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reportROC - An Easy Way to Report ROC Analysis

Provides an easy way to report the results of ROC analysis, including: 1. an ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (accuracy), SEN (sensitivity), SPE (specificity), PLR (positive likelihood ratio), NLR (negative likelihood ratio), PPV (positive predictive value), NPV (negative predictive value), PPA (percentage of positive accordance), NPA (percentage of negative accordance), TPA (percentage of total accordance), KAPPA (kappa value).

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2.84 score 2 dependents 38 scripts 390 downloads

stddiff - Calculate the Standardized Difference for Numeric, Binary and Category Variables

Contains three main functions including stddiff.numeric(), stddiff.binary() and stddiff.category(). These are used to calculate the standardized difference between two groups. It is especially used to evaluate the balance between two groups before and after propensity score matching.

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2.75 score 2 dependents 24 scripts 1.3k downloads

CATT - The Cochran-Armitage Trend Test

This function conducts the Cochran-Armitage trend test to a 2 by k contingency table. It will report the test statistic (Z) and p-value.A linear trend in the frequencies will be calculated, because the weights (0,1,2) will be used by default.

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2.48 score 1 dependents 2 scripts 248 downloads

nomogramEx - Extract Equations from a Nomogram

A nomogram can not be easily applied, because it is difficult to calculate the points or even the survival probability. The package, including a function of nomogramEx(), is to extract the polynomial equations to calculate the points of each variable, and the survival probability corresponding to the total points.

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2.04 score 1 stars 11 scripts 338 downloads

FlexScan - Flexible Scan Statistics

An easy way to conduct flexible scan. Monte-Carlo method is used to test the spatial clusters given the cases, population, and shapefile. A table with formal style and a map with clusters are included in the result report. The method can be referenced at: Toshiro Tango and Kunihiko Takahashi (2005) <doi:10.1186/1476-072X-4-11>.

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2.00 score 2 scripts 266 downloads

CsChange - Testing for Change in C-Statistic

Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) <doi:10.1001/jama.2016.5951>.

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1.85 score 7 scripts 753 downloads

reportReg - An Easy Way to Report Regression Analysis

Provides an easy way to report the results of regression analysis, including: 1. Proportional hazards regression from function 'coxph' of package 'survival'; 2. Conditional logistic regression from function 'clogit' of package 'survival'; 3. Ordered logistic regression from function 'polr' of package 'MASS'; 4. Binary logistic regression from function 'glm' of package 'stats'; 5. Linear regression from function 'lm' of package 'stats'; 6. Risk regression model for survival analysis with competing risks from function 'FGR' of package 'riskRegression'; 7. Multilevel model from function 'lme' of package 'nlme'.

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1.48 score 1 scripts 177 downloads

con2aqi - Calculate the AQI from Pollutant Concentration

To calculate the AQI (Air Quality Index) from pollutant concentration data. O3, PM2.5, PM10, CO, SO2, and NO2 are available currently. The method can be referenced at Environmental Protection Agency, United States as follows: EPA (2016) <https://www3.epa.gov/airnow/aqi-technical-assistance-document-may2016.pdf>.

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1.41 score 26 scripts 132 downloads

VIMean - Variability Independent of Mean

To computed the variability independent of mean (VIM) or variation independent of mean (VIM). The methodology can be found at Peter M Rothwell et al. (2010) <doi:10.1016/S1474-4422(10)70067-3>.

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1.00 score 198 downloads

RHSDB - Ryan-Holm Step-Down Bonferroni or Sidak Procedure

The Ryan-Holm step-down Bonferroni or Sidak procedure is to control the family-wise (experiment-wise) type I error rate in the multiple comparisons. This procedure provides the adjusting p-values and adjusting CIs. The methods used in this package are referenced from John Ludbrook (2000) <doi:10.1046/j.1440-1681.2000.03223.x>.

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1.00 score 247 downloads

easyDes - An Easy Way to Descriptive Analysis

Descriptive analysis is essential for publishing medical articles. This package provides an easy way to conduct the descriptive analysis. 1. Both numeric and factor variables can be handled. For numeric variables, normality test will be applied to choose the parametric and nonparametric test. 2. Both two or more groups can be handled. For groups more than two, the post hoc test will be applied, 'Tukey' for the numeric variables and 'FDR' for the factor variables. 3. T test, ANOVA or Fisher test can be forced to apply. 4. Mean and standard deviation can be forced to display.

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1.00 score 1 scripts 237 downloads

Gini - Gini Coefficient

Providing various equations to calculate Gini coefficients. The methods used in this package can be referenced from Brown MC (1994) <doi: 10.1016/0277-9536(94)90189-9>.

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1.00 score 5 scripts 237 downloads

SEofM - Standard Error of Measurement

To calculate the standard error of measurement (SEM) to assess the observer variability (inter- and intra-observer variation). The methods used in this package are referenced from Zoran B. Popović (2017) <doi:10.21037/cdt.2017.03.12>.

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1.00 score 201 downloads

HSEtest - Homogeneity of Stratum Effects Test

To test the homogeneity of stratum effects in stratified paired binary data.

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1.00 score 118 downloads

numKM - Create a Kaplan-Meier Plot with Numbers at Risk

To add the table of numbers at risk below the Kaplan-Meier plot.

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1.00 score 1 scripts 156 downloads

gamRR - Calculate the RR for the GAM

To calculate the relative risk (RR) for the generalized additive model.

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1.00 score 10 scripts 168 downloads

DTAXG - Diagnostic Test Assessment in the Absence of Gold Standard

To calculate the sensitivity and specificity in the absence of gold standard using the Bayesian method. The Bayesian method can be referenced at Haiyan Gu and Qiguang Chen (1999) <doi:10.3969/j.issn.1002-3674.1999.04.004>.

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1.00 score 2 scripts 136 downloads

IDCard - Update Chinese ID Card Number to Eighteen Digits

The digits of the old version (before 2000 year) of 'Chinese ID Card Number' is 15, this package aims to update to the current version of 18 digits. Besides, this package can help check whether the given 'ID' is right or not.

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1.00 score 4 scripts 120 downloads

easyAHP - Analytic Hierarchy Process (AHP)

Given the scores from decision makers, the analytic hierarchy process can be conducted easily.

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1.00 score 1 scripts 141 downloads

rocNIT - Non-Inferiority Test for Paired ROC Curves

Non-inferiority test and diagnostic test are very important in clinical trails. This package is to get a p value from the non-inferiority test for ROC curves from diagnostic test.

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1.00 score 1 scripts 153 downloads