.edu">lishanpeng0913@ucla.edu</a>

Author

Combine biomarker measurements across multiple data frames — combine_biomarkers

<dl>

<dt>data_list</dt>
<dd>A non-empty list of data frames containing subject-level
biomarker measurements.</dd>


<dt>biomarkers</dt>
<dd>A character vector of biomarker column names to search for
across the supplied data frames.</dd>


<dt>id_col</dt>
<dd>A character string giving the subject ID column name. This
column must be present in every data frame in <code>data_list</code>.</dd>


<dt>time_col</dt>
<dd>An optional character string giving the time variable column
name, such as days from baseline. If supplied, this column must be present
in every data frame in <code>data_list</code>, and it is standardized to
<code>"time"</code> in the returned long-format output.</dd>


<dt>dataset_names</dt>
<dd>An optional character vector of names for the supplied
data frames. If omitted, the function uses <code>names(data_list)</code> when
available; otherwise it creates default names of the form
<code>"dataset_1"</code>, <code>"dataset_2"</code>, and so on.</dd>

</dl>

Shanpeng Li <a href='mailto:lishanpeng0913@ucla.edu'>lishanpeng0913@ucla.edu</a>

combine_biomarkers: Combine biomarker measurements across multiple data frames

Description

Usage

Value

Arguments

Author

Examples