update for travis

DESCRIPTION

@@ -50,7 +50,6 @@ Imports:
     infotheo,
     methods,
     RColorBrewer,
-    patchwork,
     tibble
 Suggests: knitr,
     rmarkdown,

NAMESPACE

@@ -45,7 +45,6 @@ export(plotNET_SW)
 export(plotNET_groupColour)
 export(plotNET_groupWeight)
 export(plotNET_prep)
-export(plotRP_crqa)
 export(plotSUR_hist)
 export(recmat)
 export(recmat_plot)

R/CasNET_Merlijn.R

@@ -33,6 +33,7 @@
 #' @references Schiepek, G. (2003). A Dynamic Systems Approach to Clinical Case Formulation. European Journal of Psychological Assessment, 19, 175-184.
 #' @references Haken, H. & Schiepek, G. (2006, 2. Aufl. 2010). Synergetik in der Psychologie. Selbstorganisation verstehen und gestalten. G?ttingen: Hogrefe.
 #' @references Schiepek, G. K., St?ger-Schmidinger, B., Aichhorn, W., Sch?ller, H., & Aas, B. (2016). Systemic case formulation, individualized process monitoring, and state dynamics in a case of dissociative identity disorder. Frontiers in psychology, 7, 1545.
+#'
 dyn_comp = function(df, col_first, col_last, scale_min, scale_max, win=NROW(df),  doPlot = FALSE){
 
 
@@ -229,9 +230,11 @@ DC_D = function (df, win, xmin, xmax, col_first, col_last){
 #' @description Computes significant peaks in the dynamic complexity time series. Example: Schiepek, Tominschek & Heinzel, 2014.
 #'
 #' @param df A dataframe of dynamic complexity values, e.g. output data from dyn_comp
-#' @param win Window size over which dynamic complexity was calculated (nescesary for plot)
+#' @param win Window size over which dynamic complexity was calculated (neccesary for plot)
+#' @param doPlot If \code{TRUE} shows a plot and returns a \code{\link[ggplot2]{ggplot}} object in a list. If \code{FALSE}, no plot will be drawn and no object will be returned (default = \code{FALSE})
 #'
 #' @return A list with a dataframe of binary critical instability indices and a summed critical intability index, a ggplot object containing a critical instability diagram.
+#'
 #' @export
 #'
 #' @author Merlijn Olthof
@@ -241,7 +244,7 @@ DC_D = function (df, win, xmin, xmax, col_first, col_last){
 #' @references Haken, H. & Schiepek, G. (2006, 2. Aufl. 2010). Synergetik in der Psychologie. Selbstorganisation verstehen und gestalten. G?ttingen: Hogrefe.
 #' @references Schiepek, G. K., Tominschek, I., & Heinzel, S. (2014). Self-organization in psychotherapy: testing the synergetic model of change processes. Frontiers in psychology, 5, 1089.
 #'
-crit_in = function(df, win){
+crit_in = function(df, win, doPlot = TRUE){
 
   df.ci <- matrix(data=NA, nrow=nrow(df), ncol=ncol(df))
   df.ci <- data.frame(df.ci)

R/nlRtsa_SOURCE.R

@@ -250,7 +250,7 @@ crqa_cl_main <- function(data,
 #' @param silent Do not display any messages (default = \code{TRUE})
 #' @param surrogateTest Perform surrogate tests. If \code{TRUE}, will run surrogate tests using default settings for a two-sided test of \eqn{H_0: The data generating process is a rescaled linear Gaussian process} at \eqn{\alpha = .05} (arguments \code{ns = 39, fft = TRUE, amplitude = TRUE})
 #' @param targetValue A value passed to \code{crqa_radius(...,type="fixed", targetMeasure="RR")} if \code{is.na(emRad)==TRUE}. This is useful for windowed analysis, it will estimate a new radius for each window.
-#' @param useParallel Speed up calculations by using the parallel processing options provided by \code{\link[multidplyr]{partition}} to assign a seperate process/core for each window in windowed (C)RQA analysis using \code{\link[purrr]{map2}} to assign data and \code{\link[parallel]{detectCores}} with  \code{logical = TRUE} to decide on the available cores (default = \code{FALSE})
+#' @param useParallel Speed up calculations by using the parallel processing options provided by `parallel` to assign a seperate process/core for each window in windowed (C)RQA analysis using \code{\link[purrr]{map2}} to assign data and \code{\link[parallel]{detectCores}} with  \code{logical = TRUE} to decide on the available cores (default = \code{FALSE})
 #' @param ... Additional parameters (currently not used)
 #'
 #' @details The \code{rp} executable is installed when the function is called for the first time and is renamed to \code{rp}, from a platform specific filename downloaded from \url{http://tocsy.pik-potsdam.de/commandline-rp.php} or extracted from an archive located in the directory: \code{...\\casnet\\commandline_rp\\}.
@@ -4372,8 +4372,6 @@ plotSUR_hist <- function(surrogateValues,
 
 
 
-
-
 #' Add transparency to a colour
 #'
 #' @param col A colour name, hexadecimal string or positive integer \code{i}, such that palette()[i]
@@ -4388,89 +4386,6 @@ add_alpha <- function(col, alpha=1){
 }
 
 
-#' plotRP
-#'
-#' @param crqaOutput    List output from \code{\link[crqa]{crqa}}
-#'
-#' @return A list
-#' @export
-#' @author Fred Hasselman
-#' @description Creates a recurrence plot from the sparse matrix output generated by \code{\link[crqa]{crqa}}.
-plotRP_crqa <- function(crqaOutput){
-
-  AUTO <- FALSE
-
-  # Is is crqa output?
-  if(all(names(crqaOutput)%in%c("RR","DET","NRLINE","maxL","L","ENTR","rENTR","LAM","TT","RP"))){
-
-    # RP dimensions
-    nr <- dim(crqaOutput$RP)[1]
-    nc <- dim(crqaOutput$RP)[2]
-
-    RP <- crqaOutput$RP
-
-    # AUTO or CROSS?
-    if(class(RP)=="dtCMatrix"){
-      message("\nRP in crqa output is a Triangular Sparse Matrix, this implies auto-recurrence...\n")
-      AUTO <- TRUE
-    }
-    if(isSymmetric(RP)){
-      message("\nRP in crqa output is a Symmetric Sparse Matrix, this implies auto-recurrence: \n >> RP Measures will include the Line of Identity, unless:\n >> crqa() with side = 'upper' or 'lower' was used.\n >> crqa() with Theiler window (tw) of 1 was used.")
-      AUTO <- TRUE}
-
-    if(nc*nr>10^6){
-      message(paste("\nLarge RP with",nc*nr,"elements... \n >> This could take some time to plot!\n"))
-    }
-
-    ifelse(AUTO,
-           Titles <- list(main="Auto Recurrence Plot", X = expression(Y[t]), Y = expression(Y[t])),
-           Titles <- list(main="Cross Recurrence Plot", X = expression(X[t]), Y = expression(Y[t]))
-    )
-
-
-    # Thresholded or Distance matrix?
-    ifelse(is.logical(as.array(RP)),
-           distPallette <- grDevices::colorRampPalette(c("white", "black"))(2),
-           distPallette <- grDevices::colorRampPalette(c("red", "white", "blue")) #( length(unique(as.vector(RP))))
-    )
-
-    #distPallette <- grDevices::colorRampPalette(c("white", "black"))(2)
-
-    lp <- levelplot(Matrix::as.matrix(RP),
-                    #colorkey = TRUE,
-                    region = TRUE, col.regions = distPallette, useRaster = TRUE, aspect = nc/nr,
-                    main = Titles$main,
-                    xlab = Titles$X,
-                    ylab = Titles$Y)
-
-    txt <- grid.text(paste0("\n   RR: ", round(crqaOutput$RR, digits = 1),
-                            "\n  DET: ", round(crqaOutput$DET, digits = 1),
-                            "\nmeanL: ", round(crqaOutput$maxL, digits = 1),
-                            "\n maxL: ", round(crqaOutput$NRLINE, digits = 1),
-                            "\n  LAM: ", round(crqaOutput$LAM, digits = 1),
-                            "\n   TT: ", round(crqaOutput$TT, digits = 1),
-                            "\n  ENT: ", round(crqaOutput$ENT, digits = 1),
-                            "\n rENT: ", round(crqaOutput$rENTR, digits = 1)),
-                     .02,.7, just = "left", draw = FALSE, gp = gpar(fontfamily = "mono", cex = .7))
-    # ,)
-
-    grid.arrange(lp, txt, ncol=2, nrow=1, widths=c(4, 1), heights=c(4))
-
-  } else {
-    warning("\nInput is not list output from function crqa().\n")
-  }
-
-}
-
-plotRP_fnn <- function(FNNoutput){
-  graphics::plot(FNNoutput["combined",],type="b",pch=16, cex=2, col="grey80", ylim=c(0,100), xaxt="n",
-       xlab = "Embedding Dimension", ylab = "False Nearest Neighbours")
-  graphics::lines(FNNoutput["atol",],type="b",pch="a",col="grey30", lty=2)
-  graphics::lines(FNNoutput["rtol",],type="b",pch="r", col="grey30",lty=2)
-  graphics::Axis(side=1,at=seq_along(FNNoutput[1,]),labels = dimnames(FNNoutput)[[2]])
-  graphics::legend("topright",c("Combined","atol","rtol"), pch = c(16,97,114), lty = c(1,2,2), col = c("grey80","grey30","grey30"), pt.cex=c(2,1,1))
-}
-
 # Complex Networks# graph2svg <- function(TDM,pname){
 #
 #   # Create weighted Term-Term matrix

inst/doc/cl_RQA.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Fred Hasselman" />
 
-<meta name="date" content="2018-03-28" />
+<meta name="date" content="2018-03-29" />
 
 <title>Using the CRQA command line interface (crqa_cl)</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Using the CRQA command line interface (crqa_cl)</h1>
 <h4 class="author"><em>Fred Hasselman</em></h4>
-<h4 class="date"><em>2018-03-28</em></h4>
+<h4 class="date"><em>2018-03-29</em></h4>