An extended function of the standard z-score standardization of a vector in R (i.e. function 'scale'). Supports filling in non-finite values as well as re-naming variables to distinguish them from non-standardized variables.

The top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge <https://www.synapse.org/ProstateCancerChallenge> presented in Guinney J, Wang T, Laajala TD, et al. (2017) <doi:10.1016/S1470-2045(16)30560-5> is provided here-in, together with the corresponding follow-up work. While initially aimed at modeling the most advanced stage of prostate cancer, metastatic Castration-Resistant Prostate Cancer (mCRPC), the modeling framework has subsequently been extended to cover also the non-metastatic form of advanced prostate cancer (CRPC). Readily fitted ensemble-based model S4-objects are provided, and a simulated example dataset based on a real-life cohort is provided from the Turku University Hospital, to illustrate the use of the package. Functionality of the ePCR methodology relies on constructing ensembles of strata in patient cohorts and averaging over them, with each ensemble member consisting of a highly optimized penalized/regularized Cox regression model. Various cross-validation and other modeling schema are provided for constructing novel model objects.

Teemu Daniel Laajala

ePCR

Ensemble Penalized Cox Regression for Survival Prediction

zt function

<dl><dt>x</dt>
<dd>A data matrix for which the columns are to be standardized</dd>
<dt>fillfinite</dt>
<dd>The value to fill non-finite values with, by default zero.</dd>
<dt>addz</dt>
<dd>Boolean indicating whether letter 'z' should be appended to the variable names to indicate the standardization</dd>
<dt>saveattr</dt>
<dd>Boolean for if an 'attr' should be attached to the standardized vector, similar to how the R default function 'scale' conserves the centering and scaling values</dd></dl>

Arguments

Extended function for z-transformation, filling non-finite values and changes column names at will — zt

<dl>

<dt>x</dt>
<dd>A data matrix for which the columns are to be standardized</dd>


<dt>fillfinite</dt>
<dd>The value to fill non-finite values with, by default zero.</dd>


<dt>addz</dt>
<dd>Boolean indicating whether letter 'z' should be appended to the variable names to indicate the standardization</dd>


<dt>saveattr</dt>
<dd>Boolean for if an 'attr' should be attached to the standardized vector, similar to how the R default function 'scale' conserves the centering and scaling values</dd>

</dl>

zt: Extended function for z-transformation, filling non-finite values and changes column names at will

Description

Usage

Value

Arguments

Examples