version 0.1-32

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: refund
 Type: Package
 Title: Regression with Functional Data
-Version: 0.1-31
-Date: 2023-06-26
+Version: 0.1-32
+Date: 2023-07-17
 Authors@R: c(
     person("Jeff", "Goldsmith", role = "aut", email = "jeff.goldsmith@columbia.edu"),
     person("Fabian", "Scheipl", role = "aut", email = "fabian.scheipl@stat.uni-muenchen.de"),
@@ -27,9 +27,9 @@ Authors@R: c(
     person("Ruonan", "Li", role="ctb", email="rli20@ncsu.edu"),
     person("Zheyuan", "Li", role="ctb"))
 Depends: R (>= 3.5.0)
-Imports: fda, Matrix, lattice, boot, mgcv (>= 1.8-23), MASS, magic,
-        nlme, gamm4, lme4, RLRsim, splines, grpreg, ggplot2, stats,
-        pbs, methods
+Imports: fda, Matrix, lattice, boot, mgcv (>= 1.9), MASS, magic, nlme,
+        gamm4, lme4, RLRsim, splines, grpreg, ggplot2, stats, pbs,
+        methods
 Suggests: RColorBrewer, reshape2, testthat
 Description: Methods for regression for functional
     data, including function-on-scalar, scalar-on-function, and
@@ -66,7 +66,7 @@ Collate: 'Omegas.R' 'af.R' 'af_old.R' 'amc.R' 'ccb.fpc.R'
 RoxygenNote: 7.2.3
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2023-06-27 15:25:37 UTC; wrobelj
+Packaged: 2023-07-17 20:30:53 UTC; wrobelj
 Author: Jeff Goldsmith [aut],
   Fabian Scheipl [aut],
   Lei Huang [aut],
@@ -90,4 +90,4 @@ Author: Jeff Goldsmith [aut],
   Ruonan Li [ctb],
   Zheyuan Li [ctb]
 Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
-Date/Publication: 2023-06-29 12:50:02 UTC
+Date/Publication: 2023-07-23 16:40:02 UTC

MD5

@@ -1,4 +1,4 @@
-bfc9b2ea88a3cbaded0bb22b558488b9 *DESCRIPTION
+e6fc92c9468cb010919f506ad71be75b *DESCRIPTION
 d07c8587c80600b57b321d602ef61928 *NAMESPACE
 9e8ee7293f8e631aa493bec1a19c0c45 *R/CD4-data.R
 423e0e7e78259f82ac03416c532deb49 *R/COVID19-data.R
@@ -63,13 +63,13 @@ dfc9b0b4802607bd388f8f736ccd0ba1 *R/mfpca.face.R
 bde2d12a84269416bb06b401efb1382d *R/peer.R
 78e3ca1fd1d490e453b040d801b31260 *R/peer_old.R
 5edd5816a48757991887f6d83b6dfc0b *R/pffr-ff.R
-5c930dded727731d474f5b493dab36a4 *R/pffr-ffpc.R
+2e84254549d9fe03c6c1aab59a7fe1e3 *R/pffr-ffpc.R
 3fe43fb9b33515088d4fd0e945b7f3e4 *R/pffr-methods.R
 7ebd45e78e494092edc5850edf0b7afa *R/pffr-pcre.R
 b00a440b3fc2c554c314254a5f7730ce *R/pffr-robust.R
 0d22801c3dd9c9c502720625d25f9ad9 *R/pffr-sff.R
 21121a37471fbba396a8c109cdac9291 *R/pffr-utilities.R
-e645640bdabd5391cf7ccf9aa63ed2b1 *R/pffr.R
+58022a0991d2dc5590a0eb8f9d990c90 *R/pffr.R
 6ec53d1271d9708bd4d5eefcd88efe6d *R/pfr.R
 c20ddd15fa55c6e88432fc6e43585fb2 *R/pfr_old.R
 ca16e2f6965f670300cfbc01779d6b19 *R/pi_basis.R
@@ -79,7 +79,7 @@ b5e5847b43605f81f0d4a7f89e2af911 *R/plot.fosr.vs.R
 9d878231cf9dee0071ade44a6d70f3cc *R/plot.fpcr.R
 cfb9f89ce8ff988130e55c218eaeb976 *R/plot.lpeer.R
 77cdf94d964e56febef584e39c13a14b *R/plot.peer.R
-03bb19c7f5fab079f9e8cef40770d53c *R/plot.pfr.R
+36365b607b14ff60c7f721d709a926de *R/plot.pfr.R
 c969d9f72fd6d62855aef789faafce53 *R/poridge.R
 24968d3466ceba2286b1c656653ca3c9 *R/postprocess.pfr.R
 dc153c771713f874d978c26ef3e633eb *R/predict.fbps.R
@@ -136,7 +136,7 @@ d3fd98f4418925932eb7424741371b85 *man/f_sum4.Rd
 be02262fa89556791e100642ce1b43d2 *man/f_trace.Rd
 2f2dc572a9523a743cfd970312c11aca *man/fbps.Rd
 983508a628b33d3fdd619eb0802c2596 *man/ff.Rd
-038c26529b691720ab87bef657235cb9 *man/ffpc.Rd
+575dde02f7cbcd67a98e63be79d10d62 *man/ffpc.Rd
 f84e1a0ade8af6ff124405a32857efbd *man/ffpcplot.Rd
 c51ae9d3445f98caf851d11fbfa6d771 *man/fgam.Rd
 00588c383abb8313141e78db0a6bd030 *man/fosr.Rd
@@ -171,13 +171,13 @@ dca002e0a13860f4c041f4c6951ddeb3 *man/model.matrix.pffr.Rd
 da1df1f46bcc8eae50c29ae4742ae4a8 *man/pcre.Rd
 3a15a08fd6470d116521ad85e22d710d *man/peer.Rd
 a91d3dacb5be61666a6a197394b0b4ee *man/peer_old.Rd
-f70171bcb8975f7ca083621ce9a48c90 *man/pffr.Rd
+5b258b1bff5dbd59b2f8b0032a047106 *man/pffr.Rd
 397f27d06014db23a438e4238ce47cd1 *man/pffr.check.Rd
 c8ec2f1a933191e399a0e92ccfa0f86b *man/pffrGLS.Rd
 6d6d5df970f7a5981ba66c09e305d9c3 *man/pffrSim.Rd
 75830d70ae7f4412f4dead6413be70a6 *man/pfr.Rd
 5aa5d30f2ecffcd6b908ae09a399bab0 *man/pfr_old.Rd
-87c31cf4885f5a83981b049d98489285 *man/pfr_plot.gam.Rd
+0ee86d52b3088e51fbe0a9466385dfaf *man/pfr_plot.gam.Rd
 7aa64640f1eb0bb496b5e0f16b0fdf9e *man/plot.fosr.Rd
 d3930765745734c125046717177fbfda *man/plot.fosr.vs.Rd
 5cd8d657949646f99b103378d422e1c1 *man/plot.fpcr.Rd
@@ -196,8 +196,6 @@ d520fc399d537aa0c2d2a50142f7fcd5 *man/predict.fosr.Rd
 aa2b0f6ed709c7653be426c2f9340794 *man/qq.pffr.Rd
 8fe2dac6c39388810494ff7e05297f02 *man/quadWeights.Rd
 c4976cf030cd5210c1922b6aeb3c42ea *man/re.Rd
-aa9973bb933fa3b1e8b962406271303a *man/refund-internal.Rd
-0f825b85c6afa166407d441127f9d442 *man/refund-package.Rd
 25501a6d7edd07e7f914cd06414767c9 *man/residuals.pffr.Rd
 fcdcf1ecea47fded75c171d0d16a339f *man/rlrt.pfr.Rd
 f778a4a5b2a11c6a240c441f43adb368 *man/sff.Rd

R/pffr-ffpc.R

@@ -67,7 +67,7 @@
 #' layout(t(1:3))
 #' persp(t, s, t(beta.st), theta=50, phi=40, main="Truth",
 #'     ticktype="detailed")
-#' plot(m.ff, select=1, pers=TRUE, zlim=range(beta.st), theta=50, phi=40,
+#' plot(m.ff, select=1, zlim=range(beta.st), theta=50, phi=40,
 #'     ticktype="detailed")
 #' title(main="ff()")
 #' ffpcplot(m.pc, type="surf", auto.layout=FALSE, theta = 50, phi = 40)

R/pffr.R

@@ -188,7 +188,7 @@
 #' s <- attr(data1, "xindex")
 #' m1 <- pffr(Y ~ ff(X1, xind=s), yind=t, data=data1)
 #' summary(m1)
-#' plot(m1, pers=TRUE, pages=1)
+#' plot(m1, pages=1)
 #'
 #' \dontrun{
 #' ###############################################################################
@@ -206,7 +206,7 @@
 #'         yind=t,
 #'         data=data2)
 #' summary(m2)
-#' plot(m2, pers=TRUE)
+#' plot(m2)
 #' str(coef(m2))
 #' # convenience functions:
 #' preddata <- pffrSim(scenario="all", n=20)
@@ -224,7 +224,7 @@
 #' t <- attr(data3, "yindex")
 #' m3.sparse <- pffr(Y ~ s(xsmoo), data=data3$data, ydata=data3$ydata, yind=t)
 #' summary(m3.sparse)
-#' plot(m3.sparse, pers=TRUE, pages=1)
+#' plot(m3.sparse,pages=1)
 #' }
 pffr <- function(
   formula,

R/plot.pfr.R

@@ -53,7 +53,7 @@ plot.pfr <- function(x, Qtransform=FALSE, ...) {
 #' @seealso \code{\link[mgcv]{plot.gam}}
 #' @keywords internal
 pfr_plot.gam <- function (x, residuals = FALSE, rug = TRUE, se = TRUE, pages = 0,
-                         select = NULL, scale = -1, n = 100, n2 = 40, n3=3, pers = FALSE,
+                         select = NULL, scale = -1, n = 100, n2 = 40, n3=3,
                          theta = 30, phi = 30, jit = FALSE, xlab = NULL, ylab = NULL,
                          main = NULL, ylim = NULL, xlim = NULL, too.far = 0.1, all.terms = FALSE,
                          shade = FALSE, shade.col = "gray80", shift = 0, trans = I,
@@ -142,7 +142,7 @@ pfr_plot.gam <- function (x, residuals = FALSE, rug = TRUE, se = TRUE, pages = 0
       attr(x$smooth[[i]], "coefficients") <- x$coefficients[first:last]
       P <- plot(x$smooth[[i]], P = NULL, data = x$model,
                 partial.resids = partial.resids, rug = rug, se = se,
-                scale = scale, n = n, n2 = n2, pers = pers, theta = theta,
+                scale = scale, n = n, n2 = n2, theta = theta,
                 phi = phi, jit = jit, xlab = xlab, ylab = ylab,
                 main = main, label = term.lab, ylim = ylim, xlim = xlim,
                 too.far = too.far, shade = shade, shade.col = shade.col,
@@ -301,7 +301,7 @@ pfr_plot.gam <- function (x, residuals = FALSE, rug = TRUE, se = TRUE, pages = 0
                                              i == select)) {
       plot(x$smooth[[i]], P = pd[[i]], partial.resids = partial.resids,
            rug = rug, se = se, scale = scale, n = n, n2 = n2,
-           pers = pers, theta = theta, phi = phi, jit = jit,
+          theta = theta, phi = phi, jit = jit,
            xlab = xlab, ylab = ylab, main = main, ylim = ylim,
            xlim = xlim, too.far = too.far, shade = shade,
            shade.col = shade.col, shift = shift, trans = trans,
@@ -336,7 +336,7 @@ pfr_plot.gam <- function (x, residuals = FALSE, rug = TRUE, se = TRUE, pages = 0
 #' @keywords internal
 plot.mgcv.smooth <- function (x, P = NULL, data = NULL, label = "", se1.mult = 1,
                               se2.mult = 2, partial.resids = FALSE, rug = TRUE, se = TRUE,
-                              scale = -1, n = 100, n2 = 40, pers = FALSE, theta = 30, phi = 30,
+                              scale = -1, n = 100, n2 = 40,  theta = 30, phi = 30,
                               jit = FALSE, xlab = NULL, ylab = NULL, main = NULL, ylim = NULL,
                               xlim = NULL, too.far = 0.1, shade = FALSE, shade.col = "gray80",
                               shift = 0, trans = I, by.resids = FALSE, scheme = 0, ...) {
@@ -625,8 +625,6 @@ plot.mgcv.smooth <- function (x, P = NULL, data = NULL, label = "", se1.mult = 1
       }
       else if (x$dim == 2) {
         P$fit[P$exclude] <- NA
-        if (pers)
-          scheme <- 1
         if (scheme == 1) {
           persp(P$x, P$y, matrix(trans(P$fit + shift),
                                  n2, n2), xlab = P$xlab, ylab = P$ylab, zlab = P$main,
@@ -692,8 +690,6 @@ plot.mgcv.smooth <- function (x, P = NULL, data = NULL, label = "", se1.mult = 1
         P$fit[P$exclude] <- NA
         if (!is.null(main))
           P$title <- main
-        if (pers)
-          scheme <- 1
         if (scheme == 1) {
           persp(P$x, P$y, matrix(trans(P$fit + shift),
                                  n2, n2), xlab = P$xlab, ylab = P$ylab, zlab = P$main,