version 0.2.1

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: ibdreg
-Version: 0.1.3
-Date: 2010-2
+Version: 0.2.1
+Date: 2012-11-16
 Title: Regression Methods for IBD Linkage With Covariates
 Author: Jason P. Sinnwell and Daniel J. Schaid
-Maintainer: Jason P. Sinnwell <sinnwell@mayo.edu>
+Maintainer: Jason P. Sinnwell <Sinnwell.Jason@mayo.edu>
 Description: A method to test genetic linkage with covariates by
         regression methods with response IBD sharing for relative
         pairs.  Account for correlations of IBD statistics and
         covariates for relative pairs within the same pedigree.
 License: GPL-2 | file LICENSE
-Depends: R (>= 2.6.1)
+Depends: R (>= 2.14.0)
 URL: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
-Packaged: 2012-10-29 08:59:00 UTC; ripley
+Packaged: 2012-11-16 12:35:23 UTC; sinnwell
 Repository: CRAN
-Date/Publication: 2012-10-29 08:59:00
+Date/Publication: 2012-11-16 14:02:27

MD5

@@ -1,22 +1,21 @@
-6cde07c1734dbc9e2e908db89f902574 *DESCRIPTION
-a0d48861bf3b074162e78ef1ddb3fe16 *INDEX
+0c726e5e32a24cece605dd9c95b05712 *DESCRIPTION
 27bf59c2a37bff07a78c9730061e532b *LICENSE
-9fdfeb11f7ddba6f3aab9aaa6b1ac5dd *NAMESPACE
+6a1d7de4f64a74e51469d619b05e30bc *NAMESPACE
 3c3314613f983d73f7a4e47e79fd51ca *R/Ginv.R
 da00d790b86e88df9a7441c2fd0186bd *R/align.ibd.var.q
 3ba56b64c55320241d1bd370716152c7 *R/chibar3.w.q
-d8942d337cc70fbd1755e5e2379a1431 *R/create.ibd.dat.q
+9cb27ea687f6acf0cd2db4e1dad8881e *R/create.ibd.dat.q
 7857ef210b764d1f08c96b5494ce3b83 *R/create.pairs.frame.cvec.q
-e2907620cf3c619f0fbf260a3df3a04a *R/create.pairs.frame.q
-8d013c5d11a24a9260c0670b610a9b99 *R/exact.ibd.var.q
-2e2bc00e5db9763c0e38faa8ac941049 *R/ibd.df.merlin.q
+3d27060f9fb360088bcde3f0b222d312 *R/create.pairs.frame.q
+e4afcf095b0b01fddb493cd8bf084a30 *R/exact.ibd.var.q
+bb31c0158c648095b7134d4244ac7bc7 *R/ibd.df.merlin.q
 15ea877d29d5723e8cffd68ee9520b47 *R/ibd.moments.q
-f5d58c10f8e88a034f0b90c09cce7e4d *R/ibdreg.q
+e96ec47a2b995afa3aaa6e5e6f6f2478 *R/ibdreg.q
 501772a7a6c5d188ca98c30f3a5918f7 *R/linkage.all.pedloop.q
-7e897dff7f8dd46aed5acc1323e733c3 *R/linkage.all.q
+d4eb2ab74ad83293198b6784e84ec353 *R/linkage.all.q
 ef89bac3f798e1cf6aa8fcf541b9264b *R/linkage.tests.B0.q
 2423658836319474a1dfb213d31d9fce *R/linkage.tests.pedloop.q
-ae8e77b95b660afb6a3f32f307323210 *R/linkage.tests.q
+25d21166e8f6f20379234e229f6a4014 *R/linkage.tests.q
 38c6479f9b432fb53a8cf33c670daf9f *R/lsConstrain.fit.q
 61d5037e10e654661266605fadfe15d9 *R/mergeIBD.q
 b58ae1e1636a1fdca01e1f25cb59ad9e *R/minpRows.q
@@ -28,21 +27,18 @@ da7c06a8320b5845933e18d76e824a60 *R/plot.ibdreg.unexpect.q
 344a01d0f9bc3f46ef49b524db8f6bcb *R/plot.linkage.all.q
 acc700e0660fb7663b49cc6234f27b99 *R/plot.linkage.tests.q
 2bcf46290e6ed1348009e413891517d4 *R/plotpval.q
-4315e9f4d44432122758303cc62618f3 *R/print.ibd.var.q
+70bf08375800a91ea7ba937e9166dc1c *R/print.ibd.var.q
 e55e09fb4e4b5ccb8f2931fbd85fc485 *R/print.ibdreg.q
-40789e9f58a8e01905cf21a136a278dd *R/print.linkage.all.q
-f366b4f6e7f401a4315c66baba5d25e6 *R/print.linkage.tests.q
+8e172c0e2d0ee3d4a8dedea462d1306e *R/print.linkage.all.q
+087ed7433315a6c7000c452697fbc4fe *R/print.linkage.tests.q
 ac041fc616815527ef260c22d8cdd77a *R/printBanner.q
-c0c9d01cfb1e468f0ff069bc05822c51 *R/resources.q
-a8efdb3e48a86dc555750a7b60c1d93f *R/setFounderAlleles.q
+033dc9145bafbe2d1cf690c04e40ccf8 *R/resources.q
+f9e43bc844bce718e16b3e6e293e7a85 *R/setFounderAlleles.q
 447b635fa0ca8b7066a0f4862cade7a1 *R/sim.ibd.setup.q
-d6cd5561d69bb5e80aa5ac019f394e75 *R/sim.ibd.var.q
+88d503e80aaa027a81f6bcca016953f0 *R/sim.ibd.var.q
 7ed5f7e847b363ffef7e999f9b03ab21 *R/sim.mark.prop.q
-ec3faa0324135b3790f3266c57696a46 *R/sr.class.q
-518f9fe65b0c8f5805980da5b2f309f6 *R/sr.strsplit.q
-2bcb527ddf69e8140d355079fc482e20 *R/zzz.ibdreg.q
-c33dae15f90affda6d4fa5b2d1826e17 *README.ibdreg
-7907f8125dc4703149930d82d78123b8 *TODO
+22703b57b4838ae561e8a33f09f35c06 *R/zzz.ibdreg.q
+5999a3cb4c109c28cc39aba504ef087a *inst/NEWS.Rd
 d368405f1c604912f51ba286eed9944a *inst/doc/GPL.txt
 a76a669bd962800e876c2e6d9d2696ea *inst/doc/manualIBDReg.pdf
 64f1b79f244ceabc71c0e7ea8ddc1a58 *man/Ginv.Rd
@@ -71,16 +67,14 @@ bd2f1a09a17d8062d4d33af0fe711b91 *man/print.ibd.var.Rd
 5783397a0f5a93b907356f3c5cf36201 *man/print.linkage.all.Rd
 582502293b925ddcda1ff118279cd468 *man/print.linkage.tests.Rd
 762376e04f9645efe153085ff92fdca2 *man/printBanner.Rd
-88201552520e8a57a55999818eeed8cf *man/resources.Rd
+bd1064ab77455c4db2cc517c0939522d *man/resources.Rd
 cd4a6e156ad0f1de5b9dee18c8af9ee2 *man/sim.ibd.setup.Rd
 e9e10b596013816b4a50beeefa5ff5e8 *man/sim.ibd.var.Rd
 56d07f3ad9716f327843e77fd1262a17 *man/sim.mark.prop.Rd
-7d157863eaaf5a5c3f39cbad017fee2a *man/sr.class.Rd
-2a333bf53903eb1a49d48d8dbe5c2bd2 *man/sr.strsplit.Rd
 8d19e38856d01ad19787c321e8cc5756 *perl/exact.ibd.var.pl
 a31859e2d359ec4aaa7fbbe4958be65c *perl/gws.merlin.ibd.pl
 f3e6a55d104c21d753f1d26f908c099e *perl/merlin.post.ibd.pl
 1b2fd16a99e3a0bcf0ced3b6b8ef9809 *perl/merlin.prior.ibd.pl
 253cdd482b07d5e640b59364a304b9c0 *src/lsConstrain.c
 ed1cacad8ae54f70022e0bb89386b8cb *src/mcmemory.h
-7374e106dddcacef3e91379d627e12b9 *src/sim.mark.prop.c
+e9fcdae4746f5aa441276588921aa17c *src/sim.mark.prop.c

NAMESPACE

@@ -1,5 +1,39 @@
-# Default NAMESPACE created by R
-# Remove the previous line if you edit this file
+useDynLib(ibdreg)
+export(align.ibd.var,
+create.ibd.dat,
+create.pairs.frame,
+exact.ibd.var,
+Ginv,
+ibd.df.merlin,
+ibd.moments,
+ibdreg,
+linkage.all,
+linkage.tests,
+lsConstrain.fit,
+mergeIBD,
+minpRows,
+pairSum, pairDiff,
+pchibar, chibar3.w,
+plot.ibdreg,
+plot.ibdreg.unexpect,
+plot.linkage.all,
+plot.linkage.tests,
+plotpval,
+printBanner,
+print.ibdreg,
+print.ibd.var,
+print.linkage.all,
+print.linkage.tests,
+resources,
+sim.ibd.setup,
+sim.ibd.var,
+sim.mark.prop)
 
-# Export all names
-exportPattern(".")
+S3method(print, ibdreg)
+S3method(plot, ibdreg)
+S3method(plot, linkage.all)
+S3method(print, linkage.all)
+S3method(plot, linkage.tests)
+S3method(print, linkage.tests)
+S3method(plot, ibdreg.unexpect)
+S3method(print, ibd.var)

R/create.ibd.dat.q

@@ -182,7 +182,7 @@ create.ibd.dat <- function(postfile,          # ibd file with all loci, all alle
   }
 
 
-  sr.class(ibd.df) <- c("ibd.dat" , "data.frame")
+  class(ibd.df) <- c("ibd.dat" , "data.frame")
 
   ibd.df
 

R/create.pairs.frame.q

@@ -100,7 +100,7 @@ create.pairs.frame <- function(ibd.dat,
     for(term in formula.terms) {
 
       # split up the term by an open paren '(', use S::unpaste R::strsplit
-      split.term <- sr.strsplit(term, sep='(')
+      split.term <- strsplit(term, split='(')
 
       # extract the function name to apply to the covariate pair
       fname <- split.term[[1]][1]

R/exact.ibd.var.q

@@ -64,7 +64,7 @@ exact.ibd.var <- function(file){
     list.index <- list.index+1
   }
 
-  sr.class(var.lst) <- c("ibd.var", "list")
+  class(var.lst) <- c("ibd.var", "list")
   return(var.lst)
 
 }

R/ibd.df.merlin.q

@@ -89,7 +89,7 @@ ibd.df.merlin <- function(ibd.dat){
 
 
 # data.frame methods need to work on ibd.df
- # sr.class(dat) <- c("ibd.df", "data.frame")
+ # class(dat) <- c("ibd.df", "data.frame")
 
   return(dat)
 

R/ibdreg.q

@@ -73,10 +73,10 @@ ibdreg <- function(formula,
 # CHECK INPUT PARAMETERS
 #--------------------------------------------------------- 
   # check classes of ibd.var and ibd.dat objects
-  if(!sr.class(ibd.var)[1]=='ibd.var')
+  if(!class(ibd.var)[1]=='ibd.var')
     stop(paste(deparse(substitute(ibd.var)), " must be an object with class ibd.var"))
 
-  if(!sr.class(ibd.dat)[1]=='ibd.dat')
+  if(!class(ibd.dat)[1]=='ibd.dat')
     stop("ibd.dat must be an object with class ibd.dat")
     ibd.dat.names <-  c("ped.id", "person1.id", "person2.id",
                             "post0", "post1", "post2", "prior0", "prior1", "prior2")
@@ -270,7 +270,7 @@ ibdreg <- function(formula,
                      AU.linkage=AU.linkage,
                      ALL.linkage=ALL.linkage)
 
-  sr.class(ibdreg.obj) <- c("ibdreg", "list")
+  class(ibdreg.obj) <- c("ibdreg", "list")
 
   return(ibdreg.obj)
 

R/linkage.all.q

@@ -116,7 +116,7 @@ linkage.all <- function(
                 dof3=rep(3,npos), pval.all=pval.all)
               )
 
-  sr.class(obj) <- "linkage.all"
+  class(obj) <- "linkage.all"
 
   return(obj)
 

R/linkage.tests.q

@@ -207,7 +207,7 @@ linkage.tests <- function(
   }
 
 
-  sr.class(obj) <- c("linkage.tests", "list")
+  class(obj) <- c("linkage.tests", "list")
 
   return(obj)
 

R/print.ibd.var.q

@@ -24,7 +24,7 @@ print.ibd.var <- function(x,
                           ...) {
 
   # check ibd.var class
-  if(!match("ibd.var", sr.class(x))) stop("Not an ibd.var object\n")
+  if(!match("ibd.var", class(x))) stop("Not an ibd.var object\n")
 
 
   ##-- if ped.id is NULL and sinkfile is NULL, don't print anything--TOO BIG
@@ -51,7 +51,7 @@ print.ibd.var <- function(x,
     }
 
     cat(paste("Sinking all pedigree ibd.var data to file", sinkfile, "...\n"))
-    sr.class(x) <- "list"
+    class(x) <- "list"
     sink(sinkfile)
     print(x, digits=digits)
     sink()

R/print.linkage.all.q

@@ -20,7 +20,7 @@ print.linkage.all <- function(x,
                               digits=max(options()$digits - 2, 5),
                               ...) {
 
-  if(sr.class(x)[1] != "linkage.all") stop("x must be a linkage.all object")
+  if(class(x)[1] != "linkage.all") stop("x must be a linkage.all object")
   test.df.names <-  c("pos(cM)", "Score Test", "d.f.", "pvalue")
   all.frame <- minpRows(obj=data.frame(x$all.frame[,1:2],
                           apply(x$all.frame[,3:6], 1, paste, collapse=":"),

R/print.linkage.tests.q

@@ -39,7 +39,7 @@ print.linkage.tests <- function(x, digits = max(options()$digits - 2, 5), show.m
   # Tests include linkage-only
   # and additional tests with covariates if x$ncov > 1
 
-  if(sr.class(x)[1] != "linkage.tests") stop("x must be a linkage.tests object")
+  if(class(x)[1] != "linkage.tests") stop("x must be a linkage.tests object")
 
   index <- 1:nrow(x$linkage.frame)
 

R/resources.q

@@ -1,4 +1,4 @@
-## $Id: resources.q,v 1.3 2008/10/15 19:57:55 sinnwell Exp $
+## $Id: resources.q,v 1.1.1.1 2011/02/24 14:16:27 sinnwell Exp $
 ##
 
 ## S: Beth Atkinson and SR: Jason Sinnwell
@@ -15,7 +15,7 @@
 #  mat <- 2*mat
 #})
 
-resources <- function(expr) {
+resources <- function(expr, doPrint=TRUE) {
 
 # Returns and prints the following information for the current S-PLUS session.
 # Note: All times are expressed in units of seconds.
@@ -34,37 +34,31 @@ resources <- function(expr) {
   on.exit(cat("Timing stopped at:", proc.time() - time, "\n"))
   expr <- substitute(expr)
   stime <- proc.time()
-  if(is.R()) {
-    mem1 <- gc(reset=TRUE)
-    w <- eval(expr, envir=loc)
-  } else {
-    mem.tally.reset()
-    w <- eval(expr, local=loc)
-  }
 
+  mem1 <- gc(reset=TRUE)
+  w <- eval(expr, envir=loc)
+
   etime <- proc.time()
 
-  if(is.R()) {
-    mem2=gc(reset=TRUE)
-    mem <- data.frame(mem2[2,1]-mem1[2,1])
-    names(mem) <- "Vcells"
-
-  } else {
-    mem <- data.frame(mem.tally.report()[2])
-    names(mem) <- "Working"
-  }
+  mem2=gc(reset=TRUE)
+  mem <- data.frame(mem2[2,1]-mem1[2,1])
+  names(mem) <- "Vcells"
+
 
   on.exit()
 
   if(length(stime)==3) stime <- c(stime,0,0)
   if(length(etime)==3) etime <- c(etime,0,0)
   time <- etime-stime
   time[3] <- max(time[3], time[1] + time[2])
-  print(data.frame(CPU = time[1] + time[2],
+  df <- data.frame(CPU = time[1] + time[2],
           Elapsed=time[3],
           CPU.pct=round((100*(time[1]+time[2]))/time[3],4),
           Child=time[4]+time[5],
-          mem))
-  invisible(w)
-
+          mem)
+  if(doPrint) {
+    print(df)
+  }
+  invisible(df)
+
 }

R/setFounderAlleles.q

@@ -58,12 +58,12 @@ setFounderAlleles <- function(ped, x.linked=FALSE)
 
 	chrom1[founder & male,  ] <- a1.male
         chrom1[founder & (!male), ] <- a1.female
-	sr.class(chrom1) <- "model.matrix"
+	class(chrom1) <- "model.matrix"
 
 	chrom2[founder & male,  ] <- a2.male
         chrom2[founder & (!male), ] <- a2.female
 
-	sr.class(chrom2) <- "model.matrix"
+	class(chrom2) <- "model.matrix"
 	ped <- data.frame(ped, chrom1 = chrom1, chrom2 = chrom2)
 	return(ped)
 }

R/sim.ibd.var.q

@@ -81,6 +81,6 @@ sim.ibd.var <- function(pedfile, male.code=1, female.code=2,
        save[[i]]$sv <- tmp$sv
      }   
 
-   sr.class(save) <- c("ibd.var", "list")
+   class(save) <- c("ibd.var", "list")
    return(save)
  }