minor updates to fda code

Author: JamesRamsay5

.DS_Store

@@ -4,3 +4,4 @@
 .Ruserdata
 .Rbuildignore
 
+inst/doc

.gitignore

@@ -1,13 +1,16 @@
 Package: fda
-Version: 5.5.1
-Date: 2021-11-16
+Version: 5.5.2
+Date: 2022-03-04
 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), splines, Matrix, fds, deSolve
-Suggests: lattice
+Depends: R (>= 3.5), splines, fds, deSolve
+Suggests: 
+    rmarkdown,
+    knitr,
+    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 
@@ -21,3 +24,4 @@ License: GPL (>= 2)
 URL: http://www.functionaldata.org
 LazyData: true
 NeedsCompilation: no
+VignetteBuilder: knitr

DESCRIPTION

@@ -97,7 +97,8 @@ export(AmpPhaseDecomp,
        monhess,
        monomial,
        monomialpen,
-       norder, norder.bspline,
+       norder, 
+       norder.bspline,
        objAndNames,
        odesolv,
        pca.fd,
@@ -127,10 +128,10 @@ export(AmpPhaseDecomp,
        predict.fdSmooth, 
        project.basis,
        quadset,
-	     reconsCurves,
+       reconsCurves,
        register.fd,
        register.newfd,
-	     scoresPACE,
+       scoresPACE,
        sd.fd, 
        std.fd, 
        stdev.fd, 
@@ -142,7 +143,6 @@ export(AmpPhaseDecomp,
        smooth.fdPar,
        smooth.monotone,
        smooth.morph,
-       smooth.morph2,
        smooth.pos,
        smooth.basis.sparse,
        smooth.sparse.mean,
@@ -170,7 +170,6 @@ export(AmpPhaseDecomp,
 import("graphics")
 import("stats")
 import("splines")
-import("Matrix")
 import("fds")
 import("deSolve")
 

NAMESPACE

@@ -20,6 +20,7 @@ basisfd <- function(type, rangeval, nbasis, params, dropind=vector("list",0),
   #             "power" "pow"
   #  RANGEVAL...an array of length 2 containing the lower and upper
   #             boundaries for (the rangeval of argument values
+  #             If basis is of FEM type, rangeval is not used
   #  NBASIS ... the number of basis functions
   #  PARAMS ... If the basis is "fourier", this is a single number indicating
   #               the period.  That is, the basis functions are periodic on
@@ -212,13 +213,15 @@ basisfd <- function(type, rangeval, nbasis, params, dropind=vector("list",0),
     stop("'type' unrecognizable.")
   }
 
-  #  check rangeval
+  #  check rangeval if the object is not of type FEM
 
-  rangeval = as.vector(rangeval)
-  if (!is.numeric(rangeval)) stop("Argument rangeval is not numeric.")
-  if (length(rangeval) != 2) stop("Argument rangeval is not of length 2.")
-  if (!(rangeval[2] > rangeval[1]))
-    stop("Argument rangeval is not strictly increasing.")
+  if (!type == "FEM") {
+    rangeval = as.vector(rangeval)
+    if (!is.numeric(rangeval)) stop("Argument rangeval is not numeric.")
+    if (length(rangeval) != 2) stop("Argument rangeval is not of length 2.")
+    if (!(rangeval[2] > rangeval[1]))
+      stop("Argument rangeval is not strictly increasing.")
+  }
 
   #  check nbasis
 

R/.DS_Store

@@ -47,7 +47,7 @@ bsplineS <- function (x, breaks, norder=4, nderiv=0, returnMatrix=FALSE)
   nbasis <- nbreaks + norder - 2
   if (nbasis >= norder) {
       if (nbasis > 1) {
-  	    basismat <- Matrix(splines::spline.des(knots, x, norder, derivs)$design)
+  	    basismat <- splines::spline.des(knots, x, norder, derivs)$design
       } else {
   	    basismat <- as.matrix(splines::spline.des(knots, x, norder, derivs)$design)
       }

R/basisfd.R

@@ -95,7 +95,7 @@ create.bspline.basis <- function (rangeval=NULL, nbasis=NULL,
 #  Returns
 #  BASISFD ...a functional data basis object
 
-#  Last modified  11 February 2015 by Jim Ramsay
+#  Last modified  19 November 2021 by Jim Ramsay
 
 #  -------------------------------------------------------------------------
 #  Default basis for missing arguments:  A B-spline basis over [0,1] of

R/bsplineS.R

@@ -16,4 +16,5 @@ fdParcheck = function(fdParobj, ncurve=NULL) {
     }
   }
   return(fdParobj)
+  
 }

R/create.bspline.basis.R

@@ -1,6 +1,6 @@
 landmarkreg <- function(fdobj, ximarks, x0marks=xmeanmarks,
                         WfdPar=NULL, monwrd=FALSE, ylambda=1e-10)
-{
+    {
 #  Arguments:
 #  FDOBJ   ... functional data object for curves to be registered
 #  XIMARKS ... N by NL array of times of interior landmarks for
@@ -125,8 +125,7 @@ landmarkreg <- function(fdobj, ximarks, x0marks=xmeanmarks,
     #  smooth relation between this curve"s values and target"s values
     if (monwrd) {
        #  use monotone smoother
-#       Wfd       <- smooth.morph(xval, yval, WfdPar)$Wfdobj
-       Wfds       <- smooth.morph(xval, yval, WfdPar)
+       Wfds       <- smooth.morph(xval, yval, wrange, WfdPar)
        Wfd <- Wfds$Wfdobj
        h         <- monfn(x, Wfd)
        b         <- (rangeval[2]-rangeval[1])/(h[n]-h[1])
@@ -160,7 +159,7 @@ landmarkreg <- function(fdobj, ximarks, x0marks=xmeanmarks,
        wcoef        <- Wfd$coefs
        Wfdinv       <- fd(-wcoef,wbasis)
        WfdParinv    <- fdPar(Wfdinv, wLfd, wlambda)
-       Wfdinv       <- smooth.morph(h, x, WfdParinv)$Wfdobj
+       Wfdinv       <- smooth.morph(h, x, wrange, WfdParinv)$Wfdobj
        hinv         <- monfn(x, Wfdinv)
        b            <- (rangeval[2]-rangeval[1])/(hinv[n]-hinv[1])
        a            <- rangeval[1] - b*hinv[1]