version 1.2.1

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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: CryptRndTest
 Type: Package
 Title: Statistical Tests for Cryptographic Randomness
-Version: 1.1.5
-Date: 2015-09-01
+Version: 1.2.1
+Date: 2015-12-24
 Author: Haydar Demirhan 
 Maintainer: Haydar Demirhan <haydarde@hacettepe.edu.tr>
-Description: Performs cryptographic randomness tests on a sequence of random integers or bits. Most of the included tests are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests. Additionally, it includes functions for the calculation of greatest common divisor, the Stirling numbers of the second kind, critical value of the topological binary test, and base conversions from base 2 to 10 and vice versa.
+Description: Performs cryptographic randomness tests on a sequence of random integers or bits. Included tests are greatest common divisor, birthday spacings, book stack, adaptive chi-square, topological binary, and three random walk tests. Tests except greatest common divisor and birthday spacings are not covered by standard test suites. In addition to the chi-square goodness-of-fit test, results of Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera tests are also generated by some of the cryptographic randomness tests.
 Depends: MissMech, kSamples, sfsmisc, Rmpfr, parallel
 Imports: LambertW, gmp, tseries, methods
 License: GPL-3
 NeedsCompilation: no
-Packaged: 2015-09-01 09:14:41 UTC; 114F249_Nihan
+Packaged: 2016-01-04 14:02:49 UTC; Stat
 Repository: CRAN
-Date/Publication: 2015-09-01 17:39:23
+Date/Publication: 2016-01-04 15:28:45
diff --git a/MD5 b/MD5
@@ -1,37 +1,51 @@
-5c65d88be15ddafb4e9ae2af173cfd91 *DESCRIPTION
-b6c7f28a9724b837801d87eb0a3fb5c0 *NAMESPACE
-6225a0183f2419adc72ff8f788ff2835 *R/CryptRndTest-internal.R
+89ff16fe4b2d24a05939a1041d6e21b6 *DESCRIPTION
+0963ce0eccb698dace2a13f4c2374f5f *NAMESPACE
 a932de32fc9531dc82b578764ed2a871 *R/GCD.R
 1b7c36ec62dbbabfecd8a2f51a23ac7b *R/GCD.big.R
 991a5fdabd63162144bf066ae0239952 *R/GCD.q.R
-f801c358709129a4bbd7d2d833f9c93a *R/GCD.test.R
+3ae5da7ed136aac85a8518f33f23a372 *R/GCD.test.R
+a9c19cd33bb198ae37669ed3d8a44bbb *R/GCD.test.default.R
+39ca022cbc9abbd5e6b125cb5f31e925 *R/GCD.test.main.R
 1d0b330f6fbf6df7cede853d1654702d *R/KSADCHRY.R
 4b1f39183e0f932064e57c0e776e5489 *R/KSADdga.R
 674b384db89264e1cd498000c1bf4cac *R/Random.walk.D.R
-4744acec9b67818f76ffa56b72d98d67 *R/Random.walk.G.R
+49b1ffdad04d96463b6e7fbdd2e509ae *R/Random.walk.G.R
 44c5acbbf64b2ce7a6185ea1cfde1b75 *R/Random.walk.Y.R
 c0e1d7d5b2e99f12381baff7bcc83557 *R/Strlng2.R
 b146cdcc7754738270f83214953c81b2 *R/TBT.criticalValue.R
-9a4f919dd36740d9c1b0bc1987435b94 *R/adaptive.chi.square.R
-f3dd9aec704b86a34271350017b1863e *R/birthday.spacings.R
-8a60af1f95810f0490df2a3d46ba78d6 *R/book.stack.R
-a9608f0bbc95ddca7bd716f63e3d6704 *R/dogumGunuAraliklari.R
-4ea3016f4cab1d61fb7ee837b9369f6c *R/random.walk.tests.R
+27ab4c3a917cd0bae30f7f6f7a0e19b8 *R/adaptive.chi.square.R
+4c6d3f2a968d8da73e15ee1f39816452 *R/adaptive.chi.square.default.R
+73d0184dd76ae4ef9e6dff29ab5f2497 *R/adaptive.chi.square.main.R
+f26b10871afe4a43a5bbfe9ae287bb94 *R/birthday.spacings.R
+77cfb3f086ee6c74da489d667d030f12 *R/birthday.spacings.default.R
+6b07f97a62a977bcf86fdab38e2b8e1d *R/birthday.spacings.main.R
+7b18a6290a22288cfe9694d65744db86 *R/book.stack.R
+5597e999245639ac80823c6cacfcecdc *R/book.stack.default.R
+bfbc1d56f97ceb05808651095f9b8874 *R/book.stack.main.R
+5f4bd284f4e8ca31298533ea5cfb95cb *R/check.R
+b1fbe8fbf7a8d1430168769b8abe4df2 *R/dogumGunuAraliklari.R
+544138ab7e3960a5b8081b51d6c264ee *R/print.CryptRndTest.R
+51438bc546b86700112474a1f871f36b *R/random.walk.tests.R
+a20eb094a838f5e93b4c295bb6501060 *R/random.walk.tests.default.R
+d4d7cf67230cf1eeaf304922e40e53d4 *R/random.walk.tests.main.R
 0c5b628c60a42b21e695e92bda4467f5 *R/toBaseTen.R
 2bb031d6101c523751cd573730231ff5 *R/toBaseTwo.R
-330c965d7d7ccfab85d791687bc74c98 *R/topological.binary.R
-c378b15518874d3bb760fe9b3e56168c *man/CryptRndTest-internal.Rd
-3475becdda643b5cb2a7954aa27e756b *man/CryptRndTest-package.Rd
+a32856d16ca0bc9115ff315de240a8b0 *R/topological.binary.R
+e2c3869bc7ac9778cc91f540ca626a02 *R/topological.binary.default.R
+eeff0d1eb017d5816107be7adb6fa1e6 *R/topological.binary.main.R
+9b78c028ccdde86a855a1044e308045d *man/CryptRndTest-internal.Rd
+8417e8482197942e52749537d0abb273 *man/CryptRndTest-package.Rd
 46426b0a1c9aa431340b333f7a425b58 *man/GCD.Rd
 1dd353fe833e9128ba46aa48971c781c *man/GCD.big.Rd
 1349f0f5ed2ad37201f883d75b3c06d0 *man/GCD.q.Rd
-7d20cca810e0bf0301c902aef53c193b *man/GCD.test.Rd
+475c50f123690dcdfe555ad3a94b8c31 *man/GCD.test.Rd
 2bcf2f6e1c7162ba0d259aad3a323485 *man/Strlng2.Rd
 31ed38336ca337fbe27ed32e5ea318c5 *man/TBT.criticalValue.Rd
-19f1c9b686b930835094f349eba8bd4a *man/adaptive.chi.square.Rd
-55ba059b1f66cb2b5015edf64666a991 *man/birthday.spacings.Rd
-09d7621ab337045ec08f3924573c9b24 *man/book.stack.Rd
-af675753f6b7b09c91db40e5975e3c28 *man/random.walk.tests.Rd
+50dd11664dbc804c6ed8ccdce4aa7a2a *man/adaptive.chi.square.Rd
+ed00fe05150d9001fcbb4f69ff04419b *man/birthday.spacings.Rd
+0babf1004e341378ce5e6b3746d2201f *man/book.stack.Rd
+060765a6f1e7ffcf9dd75cdd158f2f06 *man/print.CryptRndTest.Rd
+000f0562fdf36ef9dd71a86fda1cabd3 *man/random.walk.tests.Rd
 0f3a9dc2818890821b8f6c0ff1a1062d *man/toBaseTen.Rd
 cdd3c1619aeec3a159da599e83cc4008 *man/toBaseTwo.Rd
-84fb73bbe16f992208e5da0f71a07917 *man/topological.binary.Rd
+f8273920ea3772dd41a149405b8315e7 *man/topological.binary.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,17 +1,57 @@
-exportPattern("^[[:alpha:]]+")
+exportPattern("^[[:alpha:]]+")
+
 importFrom(sfsmisc,digitsBase)
+
 importFrom(tseries,jarque.bera.test)
-importFrom(kSamples,ad.test)
+
+importFrom(kSamples,ad.test)
+
 importFrom(MissMech,AndersonDarling)
+
 importFrom(LambertW,W)
+
 importFrom(gmp,Stirling2)
-importFrom(Rmpfr,mpfr)
+
+importFrom(Rmpfr,mpfr)
+
 importFrom(Rmpfr,mpfrArray)
+
 importFrom(parallel,makePSOCKcluster)
+
 importFrom(parallel,setDefaultCluster)
 importFrom(parallel,clusterExport)
+
 importFrom(parallel,parLapply)
+
 importFrom(parallel,stopCluster)
+
 importFrom("stats", "chisq.test", "dpois", "ks.test", "pchisq","rnorm", "runif")
+
 importFrom("methods", "new")
+
 importFrom("utils", "write.table")
+
+S3method(adaptive.chi.square,default)
+
+S3method(birthday.spacings,default)
+
+S3method(book.stack,default)
+
+S3method(GCD.test,default)
+
+S3method(random.walk.tests,default)
+S3method(topological.binary,default)
+
+
+S3method(adaptive.chi.square,main)
+
+S3method(birthday.spacings,main)
+
+S3method(book.stack,main)
+
+S3method(GCD.test,main)
+
+S3method(random.walk.tests,main)
+S3method(topological.binary,main)
+
+S3method(print,CryptRndTest)
diff --git a/R/CryptRndTest-internal.R b/R/CryptRndTest-internal.R
diff --git a/R/GCD.test.R b/R/GCD.test.R
@@ -1,144 +1 @@
-GCD.test=function(x,B=32,KS=TRUE,CSQ=TRUE,AD=TRUE,JB=TRUE,test.k=TRUE,test.g=TRUE,mu,sd,alpha=0.05){
-    if (sum(x==0)>0){
-        stop("Input includes invalid value: 0.")
-    }
-    num=as.matrix(x)
-    N=nrow(num)
-    y=0
-    z=0
-    y2=0
-    oklit=0
-    sig.value.k=array(NA,dim=4)
-    sig.value.g=array(NA,dim=2)
-
-    if (B<=64){
-        for (i in 1:N){
-            oklit=GCD.q(num[i,1],num[i,2])
-            y[i]=oklit$k
-            if (oklit$g<3) {
-                y2[i]=3
-            }else if (oklit$g>35){
-                y2[i]=35
-            }else{
-                y2[i]=as.numeric(oklit$g)
-            }
-        }
-    }else {
-        for (i in 1:N){
-            y[i]=GCD(num[i,1],num[i,2])$k  #uses recursive algo
-            #tests for g will not be applied for 128 bit numbers         
-        }
-
-    }
-  if (test.k==TRUE){
-    teorik.Normal=round(rnorm(N,mu,sd))
-    if (KS==TRUE){
-      sig.value.k[1]=ks.test(y,teorik.Normal,alternative = "two.sided")$p.value
-      if (sig.value.k[1]<alpha){
-        KS.result.k=0
-      }else {
-        KS.result.k=1
-      }
-    }
-    if (CSQ==TRUE){
-      nbin=min(length(tabulate(teorik.Normal)),length(tabulate(y)))
-      gozl=tabulate(y,nbins=nbin)
-      bekl=tabulate(teorik.Normal,nbins=nbin)
-      gozl[which(gozl==0)]=10^-5
-      bekl[which(bekl==0)]=10^-5
-      testCSQ.p.value=pchisq(sum((gozl-bekl)^2/bekl), df=nbin-1, ncp = 0, lower.tail = FALSE, log.p = FALSE)       
-      sig.value.k[2]=testCSQ.p.value
-      if (sig.value.k[2]<alpha){
-        CSQ.result.k=0
-      }else {
-        CSQ.result.k=1
-      }
-    }
-    if (JB==TRUE){
-      testJB=  jarque.bera.test(as.matrix((y-mean(y))/sd(y)))
-      sig.value.k[3]=testJB$p.value
-      if (sig.value.k[3]<alpha){
-        JB.result.k=0
-      }else {
-        JB.result.k=1
-      }
-    }
-    if (AD==TRUE){
-      if (N>=10000){
-        testAD=kSamples::ad.test(list(y[1:5000],teorik.Normal[1:5000]),method="asymptotic",dist=FALSE,Nsim=500)      
-      }else{
-        testAD=kSamples::ad.test(list(y[1:(N/2)],teorik.Normal[1:(N/2)]),method="asymptotic",dist=FALSE,Nsim=500)      
-      }
-      sig.value.k[4]=testAD$ad[1,3]
-      if (sig.value.k[4]<alpha){
-        AD.result.k=0
-      }else {
-        AD.result.k=1
-      }
-    }
-  }
-
-  if (test.g==TRUE){
-    kuramsalDF=0
-    teo=0
-    teorik=0
-    rasgele=runif(N,0,1)
-    bsl=1
-    i=0
-    while ((sum(teo)<N)){
-      i=i+1      
-      kuramsalDF[i]=0
-      j=1:i
-      kuramsalDF[i]=sum(6/((pi*j)^2))
-      if (kuramsalDF[i]==0){
-        kuramsalDF[i]=1
-      }
-      if (i==1){
-        teo[i]=sum(rasgele<=kuramsalDF[i])
-        teorik[bsl:(bsl+teo[i]-1)]=3
-        bsl=bsl+teo[i]
-      }else{
-        teo[i]=sum(rasgele<=kuramsalDF[i])-sum(teo[1:i-1])
-        if (i>35){         
-          teorik[bsl:N]=35
-          teo[i]=N+1
-        }else if(i<3){          
-          teorik[bsl:(bsl+teo[i]-1)]=3   
-          bsl=bsl+teo[i]
-        }else{         
-          teorik[bsl:(bsl+teo[i]-1)]=i
-          bsl=bsl+teo[i]
-        }       
-      } 
-    }
-
-    if (KS==TRUE){      
-      sig.value.g[1]=ks.test(y2,teorik,alternative = "two.sided")$p.value
-      if (sig.value.g[1]<alpha){
-        KS.result.g=0
-      }else {
-        KS.result.g=1
-      }
-    }
-    if (CSQ==TRUE){
-      test2=chisq.test(y2, teorik, correct = FALSE)
-      sig.value.g[2]=test2$p.value
-      if (sig.value.g[2]<alpha){
-        CSQ.result.g=0
-      }else {
-        CSQ.result.g=1
-      }
-    }
-  }
-
-  if ((test.g==TRUE) & (test.k==TRUE)) {
-    result=list(sig.value.k=sig.value.k,sig.value.g=sig.value.g,KS.result.k=KS.result.k,CSQ.result.k=CSQ.result.k,
-                AD.result.k=AD.result.k,JB.result.k=JB.result.k,KS.result.g=KS.result.g,CSQ.result.g=CSQ.result.g)
-  }else if ((test.g==TRUE) & (test.k==FALSE)) {
-    result=list(sig.value.g=sig.value.g,KS.result.g=KS.result.g,CSQ.result.g=CSQ.result.g)
-  }else if ((test.g==FALSE) & (test.k==TRUE)) {
-    result=list(sig.value.k=sig.value.k,KS.result.k=KS.result.k,CSQ.result.k=CSQ.result.k,AD.result.k=AD.result.k,
-                JB.result.k=JB.result.k)
-  }
-  return(result)
-}
+GCD.test=function(x,B=32,KS=TRUE,CSQ=TRUE,AD=TRUE,JB=TRUE,test.k=TRUE,test.g=TRUE,mu,sd,alpha=0.05) UseMethod("GCD.test")
diff --git a/R/GCD.test.default.R b/R/GCD.test.default.R
@@ -0,0 +1,9 @@
+GCD.test.default=function(x,B=32,KS=TRUE,CSQ=TRUE,AD=TRUE,JB=TRUE,test.k=TRUE,test.g=TRUE,mu,sd,alpha=0.05){
+  options(warn=-1)
+  check(test=4,x=x,B=B,alpha=alpha,KS=KS,CSQ=CSQ,AD=AD,JB=JB,test.k=test.k,test.g=test.g,mu=mu,sd=sd)
+
+  res.tbl=GCD.test.main(x=x,B=B,KS=KS,CSQ=CSQ,AD=AD,JB=JB,test.k=test.k,test.g=test.g,mu=mu,sd=sd,alpha=alpha)
+  res.tbl$call = match.call()
+  class(res.tbl) = c("GCD.test","CryptRndTest")
+  res.tbl
+}