| Title: | Refining Evaluation Methodology on Stage System |
| Version: | 1.0.1 |
| 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. |
| Depends: | R (≥ 3.5.0) |
| License: | GPL-2 |
| Encoding: | UTF-8 |
| LazyData: | true |
| Imports: | survival |
| RoxygenNote: | 6.1.1 |
| Suggests: | knitr, rmarkdown, testthat |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2021-01-14 03:35:22 UTC; Yi |
| Author: | Wei Xu [aut], Susie Su [aut], Yi Zhu [cre] |
| Maintainer: | Yi Zhu <yizhu87@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-01-14 06:10:02 UTC |
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.
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.
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)