address check warnings

.Rbuildignore

 .gitignore
 test
-man_old
+old_man
 ^data-raw$
 .Rprofile
 TODO

DESCRIPTION

 Package: gtseries
 Type: Package
 Title: Time Series analysis for paleoclimate and cyclostrat purposes
-Version: 1.05-pre
+Version: 1.05
 Date: 2023-26-10
 Author: Michel Crucifix [aut, cre] (<https://orcid.org/0000-0002-3437-4911>)
 Maintainer: Michel Crucifix <michel.crucifix@uclouvain.be>
-Description: More about what it does (maybe more than one line)
-License: What license is it under?
+Description: Collection of time series analysis tools, focused on spectral decomposition and reconstruction, with an original focus on astronomical theory of paleoclimates and cyclostratigraphy. 
+License: MIT licence
 LazyLoad: yes
 RoxygenNote: 7.2.3
 Imports: Rdpack, sfsmisc

NAMESPACE

@@ -11,14 +11,24 @@ export(mfft)
 export(powerspectrum.wavelet)
 export(ssa)
 importFrom(Rdpack,reprompt)
+importFrom(graphics,axis)
+importFrom(graphics,image)
+importFrom(graphics,lines)
 importFrom(graphics,mtext)
+importFrom(graphics,par)
+importFrom(graphics,text)
 importFrom(sfsmisc,axTexpr)
 importFrom(sfsmisc,eaxis)
 importFrom(stats,ar)
 importFrom(stats,as.ts)
 importFrom(stats,coef)
+importFrom(stats,deltat)
 importFrom(stats,fft)
+importFrom(stats,lm)
+importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stats,start)
 importFrom(stats,time)
+importFrom(stats,toeplitz)
+importFrom(stats,ts)
 useDynLib(gtseries)

R/cwt_morlet.R

@@ -18,6 +18,8 @@
 ## Wavelets : theory and applications, Erlenbacher et al. eds, Oxford University Press 1996
 
 
+
+
 col_wavelet <- colorRampPalette(c('darkblue','lightblue','grey','white','red'))(100)
 
 search_ridge <- function (A,first_guess,k0=5.6,tol=1e-6, itmax=20,B=seq(along=A),window=c(0,Inf))
@@ -120,8 +122,8 @@ cross_morlet <- function(A, B, ...)
 
 #' Continous Morlet Wavelet Transform 
 
-#' @importFrom stats fft
-#' @importFrom stats time
+#' @importFrom stats fft deltat lm qnorm toeplitz ts time
+#' @importFrom graphics axis image lines par text
 #' @export cwt_morlet
 cwt_morlet <- function (A,inter=20,k0=5.6,amin=1,amax=Inf,calcmask=TRUE,scale=NA,deriv=FALSE)
 {
@@ -200,20 +202,20 @@ cwt_morlet <- function (A,inter=20,k0=5.6,amin=1,amax=Inf,calcmask=TRUE,scale=NA
 
 #' @rdname cwt_morlet
 #' @export
-plot.wavelet <- function (wave,resx=400,resy=300,xlab="Time",ylab="Period",scaling_correction=0,col=col_wavelet,legend=FALSE,Mode=Mod,plotMask=TRUE,...)
+plot.wavelet <- function (x,resx=400,resy=300,xlab="Time",ylab="Period",scaling_correction=0,col=col_wavelet,legend=FALSE,Mode=Mod,plotMask=TRUE,...)
 
 {
   require(fields)
-  xx <- attr(wave,"time")
-  period <- attr(wave,"period")
-  mask <- attr(wave,"mask")
+  xx <- attr(x,"time")
+  period <- attr(x,"period")
+  mask <- attr(x,"mask")
   if (!plotMask) mask[,] = 1  # do not hide influence cone
-  aa <- attr(wave,"scale")
+  aa <- attr(x,"scale")
   thin_factor_xx <- max(ceiling(length(xx)/ resx),1)
   thin_factor_yy <- max(ceiling(length(aa)/ resy),1)
   subx <- seq(thin_factor_xx,length(xx),thin_factor_xx)
   suba <- seq(thin_factor_yy,length(aa),thin_factor_yy)
-  wave_scaled <- Mode(wave[subx,suba])*mask[subx,suba]
+  wave_scaled <- Mode(x[subx,suba])*mask[subx,suba]
   for (i in 1:length(suba)) wave_scaled[,i] <- wave_scaled[,i]/(aa[i]^scaling_correction)
   if (legend) par(oma=c(2,2,2,5))
   image(xx[subx],period[suba],wave_scaled,log="y",ylab=ylab,xlab=xlab,axes=FALSE,col=col,...)

R/mem.R

@@ -39,10 +39,10 @@ mem <- function (A,method='burg',order.max=90,...) {
 
 #' @rdname mem
 #' @export
-plot.memObject <- function (memObject,period=FALSE,xaxp=NULL,yaxp=NULL,...)
+plot.memObject <- function (x,period=FALSE,xaxp=NULL,yaxp=NULL,...)
 {
 
-  plot(memObject$frequency,memObject$power,
+  plot(x$frequency,x$power,
        frame=FALSE,axes=FALSE,log="xy",type="l",xlab="",ylab="Power density",...)
   local({
   if (is.null(yaxp)) {yaxp <- par("yaxp"); yaxp[3] <- 1; par(yaxp=yaxp)}

R/ssa.R

@@ -18,7 +18,7 @@
 #' @param X the input series (typically a numeric)
 #' @param N if provided,  the length of the input series to beconsiderd 
 #' @param M the length of the sliding window
-#' @param Nrec: number of components to be output
+#' @param Nrec number of components to be output
 #' @importFrom sfsmisc axTexpr
 #' @importFrom sfsmisc eaxis
 
@@ -157,9 +157,9 @@ ssa <- function(X=X,N=length(X),M=M,Nrec=10) {
 
 #' @rdname ssa
 #' @export
-plot.SSAObject <- function (SSAObject,...)
+plot.SSAObject <- function (x,...)
 {
-  Nrec = length(SSAAbject$LA)
+  Nrec = length(x$LA)
   yat <- outer(seq(1:Nrec),10^(seq(-3,5)),"*")
   ylab <- 10^(-2:5)
 
@@ -168,7 +168,7 @@ plot.SSAObject <- function (SSAObject,...)
                        substitute(10^E, list(E=log10(ylab[i]))))
 
    S <- do.call("expression",ss)
-  plot(SSAObject$lambda,frame=T,axes=F,log="y",xlab="rank",ylab="Eigenvalue",...)
+  plot(x$lambda,frame=T,axes=F,log="y",xlab="rank",ylab="Eigenvalue",...)
   axis(1,xlab="rank")
   axis(2,at=yat,ylab="Eigenvalue",labels=F)
   axis(2,at=ylab,labels=axTexpr(1,at=ylab),tick=F,las=1)

README.md

+## gtseries
+
+Collection of time series analysis tools for R, focused on spectral decomposition
+and reconstruction, with an original focus on astronomical theory of paleoclimates and 
+cyclostratigraphy.
+

cleanup

-#!/bin/sh
-
-rm -f config.* src/Makevars src/config.h
+#! /bin/sh
+for f in ./config.* autom4te.cache/; do
+rm -rf $f
+done
+if [ -e src/Makevars ]; then
+rm -f src/Makevars
+fi
+exit 0
+ 

configure.ac

+
+AC_INIT
+
+# Ensure C++ is set up as R expects
+: ${R_HOME=`R RHOME`}
+if test -z "${R_HOME}"; then
+    AC_MSG_ERROR([Could not determine R_HOME.])
+fi
+CC=`"${R_HOME}/bin/R" CMD config CC`
+CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+AC_PROG_CC
+
+AC_CONFIG_SRCDIR([src/airy.c])
+
+
+#AC_CHECK_LIB(gsl, gsl_sf_airy_Ai_e,
+#             [LIBS="${LIBS} -lgsl -lgslcblas"], 
+#             [AC_MSG_ERROR([Cannot find Gnu Scientific Library.])],
+#             [-lgslcblas])
+#AC_CHECK_HEADER([gsl/gsl_version.h], ,
+#             [AC_MSG_ERROR([Cannot find GSL headers.])])
+
+# Following lines kindly supplied by Dirk Eddelbuettel
+## Use gsl-config to find arguments for compiler and linker flags
+##
+## Check for non-standard programs: gsl-config(1)
+AC_PATH_PROG([GSL_CONFIG], [gsl-config])
+## If gsl-config was found, let's use it
+if test "${GSL_CONFIG}" != ""; then
+   # Use gsl-config for header and linker arguments
+   GSL_CFLAGS=`${GSL_CONFIG} --cflags`
+   GSL_LIBS=`${GSL_CONFIG} --libs`
+   CFLAGS="$CFLAGS $GSL_CFLAGS"  # kindly supplied by Ray Brownrigg
+else
+   AC_MSG_ERROR([gsl-config not found, is GSL installed?])
+fi
+
+AC_MSG_CHECKING([if GSL version >= 2.5])
+AC_RUN_IFELSE([AC_LANG_SOURCE([[
+#include <string.h>
+#include <gsl/gsl_version.h>
+#include <stdio.h>
+#include <stdlib.h>
+int main() {
+#ifdef GSL_VERSION
+   int major, minor;
+   char *gslv = GSL_VERSION;
+   if ((sscanf(gslv, "%d.%d", &major, &minor)) != 2) {
+     exit (1);
+   }
+   exit (minor < 5);
+   exit (major < 2);
+#else
+  exit(1);
+#endif
+}
+]])],
+[gsl_version_ok=yes],
+[gsl_version_ok=no],
+[gsl_version_ok=yes])
+if test "${gsl_version_ok}" = no; then
+  AC_MSG_ERROR([Need GSL version >= 2.5])
+else
+  AC_MSG_RESULT([yes])
+fi
+
+# Now substitute these variables in src/Makevars.in to create src/Makevars
+AC_SUBST(GSL_CFLAGS) 
+AC_SUBST(GSL_LIBS)
+AC_CONFIG_FILES([src/Makevars])
+AC_OUTPUT
+

inst/REFERENCES.bib

@@ -26,7 +26,7 @@
  editor = {}, 
  year = {1997}, 
  title = {Frequency Modified Fourier Transform and its Application to Asteroids}, 
- pages = {137–148}, 
+ pages = {137-148}, 
  journal = {The Dynamical Behaviour of our Planetary System}, 
  doi = {10.1007/978-94-011-5510-6_9}, 
  url = {http://dx.doi.org/10.1007/978-94-011-5510-6_9}, 
@@ -57,7 +57,7 @@
  isbn = {9783030260507}, 
 } 
 @article{pardoiguzquiza06aa,
- author = {Pardo‐Igúzquiza, E.  and Rodríguez‐Tovar, F. J. }, 
+ author = {Pardo-Igúzquiza, E.  and Rodríguez-Tovar, F. J. }, 
  editor = {}, 
  year = {2006}, 
  title = {Maximum entropy spectral analysis of climatic time series revisited: Assessing the statistical significance of estimated spectral peaks}, 

man/cwt_morlet.Rd

@@ -18,7 +18,7 @@ cwt_morlet(
 )
 
 \method{plot}{wavelet}(
-  wave,
+  x,
   resx = 400,
   resy = 300,
   xlab = "Time",

man/mem.Rd

@@ -7,7 +7,7 @@
 \usage{
 mem(A, method = "burg", order.max = 90, ...)
 
-\method{plot}{memObject}(memObject, period = FALSE, xaxp = NULL, yaxp = NULL, ...)
+\method{plot}{memObject}(x, period = FALSE, xaxp = NULL, yaxp = NULL, ...)
 }
 \arguments{
 \item{A}{input, a time-series object}

man/ssa.Rd

@@ -7,7 +7,7 @@
 \usage{
 ssa(X = X, N = length(X), M = M, Nrec = 10)
 
-\method{plot}{SSAObject}(SSAObject, ...)
+\method{plot}{SSAObject}(x, ...)
 }
 \arguments{
 \item{X}{the input series (typically a numeric)}
@@ -16,7 +16,7 @@ ssa(X = X, N = length(X), M = M, Nrec = 10)
 
 \item{M}{the length of the sliding window}
 
-\item{Nrec:}{number of components to be output}
+\item{Nrec}{number of components to be output}
 }
 \value{
 a SSA object, compatible with the supplied plot function

src/Makevars

-# Kindly supplied by Dirk Eddelbuettel
-# set by configure
-GSL_CFLAGS = -I/usr/local/include
-GSL_LIBS   = -L/usr/local/lib -lgsl -lgslcblas -lm
-
-# combine to standard arguments for R
-PKG_CPPFLAGS =  $(GSL_CFLAGS) -I.
-PKG_LIBS = $(GSL_LIBS)
-
-