Package 'survivalVignettes'

Survival Analysis Vignettes and Optional Datasets

Description

Vignettes for the 'survival' package. Split from the 'survival' package since the vignettes were getting large. Also, since 'survival' is a recommended package it cannot make use of other packages outside of base+recommended (e.g. 'rmarkdown').

Author(s)

Terry M Therneau [aut], Elizabeth Atkinson [cre, ctb], Cynthia Crowson [ctb]

Maintainer: Elizabeth Atkinson <[email protected]>

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Survival with amyloidosis

Description

This pair of datasets is used in the external validation vignette. The amyloidmodel dataset contains survival curves from four studies, the amyloid data survival times and risk scores for 1005 subjects.

Usage

amloid
amyloidmodel

Format

A data frame with 1005 observations on the following 8 variables.

age

age in years

month

survival time in months

status

0= censored, 1= death

number.organs

number of involved organ systems

r2004

patient stage based on the 2004 model

r2012

patient stage based on the 2012 model

r2013

patient stage based on the 2013 model

r2015

patient stage based on the 2015 model

year

diagnosis year

A data frame with 832 observations on the following 4 variables.

study

which study: 2004, 2012, 2013 or 2015

stage

disease stage

month

months from study entry

survival

predicted survival

The model assement is found in Muchtar (2019), and used as an example in a package vignette. Patients with biopsy proven systemic light chain (AL) amyloidosis seen at the Mayo Clinic from 2003-01-01 to 31-08-2015 were screened for the study. The final study cohort includes all those without prior chemotherapy and with the necessary baseline data to assign patient stage, using each of the four systems.

The survival curves from the staging systems were (impefectly) digitized from the relevant papers. The 2013 publication is from a trial involving only stage 2 subjects and divided them as IIIa, IIIb and IIIc (stage 2-4 in our notation). The 2015 paper is also from a clinical trial and has 0/30 deaths in the stage 0 subjects. They label the stages as I, II, IIIa and IIIb where we have used 0-3 for consistency with the original 2004 system. E Muchtar, T Therneau, D Larson, M Gertz, M Lacy, F buadi, D Dingli, S Hayman, P Kapoor, W Gonsalves, T Kourelis, R Warsame, A Fonder, M Hobbs, Y Hwa, N Leung, S Russell, J Lust, Y Lin, R Go, S Zelderust, R Kyle, S V Rajkumar, S K Kumar, A Dispezieri. Comparitive analysis of staging systems in AL amyloidosis. Leukemia (2019) 33:811-814. doi:10.1038/s41375-018-0370-z

A Dispenzieri 2004, doi:10.1200/JCO.2004.03.029 S Kumar 2012, doi:10.1200/JCO.2011.38.5724 A Wechalekar 2013, doi:10.1182/blood-2012-12-473066 M Palladini 2015, doi: 10.1182/blood-2015-01-620302 sfit <- survfit(Surv(months, status) ~ r2012, amyloid) plot(sfit, lty=1:4, col=1:4, lwd=2, log=TRUE, xlab="Months from diagnosis", ylab="Survival") datasets

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