Package 'remss'

Title: Refining Evaluation Methodology on Stage System
Description: T (extent of the primary tumor), N (absence or presence and extent of regional lymph node metastasis) and M (absence or presence of distant metastasis) are three components to describe the anatomical tumor extent. TNM stage is important in treatment decision-making and outcome predicting. The existing oropharyngeal Cancer (OPC) TNM stages have not made distinction of the two sub sites of Human papillomavirus positive (HPV+) and Human papillomavirus negative (HPV-) diseases. We developed novel criteria to assess performance of the TNM stage grouping schemes based on parametric modeling adjusting on important clinical factors. These criteria evaluate the TNM stage grouping scheme in five different measures: hazard consistency, hazard discrimination, explained variation, likelihood difference, and balance. The methods are described in Xu, W., et al. (2015) <https://www.austinpublishinggroup.com/biometrics/fulltext/biometrics-v2-id1014.php>.
Authors: Wei Xu [aut], Susie Su [aut], Yi Zhu [cre]
Maintainer: Yi Zhu <[email protected]>
License: GPL-2
Version: 1.0.1
Built: 2025-02-12 05:26:54 UTC
Source: https://github.com/cran/remss

Help Index

Balance measurement.

Description

balance_measure returns balance measurement for the grouping scheme.

Usage

balance_measure(OS_ind, stage_list, data)

Arguments

OS_ind

OS_ind is the survival indicator variable.
stage_list

stage_list original of each scheme.
data

Data set.

Value

Ranking of balance measurement and its standardized score.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biometrics and Biostatistics 2 (2015): 1014.

Explained variation measurement.

Description

explain_var_measure returns explained variation measurement for the grouping scheme.

Usage

explain_var_measure(main_list, stage_list, stage_list_2, covar_list, data)

Arguments

main_list

main_list includes survival indicator variable, Duration time of survival variable and basic group variable.
stage_list

stage_list original of each scheme.
stage_list_2

stage_list_2 is numerical form of each scheme by using other of stages information.
covar_list

Covariate variables taking into consideration.
data

Data set.

Value

Ranking of explained variation measurement and its standardized score.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biometrics and Biostatistics 2 (2015): 1014.

Hazard consistency measurement.

Description

hz_cons_measure returns Hazard consistency for the grouping scheme.

Usage

hz_cons_measure(main_list, stage_list, covar_list, data)

Arguments

main_list

main_list includes survival indicator variable, Duration time of survival variable and basic group variable.
stage_list

stage_list is numerical form of each scheme by using other of stages information.
covar_list

Covariate variables taking into consideration.
data

Data set.

Value

Ranking of hazard consistency measurement and standardized score.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biometrics and Biostatistics 2 (2015): 1014.

Hazard discrimination measurement.

Description

hz_dis_measure returns hazard discrimination for the grouping scheme.

Usage

hz_dis_measure(main_list, stage_list, stage_list2, covar_list, data)

Arguments

main_list

main_list includes survival indicator variable, Duration time of survival variable and basic group variable.
stage_list

stage_list original of each scheme.
stage_list2

stage_list2 is numerical form of each scheme by using other of stages information.
covar_list

Covariate variables taking into consideration.
data

Data set.

Value

Ranking of hazard discrimination measurement and its standardized score.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biometrics and Biostatistics 2 (2015): 1014.

Likelihood difference measurement.

Description

lik_diff_measure returns likelihood difference for the grouping scheme.

Usage

lik_diff_measure(main_list, stage_list, covar_list, data)

Arguments

main_list

main_list includes survival indicator variable, Duration time of survival variable and basic group variable.
stage_list

stage_list is numerical form of each scheme by using other of stages information.
covar_list

Covariate variables taking into consideration.
data

Data set.

Value

Ranking of likelihood difference measurement and its standardized score.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.'Austin Biometrics and Biostatistics 2 (2015): 1014.

Overall Ranking.

Description

overall_rank returns overall ranking for the grouping scheme.

Usage

overall_rank(HCM, HDM, LDM, EVM, BM, weight)

Arguments

HCM

HCM is the hazard consistency measurement results.
HDM

HDM is the hazard discrimination measurement results.
LDM

LDM is the likelihood difference measurement results.
EVM

EVM is the explained variance measurement results.
BM

BM is the balance measurement results.
weight

weight vector of five measurements.

Value

Overall score and overall ranking.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biometrics and Biostatistics 2 (2015): 1014.

Refining evaluation methodology on stage system.

Description

rank returns five measurements for the grouping scheme and its overall rank.

Usage

rank(os, ostime, groupvar, scheme, order, covariate, weight, data)

Arguments

os

Survival indicator, 1 for death, 0 for censoring.
ostime

Duration time of survival.
groupvar

Basic group variable having the most number of stages.
scheme

Different grouping scheme, which has less stages than the basic group variable.
order

The other of stages in each grouping, from
covariate

Covariate variables taking into consideration.
weight

Weight on five measurements of grouping scheme.
data

Data set.

Value

Ranking of five measurements, which are Hazard consistency, Hazard discrimination, Explained variation, Likelihood difference and Balance. By standardized each measurement score, we provides overall ranking of schemes.

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biom Biostat 2 (2015): 1014.

Examples

data(Rdata)
Scheme=c('Scheme.1','Scheme.2','Scheme.3')
Covar=c('Age','Treatment')
weight=c(1,1,0.5,0.5,1)
Order=list(c('I','II','III'),c('I','II','III','IV'),c('I','II','III','IV'))
rank(os='OS',ostime='survmonth',groupvar='Basic_group', scheme=Scheme, order=Order,
     covariate=Covar,weight=weight,data=Rdata)

Simulation data for Genetic association models for X-chromosome SNPS

Description

A simulated dataset containing 504 observations. The variables list as follows:

Usage

data(Rdata)

Format

A data frame with 504 rows and 10 variables.

Details

  • Id Identification number.

  • Gender 1 for male, 0 for female.

  • Age Age variable.

  • OS Survival indicator, 1 for death, 0 for censoring.

  • survmonth Duration time of survival.

  • Treatment Treatment variable.

  • Basic_group Basic group variable having the most number of stages.

  • Scheme.1 Grouping scheme 1.

  • Scheme.2 Grouping scheme 2.

  • Scheme.3 Grouping scheme 3.

remss: A package for refining evaluation methodology on stage system.

Description

TNM stage is important in treatment decision-making and outcome predicting. The existing oropharyngeal Cancer (OPC) TNM stages have not made distinction of the two sub sites of HPV+ and HPV- diseases.We developed novel criteria to assess performance of the TNM stage grouping schemes based on parametric modeling adjusting on important clinical factors. These criteria evaluate the TNM stage grouping scheme in five different measures: hazard consistency, hazard discrimination, explained variation, likelihood difference, and balance.

remss functions

rank

References

Xu, W., et al. 'Refining evaluation methodology on TNM stage system: assessment on HPV-related oropharyngeal cancer.' Austin Biom Biostat 2 (2015): 1014.