add 5.1.1

Author: sbgraves237

CHANGELOG

@@ -0,0 +1,24 @@
+Package: fda
+Version: 5.1.1
+Date: 2020-03-13
+Title: Functional Data Analysis
+Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre], 
+ Spencer Graves <spencer.graves@effectivedefense.org> [ctb], 
+ Giles Hooker <gjh27@cornell.edu>  [ctb]
+Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>
+Depends: R (>= 3.5)
+Suggests: deSolve, lattice
+Description: These functions were developed to support functional data
+ analysis as described in Ramsay, J. O. and Silverman, B. W.
+ (2005) Functional Data Analysis. New York: Springer and in 
+ Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). 
+ Functional Data Analysis with R and Matlab (Springer). 
+ The package includes data sets and script files working many examples 
+ including all but one of the 76 figures in this latter book.  Matlab versions 
+ are available by ftp from 
+ <http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
+License: GPL (>= 2)
+URL: http://www.functionaldata.org
+LazyData: true
+NeedsCompilation: no
+Packaged: 2020-03-13 15:55:07 UTC; jimramsay

DESCRIPTION

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+export(AmpPhaseDecomp,
+       as.array3,
+       as.POSIXct1970,
+       axisIntervals, 
+       axesIntervals,
+       bifd,
+       bifdPar,
+       boxplot.fd, 
+       boxplot.fdPar, 
+       boxplot.fdSmooth,
+       bsplinepen,
+       bsplineS,
+       cca.fd,
+       center.fd,
+       checkDim3, 
+       checkDims3,
+       checkLogical, 
+       checkNumeric, 
+       checkLogicalInteger,
+       cor.fd,
+       covPACE,
+       create.bspline.basis, 
+       create.constant.basis,
+       create.exponential.basis,
+       create.fourier.basis,
+       create.monomial.basis,
+       create.polygonal.basis,
+       create.power.basis,
+       CSTR2in, 
+       CSTR2, 
+       CSTRfitLS, 
+       CSTRfn, 
+       CSTRres, 
+       CSTRsse,
+       cycleplot.fd,
+       Data2fd,
+       density.fd,
+       deriv.fd,
+       df2lambda,
+       dirs,
+       Eigen,
+       eigen.pda,
+       eval.basis,
+       eval.bifd,
+       eval.fd,
+       eval.monfd,
+       eval.penalty,
+       eval.posfd,
+       evaldiag.bifd,
+       expon,
+       exponentiate.fd,
+       exponpen,
+       fd, fbplot,
+       fd2list,
+       fdlabels,
+       fdPar,
+       fourier,
+       fourierpen,
+       Fperm.fd,
+       fRegress,
+       fRegressCV, 
+       fRegressStderr,
+       Fstat.fd,
+       geigen,
+       getbasismatrix,
+       getbasispenalty,
+       getbasisrange,
+       inprod,
+       inprod.bspline,
+       int2Lfd,
+       intensity.fd,
+       is.basis,
+       is.fd,
+       is.fdPar,
+       is.fdSmooth,
+       is.Lfd,
+       lambda2df,
+       lambda2gcv,
+       landmarkreg,
+       Lfd,
+       lines.fdSmooth,
+       linmod,
+       matplot, 
+       matplot.default,
+       mean.fd,
+       minus.fd, 
+       monfn,
+       monomial,
+       monomialpen,
+       norder, norder.bspline,
+       objAndNames,
+       odesolv,
+       pca.fd,
+	     pcaPACE,
+       pda.fd,
+       pda.overlay,
+       phaseplanePlot,
+       plot.cca.fd,
+       plot.fd,
+       plot.pca.fd,
+       plotbeta,
+       plotfit.fd, 
+       plotfit.fdSmooth,
+       plotreg.fd,
+       plotscores,
+       plus.fd, 
+       polyg,
+       polygpen,
+       powerbasis,
+       powerpen,
+       ppBspline,
+       project.basis,
+       quadset,
+	     reconsCurves,
+       register.fd,
+       register.newfd,
+	     scoresPACE,
+       sd.fd, 
+       std.fd, 
+       stdev.fd, 
+       stddev.fd,
+       smooth.basis,
+       smooth.bibasis,
+       smooth.fd,
+       smooth.basisPar,
+       smooth.fdPar,
+       smooth.monotone,
+       smooth.morph,
+       smooth.pos,
+	     smooth.basis.sparse,
+	     smooth.sparse.mean,
+	     sparse.list,
+	     sparse.mat,
+       svd2,
+       symsolve,
+       "[.fd",
+       times.fd,
+       tperm.fd,
+       trapzmat,
+       var.fd,
+       varmx,
+       varmx.cca.fd,
+       varmx.pca.fd,
+       vec2Lfd, 
+       wtcheck,
+       zerofind )
+
+import("graphics")
+import("stats")
+import("splines")
+
+importFrom("grDevices", "dev.new", "heat.colors")
+importFrom("utils", "data")
+
+S3method("==",         basisfd)
+S3method('*',          basisfd)
+S3method(summary,      basisfd)
+S3method(norder,       basisfd)
+S3method(plot,         basisfd)
+S3method(predict,      basisfd)
+S3method('+',          fd)
+S3method('-',          fd)
+S3method('*',          fd)
+S3method('[',          fd)
+S3method('^',          fd)
+S3method(boxplot,      fd)
+S3method(coef,         fd)
+S3method(coefficients, fd)
+S3method(density,      fd)
+S3method(deriv,        fd)
+S3method(lines,        fd)
+S3method(mean,         fd)
+S3method(norder,       fd)
+S3method(plot,         fd)
+S3method(predict,      fd)
+S3method(sqrt,         fd)
+S3method(sum,          fd)
+S3method(summary,      fd)
+S3method(fRegress,     fd)
+S3method(boxplot,      fdPar)
+S3method(coef,         fdPar)
+S3method(coefficients, fdPar)
+S3method(plot,         fdPar)
+S3method(predict,      fdPar)
+S3method(summary,      fdPar)
+S3method(fRegress,     fdPar)
+S3method(coef,         fdSmooth)
+S3method(boxplot,      fdSmooth)
+S3method(coefficients, fdSmooth)
+S3method(fitted,       fdSmooth)
+S3method(lines,        fdSmooth)
+S3method(residuals,    fdSmooth)
+S3method(plot,         fdSmooth)
+S3method(predict,      fdSmooth)
+S3method(plot,         Lfd)
+S3method(summary,      Lfd)
+S3method(fitted,       monfd)
+S3method(residuals,    monfd)
+S3method(predict,      monfd)
+S3method(fRegress,     numeric)
+S3method(matplot,      numeric)
+S3method(fitted,       posfd)
+S3method(predict,      posfd)
+S3method(residuals,    posfd)
+S3method(matplot,      Date)
+S3method(fRegress,     character)
+S3method(fRegress,     formula)
+S3method(matplot,      default)
+S3method(matplot,      POSIXct)
+S3method(norder,       bspline)
+S3method(norder,       default)
+S3method(plot,         cca.fd)
+S3method(plot,         pca.fd)
+S3method(plot,         pda.fd)
+S3method(summary,      bifd)

NAMESPACE

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+Software and datasets to support three books:
+
+James O. Ramsay, Giles Hooker, and Spencer Graves
+      (2009) Functional DAta Analysis with R and Matlab
+      (Springer)
+James O. Ramsay and Bernard W. Silverman (2005),
+      'Functional Data Analysis', 2nd ed. (Springer)
+_______ (2002) 'Applied Functional Data Analysis' (Springer)
+James O. Ramsay, Giles Hooker, and Spencer Graves (2009)
+      'Functional Data Analysis with R and Matlab' (Springer)
+
+Release 5.1.1 updates the package to conform to current CRAN requirements.  
+Changes are:
+1.  function Data2fd has been temporarily removed.  We are considering whether
+its contribution to the package is useful given the smoothing function
+smooth.basis.
+2.  functions fRegress.CV and fRgress.stderr have been changed to
+fRegressCV and fRegressStderr to avoid collisons with S3 methods.
+These functions are not methods for function fRegress.

NEWS

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+AmpPhaseDecomp <- function(xfd, yfd, hfd, rng=xrng)
+{
+#  Computes the amplitude-phase decomposition for a registration.
+
+#  Arguments:
+#  XFD  ...  FD object for unregistered functions
+#  YFD  ...  FD object for registered functions
+#  HFD  ...  FD object for warping functions
+
+#  Returns:
+#  MS.amp ... mean square for amplitude variation 
+#  MS.pha ... mean square for amplitude variation 
+#  RSQR   ... squared correlation measure of prop. phase variation 
+#  C      ... constant C
+
+#  Last modified 6 January 2020 by Jim Ramsay
+
+xbasis  <- xfd$basis
+nxbasis <- xbasis$nbasis
+nfine   <- max(201,10*nxbasis)
+xrng    <- xbasis$rangeval
+
+if (rng[1] < xrng[1] || rng[2] > xrng[2]) stop(
+    "RNG is not within the range of the other arguments.")
+if (rng[1] >= rng[2]) stop("Elements of rng are not increasing.")
+tfine   <- seq(rng[1],rng[2],len=nfine)
+delta   <- tfine[2] - tfine[1]
+
+Dhfine  <- eval.fd(tfine, hfd, 1)
+xfine   <- eval.fd(tfine, xfd, 0)
+yfine   <- eval.fd(tfine, yfd, 0)
+mufine  <- apply(xfine, 1, mean)
+etafine <- apply(yfine, 1, mean)
+
+N       <- dim(xfine)[2]
+rfine   <- yfine - outer(etafine,rep(1,N))
+
+intetasqr <- delta*trapz(etafine^2)
+intmusqr  <- delta*trapz(mufine^2)
+
+covDhSy <- rep(0,nfine)
+for (i in 1:nfine) {
+    Dhi        <- Dhfine[i,]
+    Syi        <- yfine[i,]^2
+    covDhSy[i] <- cov(Dhi, Syi)
+}
+intcovDhSy <- delta*trapz(covDhSy)
+
+intysqr <- rep(0,N)
+intrsqr <- rep(0,N)
+for (i in 1:N) {
+    intysqr[i] <- delta*trapz(yfine[,i]^2)
+    intrsqr[i] <- delta*trapz(rfine[,i]^2)
+}
+
+C      <- 1 + intcovDhSy/mean(intysqr)
+MS.amp <- C*mean(intrsqr)
+MS.pha <- C*intetasqr - intmusqr
+RSQR   <- MS.pha/(MS.amp+MS.pha)
+
+return(list("MS.amp" = MS.amp, "MS.pha" = MS.pha, "RSQR" = RSQR, "C" = C)) 
+
+}
+
+trapz = function(x) {
+n = length(x)
+intx = sum(x) - 0.5*(x[1]+x[n])
+return(intx)
+}
+

R/AmpPhaseDecomp.R

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+CSTR2 <- function(Time, y, parms){
+#function [Dy, DDy] = CSTR2(Time, y, parms)
+#%  CSTR2 is called by the ODE solving function and evaluates the
+#%  right hand side of the equation.
+#
+# 'lsoda' requires this function to return a list
+# whose first component is a vector giving the derivatives of 'y'
+#      with respect to 'Time' and 
+# whose second component (if any) "is a vector ... of global values
+#      that are required at each point in 'Time'".
+# CSTR2 provides no second component.    
+
+#%  R port 20 April 2007 by Spencer Graves
+#%  Matlab version last modified 5 May 2005
+
+  tau = 1;
+
+#[F,CA0,T0,Tcin,Fc] = CSTR2in(Time, condition, tau);
+  CSTR.in <- CSTR2in(Time, parms$condition, tau) 
+
+  fitstruct <- parms$fitstruct
+  kref   = fitstruct$kref;
+  EoverR = fitstruct$EoverR;
+  a      = fitstruct$a;
+  b      = fitstruct$b;
+
+  V      = fitstruct$V;
+  FoverV = CSTR.in[, "F."]/V;
+
+  aFc2bp = a*CSTR.in[, "Fc"]^b;
+  const1 = V*fitstruct$rho*fitstruct$Cp;
+  const2 = 2*fitstruct$rhoc*fitstruct$Cpc;
+
+  betaTTcin = (CSTR.in[, "Fc"]*aFc2bp/(    
+    const1*(CSTR.in[, "Fc"]+aFc2bp/const2)) )
+  betaTT0   = FoverV;
+
+#%  set up current values of variables
+  {
+    if( length(y) == 2 ){
+      Ci = y[1];
+      Ti = y[2];
+    }
+    else{
+      Ci = y[,1];
+      Ti = y[,2];
+    }
+  }
+# end if(length(y)==2) 
+
+  Tdif = 1/as.vector(Ti) - 1/fitstruct$Tref;
+  betaCC = kref*exp(-1e4*EoverR*Tdif);
+  betaTC = (-fitstruct$delH/const1)*betaCC;
+  betaTT = FoverV + betaTTcin;
+
+  DC = (-(FoverV + betaCC)*as.vector(Ci)  +
+    (CSTR.in[, "F."]/V)*CSTR.in[, "CA0"]); 
+  DT = (-betaTT*Ti + betaTC*Ci + (CSTR.in[, "F."]/V) * 
+        CSTR.in[, "T0"] + betaTTcin*CSTR.in[, "Tcin"]) ;
+#
+  x <- cbind(Conc=DC, Temp=DT)
+# 
+  list(x)
+}