Package nopaco. R topics documented: April 13, Type Package Title Non-Parametric Concordance Coefficient Version 1.0.
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1 Type Package Title Non-Parametric Concordance Coefficient Version Date Package nopaco April 13, 2017 A non-parametric test for multi-observer concordance and differences between concordances in (un)balanced data. License GPL (>= 3) Imports methods, Matrix (>= 1.1.5), parallel, stats Suggests MASS SystemRequirements C++11 RoxygenNote NeedsCompilation yes Author Rowan Kuiper [cre, aut], Remco Hoogenboezem [aut], Sjoerd Huisman [ctb], Pieter Sonneveld [ths], Mark van Duin [ths] Maintainer Rowan Kuiper <r.kuiper.emc@gmail.com> Repository CRAN Date/Publication :41:00 UTC R topics documented: coef concordance.test ConcordanceTest-class getpsi names,concordancetest-method rfrompsi scores $,ConcordanceTest-method Index 9 1
2 2 concordance.test coef Extract test results from the results of a concordance.test coef extract the test results from the results of a concordance.test ## S4 method for signature 'ConcordanceTest' coef(object,...) object An object of ConcordanceTest-class... Not used A matrix See Also Other concordance functions: concordance.test, getpsi, rfrompsi matrandom <- matrix(rnorm(3*20),20,3) testresult <- concordance.test(matrandom) getpsi(testresult) coef(testresult) concordance.test Perform a nonparametric concordance test. concordance.test performs a test for a random concordance (if a single matrix is given) or tests for equal concordance between two matrices. concordance.test(x, y = NULL, alternative = NULL, alpha = 0.05,...)
3 concordance.test 3 x y Details alternative a numeric matrix, subjects in the rows, repeated measurements in the columns (optional) a numeric matrix of equal size as argument x "less", "greater" or "two.sided". Only used when y is given. alpha significance level (default = 0.05)... see details Testing the deviation from random concordance: if only one matrix is given (i.e. argument x), its concordance will be tested for a deviation from a random concordance. The default alternative hypothesis is greater, thus higher concordance than would have been observed by chance. For small matrices (depending on number of replicate measurements) an exact method will be used to determine to p-value. In case of larger matrices either, the alternative beta approach (default), a beta approximation or a normal approximation is used. To enforce the use of either one method, the method argument can be used with value "exact","alt.beta","beta" or "normal". Testing for a difference between concordances: if both arguments x and y have been given, the equality of concordances of both matrices is tested. The default alternative hypothesis is two.sided. Both matrices must be of equal size and have corresponding missing entries. Eventual missing data in one matrix will also be set missing in the other. Unbalanced data due to randomly missing data or an unequal number of repeated measurements per subject is allowed. In that case, missing or unknown values must be set to NA. An object of ConcordanceTest-class References See Also P.Rothery (1979) Biometrika 66(3): Other concordance functions: coef, getpsi, rfrompsi require(mass) ##to use mvrnorm function #Generate a matrix without concordance matrandom <- matrix(rnorm(3*20),20,3) concordance.test(matrandom) #Generate a matrix with strong concordance sigma<-matrix(0.8,3,3) diag(sigma)<-1 matconcordant <- mvrnorm(20,mu=rep(0,3),sigma=sigma)
4 4 getpsi concordance.test(matconcordant) #Test concordances between matrices atest <- concordance.test(matconcordant, matrandom) getpsi(atest) coef(atest) ConcordanceTest-class Class ConcordanceTest This class stores results obtained from a concordance test. Details Class ConcordanceTest stores results from a concordance test. Slots pvalue The pvalue psi1 The concordance in matrix x psi2 The concordance in matrix y method The method used to obtain the pvalue alternative The alternative hypothesis ci.lower The lower confidence boudary ci.upper The upper confidence boudary ci.method The method used to obtain the confidence interval alpha The significance level call The call made to the concordance.test function getpsi Obtain concordance coefficients. getpsi returns the concordance coefficient(s) from a matrix or a result obtained by the concordance.test function.
5 getpsi 5 ## S4 method for signature 'ConcordanceTest,missing' getpsi(x) ## S4 method for signature 'matrix,missing' ## S4 method for signature 'data.frame,missing' ## S4 method for signature 'data.frame,data.frame' ## S4 method for signature 'matrix, NULL ' ## S4 method for signature 'matrix,matrix' x A numeric matrix or an object ConcordanceTest-class y A numeric matrix (optional)... Not used A numeric vector with coefficient(s) References P.Rothery (1979) Biometrika 66(3): See Also Other concordance functions: coef, concordance.test, rfrompsi matrandom <- matrix(rnorm(30),10,3) testresult <- concordance.test(matrandom) getpsi(testresult) getpsi(matrandom)
6 6 rfrompsi names,concordancetest-method Extract argument names from a ConcordanceTest object names extracts argument names from a ConcordanceTest-class object ## S4 method for signature 'ConcordanceTest' names(x) x An object of ConcordanceTest-class A character vector matrandom <- matrix(rnorm(3*20),20,3) testresult <- concordance.test(matrandom) names(testresult) rfrompsi Convertion between Pearson correlation and the non paramtric concordance coefficient Convertion between Pearson correlation and the non paramtric concordance coefficient rfrompsi(psi) psifromr(r) psi r a (vector of) non paramtric concordance coefficient(s) a (vector of) Pearson correlation coefficient(s)
7 scores 7 Details The convertion is performed following the relationship described by Rothery (1979). 2*cos(pi*(1-psi))-1 A (vector of) corresponding Pearson correlation coefficient(s). References Rothery, P. A nonparametric measure of intraclass correlation, Biometrika, 66, 3, (1979). See Also Other concordance functions: coef, concordance.test, getpsi #Generate a matrix without concordance matrandom <- matrix(rnorm(30),10,3) result<-concordance.test(matrandom) getpsi(result) #concordance coefficient result$ci #95% confidence interval #Corresonding Pearson correlation rfrompsi(getpsi(result)) rfrompsi(result$ci) #Plot the relation between Pearson correlation and the nonparamatric concordance coefficient. r<-seq(-1,1,0.01) psi<-psifromr(r) plot(r,psi,type='l',xlab="pearson correlation", ylab="nonparametric concordance") scores Hypothetical data of outcomes for two risk models This data is generated as explained in the nopaco vignette. It represents the outcomes of the risk models (model A and model B). Both models were applied to gene expression profiles 100 subjects, each run in duplo. data(scores)
8 8 $,ConcordanceTest-method Format Source A list with two elements named modela and modelb both containing a dataframe with outcome scores for 100 subjects in the rows each having two replicate measurements in the columns. vignette("nopaco", package = "nopaco") data(scores) str(scores) plot(scores[['modela']]) plot(scores[['modelb']]) $,ConcordanceTest-method Extract argument values from a ConcordanceTest object Extracts argument values from a ConcordanceTest-class object ## S4 method for signature 'ConcordanceTest' x$name x name An object of ConcordanceTest-class The argument to get the value of The value of the requested argument matrandom <- matrix(rnorm(3*20),20,3) testresult <- concordance.test(matrandom) names(testresult) testresult$psi
9 Index Topic datasets scores, 7 $,ConcordanceTest-method, 8 coef, 2, 3, 5, 7 coef,concordancetest-method (coef), 2 concordance.test, 2, 2, 4, 5, 7 ConcordanceTest-class, 4 get,concordancetest-method ($,ConcordanceTest-method), 8 getpsi, 2, 3, 4, 7 getpsi,concordancetest,missing-method (getpsi), 4 getpsi,data.frame,data.frame-method (getpsi), 4 getpsi,data.frame,missing-method (getpsi), 4 getpsi,matrix,matrix-method (getpsi), 4 getpsi,matrix,missing-method (getpsi), 4 getpsi,matrix,null-method (getpsi), 4 names,concordancetest-method, 6 nopaco (concordance.test), 2 psifromr (rfrompsi), 6 rfrompsi, 2, 3, 5, 6 scores, 7 9
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