version 1.1.1

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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,19 +1,18 @@
 Package: mixexp
 Type: Package
 Title: Design and analysis of mixture experiments
-Version: 1.0-5
-Date: 2011-5-24
-Author: John Lawson <lawson@byu.edu>
+Version: 1.1.1
+Date: 2014-2-13
+Author: John Lawson <lawson@byu.edu> and Cameron Willden <ccwillden@gmail.com>, with contributions from Greg Piepel
 Maintainer: John Lawson <lawson@byu.edu>
-Description: This package contains functions for creating designs for
-        mixture experiments, making ternary contour plots, and making
-        mixture effect plots.
+Description: This package contains functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
 License: GPL-2
 Depends: gdata, lattice, grid
 LazyLoad: yes
 Repository: CRAN
 Repository/R-Forge/Project: daewr
-Repository/R-Forge/Revision: 51
-Repository/R-Forge/DateTimeStamp: 2012-09-20 21:06:17
-Date/Publication: 2012-09-22 04:52:53
-Packaged: 2012-09-20 22:19:45 UTC; rforge
+Repository/R-Forge/Revision: 75
+Repository/R-Forge/DateTimeStamp: 2014-03-26 20:51:57
+Date/Publication: 2014-03-27 15:39:47
+Packaged: 2014-03-26 23:16:13 UTC; rforge
+NeedsCompilation: yes
diff --git a/MD5 b/MD5
@@ -1,29 +1,32 @@
-a2ded1cac627c8e3b3133046c0f88e05 *DESCRIPTION
-591d5d747a2a80697ac67675135e6144 *NAMESPACE
-8566a5151df8dff7fee7650faaaf107e *R/DesignPoints.R
-84a3fc3dfbfff49a7f116b2230856ea7 *R/Effplot.R
+7a37e2ad35d717cdf35c875363999f29 *DESCRIPTION
+70f353bbcf9f063d80b8ccd215315a86 *NAMESPACE
+3ec52fe3e08a373b966eced0bbbfc92b *R/DesignPoints.R
+499449d4931740e97e004e96d4ba7762 *R/Effplot.R
 3ad3c71d8af463b0f60927c48b6e748a *R/Eflags.R
 e5923423320694b42f114b885f71a72e *R/Fillv.R
-48f799ab1362785579b52bec6df7472a *R/MixturePlot.R
+7bc2189d5de6273eb0e1d398370af7f5 *R/MixturePlot.R
+5249a4ad3378db1f384f2bd9e803b688 *R/ModelPlot.R
 7c14430661e5a923dc39735d2cfa28a6 *R/Nrows.R
 1d1e41d2404b692fcb2a12609635db5a *R/SCD.R
 85308cc0960ee332036cfdc426f161f2 *R/SLD.R
 e70968351adb60ab99a8571bb4c0a18a *R/Vertcen.R
-289636bd25e5d50e2e799a5e19c50429 *R/Xvert.R
+fef7c9f2b5b951c9cd087a7e6ead8bea *R/Xvert.R
 030481ace7350906616dd1664f94e931 *R/crvtave.R
-d41d8cd98f00b204e9800998ecf8427e *TestDocument.txt
-a94d34945550adbaf299dd7551511f26 *data/conmx.rda
-1630883d19a5f740451a348f09a1a034 *man/DesignPoints.Rd
-4b80bd7c4c827e7e4759cf8a11250d40 *man/Effplot.Rd
+75a1e03e9d65616f743212e6fe8f3058 *data/SneeMq.rda
+327018175ab5d8af478faf02b6be957e *data/conmx.rda
+690bdc5266b0bd9a5633deeb7196a285 *man/DesignPoints.Rd
+1a9750a4011da10ebb6b58ed6cccdcd0 *man/Effplot.Rd
 930d16c38933f69720e0910e9f050c86 *man/Eflags.Rd
 c752862189a65e7cb34a3bb13f6db8b3 *man/Fillv.Rd
-1bfa8ec1e5b1c31d5653a59806055d01 *man/MixturePlot.Rd
+2389c92a2cd76add93a308c993e8fc00 *man/MixturePlot.Rd
+573176afe5ac0b52007df7d62a115c29 *man/ModelPlot.Rd
 71f8733f0730ff37a61618cefb0a7871 *man/Nrows.Rd
 93752cb0de5f573cc8aab1c4d3eca31c *man/SCD.Rd
 7d54d42a54f3d4c616a078c2a831d874 *man/SLD.Rd
+ef120358472acaeef56830a2e77c4003 *man/SneeMq.Rd
 870ccf1614d78de0662d33ea11262dba *man/Vertcen.Rd
-844eb6fbf7936e8baba22dcdff5071b0 *man/Xvert.Rd
+2c3a45267dc0c55a72a106322f9da309 *man/Xvert.Rd
 8d4f983e4fe013565d31f5fd4575152d *man/conmx.Rd
 0a9d64b87b580a549215010903aa65f9 *man/crvtave.Rd
-3ca50c699a506bb55464e385a2c96cd5 *man/mixexp-package.Rd
-ff941e13a03d5a0ba297a7cb17124fbf *src/cnvrt.f
+879ff06b9f0110386f01cd9806ce3b2c *man/mixexp-package.Rd
+4adf6166def03e0720733fa47d8e82c0 *src/cnvrt.f
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,12 +1,13 @@
 useDynLib(mixexp)
-
+import(gdata, lattice, grid)
 export(crvtave,
        Eflags,
 	   Nrows,
 	   Vertcen,
 	   SCD,
 	   SLD,
 	   MixturePlot,
+	   ModelPlot,
 	   DesignPoints,
 	   Xvert,
 	   Effplot,

diff --git a/R/DesignPoints.R b/R/DesignPoints.R
@@ -1,53 +1,46 @@
-DesignPoints = function(des=NULL,x=NULL,y=NULL,z=NULL,x1lower=0,x1upper=0,
-                        x2lower=0,x2upper=0,x3lower=0,x3upper=0) 
-{
-
-# Checks to See if there are design points
-
-check1<-is.null(des)
-check2<-is.null(x)
-
-#check wheter to print design points
-if (check1 & check2) {
-design=FALSE   } else {design=TRUE } 
-
-
-  if (check2) {
-# if not make dummy design points to send to MixturePlot function
-x<-c(0,0,1)
-y<-c(0,1,0)
-z<-c(1,0,0)
-              }
-if (check1) {
-            }else {
-
-x<-des$x3
-y<-des$x2
-z<-des$x1
-       }
-
-# Makes dummy response points
-w<-runif(length(x))
-
-
-# Checks to see if there are constraints
-
-Check<-x1lower+x1upper+x2lower+x2upper+x3lower+x3upper
-  if (Check==0) {
-cls<-c(rep(0,6))
-constraints=FALSE
-} else {
-cls <-c(rep(0,6))
-cls[1]<-x1lower
-cls[2]<-x1upper
-cls[3]<-x2lower
-cls[4]<-x2upper
-cls[5]<-x3lower
-cls[6]<-x3upper
-constraints=TRUE
-        }
-
-MixturePlot(x,y,z,w,x3lab="Fraction x3",
-  x2lab="Fraction x2", x1lab="Fraction x1", corner.labs=c("x3","x2","x1"),lims=cls,
-  constrts=constraints,contrs=FALSE,cols=FALSE, mod=1,n.breaks=9,despts=design)
-} 
+DesignPoints = function (des = NULL, x = NULL, y = NULL, z = NULL, x1lower = 0, 
+    x1upper = 0, x2lower = 0, x2upper = 0, x3lower = 0, x3upper = 0,
+    axislabs=c("Fraction x1","Fraction x2","Fraction x3"),
+    cornerlabs = c("x1","x2","x3")){
+    check1 <- is.null(des)
+    check2 <- is.null(x)
+    if (check1 & check2) {
+        design = FALSE
+    }
+    else {
+        design = TRUE
+    }
+    if (check2) {
+        x <- c(0, 0, 1)
+        y <- c(0, 1, 0)
+        z <- c(1, 0, 0)
+    }
+    if (check1) {
+    }
+    else {
+        x <- des$x3
+        y <- des$x2
+        z <- des$x1
+    }
+    w <- runif(length(x))
+    Check <- x1lower + x1upper + x2lower + x2upper + x3lower + 
+        x3upper
+    if (Check == 0) {
+        cls <- c(rep(0, 6))
+        constraints = FALSE
+    }
+    else {
+        cls <- c(rep(0, 6))
+        cls[1] <- x1lower
+        cls[2] <- x1upper
+        cls[3] <- x2lower
+        cls[4] <- x2upper
+        cls[5] <- x3lower
+        cls[6] <- x3upper
+        constraints = TRUE
+    }
+    MixturePlot(x, y, z, w, x3lab = axislabs[3], x2lab = axislabs[2], 
+        x1lab = axislabs[1], corner.labs = cornerlabs, 
+        lims = cls, constrts = constraints, contrs = FALSE, cols = FALSE, 
+        mod = 1, n.breaks = 9, despts = design)
+}
diff --git a/R/Effplot.R b/R/Effplot.R
@@ -1,12 +1,20 @@
-Effplot = function(des,mod=1,dir=1)
+Effplot = function(des=NULL,nfac=3,mod=1,dir=1,ufunc=NULL,dimensions = list(NULL),
+x1=c(0,1),x2=c(0,1),x3=c(0,1),x4=c(0,1),x5=c(0,1),x6=c(0,1),x7=c(0,1),x8=c(0,1),x9=c(0,1),x10=c(0,1),x11=c(0,1),x12=c(0,1))
 {
 # glimit is the resolution for the plot
 glimit<-25
 
-# get the number of factors from the design
+# check for valid mod
+if(mod < 1 | mod > 4) 
+   stop("mod must be a number between 1 and 4")
+if(mod==4 & is.null(ufunc))
+   stop("When mod=4, you must supply the user model as an lm function through ufunc=object")
 
+# get the number of factors from the design
+ if(! is.null(des)) {
 dd<-dim(des)
 nfac<-dd[2]-1
+                    }
 
 # checks for valid number of factors
 if (nfac<2 | nfac>12)
@@ -17,9 +25,8 @@ if (nfac<3 & mod>3)
    stop("Special cubic model requires at least 3 factors")
 
 
-# set up lower and upper bounds for factors
-x1=c(0,1); x2=c(0,1); x3=c(0,1); x4=c(0,1); x5=c(0,1); x6=c(0,1)
-x7=c(0,1); x8=c(0,1); x9=c(0,1); x10=c(0,1); x11=c(0,1); x12=c(0,1)
+# set up lower and upper bounds for factors if design is in des
+if(! is.null(des)) {
  if (nfac>=1) {
   x1[1]<-min(des[,1])
   x1[2]<-max(des[,1]) 
@@ -120,12 +127,16 @@ modl<-lm(y~x1+x2+x3+x4+x5+x6+x1*x2+x1*x3+x1*x4+x1*x5+x1*x6+x2*x3+x2*x4+x2*x5+x2*
 Beta<-modl$coeff 
                   }
              }
+ if (mod==4) {
+modl<-lm(y~.-1,data=des)
+Beta<-ufunc$coeff
+             }
 
 
 
+## end of calculations involving the data frame des
+              }
 
-# prints back beta
-#cat("beta=", ,"\n")
 
 
 # get constraint matrix for crvtave
@@ -136,7 +147,7 @@ v<-c(-x1[1],x1[2])
                   }
 
 
-library(gdata)
+
 Ip<-diag(nfac)
 In<--1*Ip
 conmx<-interleave(Ip,In)
@@ -161,8 +172,6 @@ pcent<-c(rep(0,times=nfac))
  for (i in 1:nfac) {
 pcent[i]<-(cent[i]-ck[1,i])/Den
                    }
-#prints centroid in pseudo component space
-#cat("pcent=",pcent,"\n")
 
 # create grid
 grid<-glimit:1
@@ -173,7 +182,7 @@ Xgrid<-array(rep(0,times=glimit*nfac*nfac))
 dim(Xgrid)<-c(nfac,glimit,nfac)
 
 
-# gets direction for Cox method
+# gets direction for Piepel method
 
 if (dir==1) {
 
@@ -279,13 +288,13 @@ if (ifac<nfac) {
                }
            }
 
-mTitle<-"Effect Plot (Cox direction)"
+mTitle<-"Effect Plot (Piepel direction)"
  } 
-# end of code for Cox direction coordinates
+# end of code for Piepel direction coordinates
 
 
 
-# get direction for Piepel method
+# get direction for Cox method
 
    if (dir==2) {
 
@@ -376,7 +385,6 @@ if (ifac<nfac){
 
 # create bottom half of xi grid
 grid<--1*(1:glimit)
-#Delta<-(pcent[ifac]-ck[1,ifac])/glimit
 Delta<-(pcent[ifac]-0)/glimit
 
 w<-Delta*grid+pcent[ifac]
@@ -405,12 +413,12 @@ for  (i in 1:nfac) {
                    }
 
 
-mTitle<-"Effect Plot (Pieple direction)"
+mTitle<-"Effect Plot (Cox direction)"
               }
 
 
 
-# end of code for Pieple direction 
+# end of code for Cox direction 
 
 # set up the plot matrix
 PX<-array(rep(0,times=nfac*2*(2*glimit+1)))
@@ -421,7 +429,7 @@ dim(PX)<-c((2*glimit+1),2*nfac)
 # get predicted values
   for (ifac in 1:nfac) {
 Xtemp<-Xgrid[ifac, , ]
- if (mod==1) {
+ if (mod==1 | mod==4) {
 Xmat<-Xtemp
              }
  if (mod==2) {
@@ -458,8 +466,18 @@ Xmat<-cbind(Xtemp,Xtemp[,1]*Xtemp[,2],Xtemp[,1]*Xtemp[,3],Xtemp[,1]*Xtemp[,4],Xt
                  }
              }
 
-
+if(mod<=3) {
 yhX<-Xmat%*%Beta
+   }
+
+if(mod==4) {
+Xmatdf<-data.frame(Xmat)
+colnames(Xmatdf)<-dimensions
+yhU<-predict(ufunc,Xmatdf)
+yhX<-yhU
+           }
+
+
 
 
 # get deviations from centroid
@@ -507,19 +525,15 @@ yaxismin<-min(ymin)
   for (i in 1:nfac) {
   xvec<-PX[(sel[,i]==1),(2*i-1)]
   yvec<-PX[(sel[,i]==1),(2*i)]
-#print(xvec)
-#print(yvec)
   lines(xvec,yvec,lty=i,col=i)
   text(xvec[length(xvec)],yvec[length(yvec)],plabs[i])
   text(xvec[1],yvec[1],plabs[i])
 
                     }
 
-#print(dim(Xgrid))
-#print(dim(Temp))
-#print(Temp)
 
 return(PX)
 }
+##############################################################
 
 
diff --git a/R/MixturePlot.R b/R/MixturePlot.R
@@ -48,10 +48,10 @@ z<-des$x1
 w<-des$y
                          }
 
-
+base = high = NULL 
 #Depends on the following libraries
-library(lattice)
-library(grid)
+#library(lattice)
+#library(grid)
 ######################
 ## Creation of Grid ##
 ######################