Move descriptive to jasp desciptives (#25)

* Move Description analysis to jaspDescriptives module

* set right jaspDescriptives

DESCRIPTION

@@ -12,9 +12,11 @@ Encoding: UTF-8
 Imports:
   jaspBase,
   jaspGraphs,
+  jaspDescriptives,
   forecast
 Suggests:
   testthat
 Remotes:
   jasp-stats/jaspBase,
-  jasp-stats/jaspGraphs
+  jasp-stats/jaspGraphs,
+  jasp-stats/jaspDescriptives

NAMESPACE

@@ -1,5 +1,16 @@
-import(jaspBase)
-export(DescriptivesTimeSeries)
 export(StationarityTimeSeries)
 export(ARIMATimeSeries)
 export(SpectralTimeSeries)
+export(DescriptivesTimeSeries)
+export(DescriptivesTimeSeriesInternal)
+import(jaspBase)
+importFrom(jaspDescriptives,.plotMarginal)
+importFrom(jaspDescriptives,.DescriptivesTimeSeries)
+importFrom(jaspDescriptives,.tsReadData)
+importFrom(jaspDescriptives,.tsErrorHandler)
+importFrom(jaspDescriptives,.tsGuessInterval)
+importFrom(jaspDescriptives,.tsDataFilterHandler)
+importFrom(jaspDescriptives,.tsDataWithMissingRowsHandler)
+importFrom(jaspDescriptives,.tsFillTimeSeriesPlot)
+importFrom(jaspDescriptives,.tsFillACF)
+

R/DescriptivesTimeSeries.R

@@ -15,220 +15,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-DescriptivesTimeSeries <- function(jaspResults, dataset, options) {
-  ready <- options$dependent != ""
-
-  datasetRaw <- .tsReadData(jaspResults, dataset, options, ready)
-
-  datasetFiltered <- .tsDataFilterHandler(datasetRaw, options, ready)
-
-  dataset <- .tsDataWithMissingRowsHandler(datasetFiltered, options, ready)
-
-  .tsErrorHandler(dataset, ready)
-
-  .tsDescriptivesTable(jaspResults, dataset, options, ready, position = 1, dependencies = c(.tsDescriptivesDependencies(), "descriptivesTableTransposed"))
-
-  .tsTimeSeriesPlotDescriptives(jaspResults, dataset, options, ready, position = 2, dependencies = c(.tsDescriptivesDependencies(), "timeSeriesPlot", "timeSeriesPlotType", "timeSeriesPlotDistribution"))
-
-  .tslagPlotDescriptives(jaspResults, dataset, options, ready, position = 3, dependencies = c(.tsDescriptivesDependencies(), "lagPlot", "lagPlotLag", "lagPlotRegressionType", "lagPlotRegressionLine", "lagPlotRegressionCi", "lagPlotRegressionCiLevel"))
-
-  .tsACFDescriptives(jaspResults, dataset, options, ready, position = 4, dependencies = c(.tsDescriptivesDependencies(), "acf", "acfCi", "acfCiLevel", "acfCiType", "acfZeroLag", "acfMaxLag"))
-
-  .tsPACFDescriptives(jaspResults, dataset, options, ready, position = 5, dependencies = c(.tsDescriptivesDependencies(), "pacf", "pacfCi", "pacfCiLevel", "pacfCiType", "pacfMaxLag"))
-}
-
-.tsDescriptivesDependencies <- function() {
-  return(c(
-    "dependent", "time",
-    "filter", "filterBy", "rowStart", "rowEnd",
-    "timeStart", "timeEnd", "dateStart", "dateEnd"
-  ))
-}
-
-.tsTimeSeriesPlotDescriptives <- function(jaspResults, dataset, options, ready, position, dependencies) {
-  if (!options$timeSeriesPlot) {
-    return()
-  }
-
-  if (is.null(jaspResults[["timeSeriesPlot"]])) {
-    plot <- createJaspPlot(title = gettext("Time Series Plot"), width = 660)
-    plot$dependOn(dependencies)
-    plot$position <- position
-
-    jaspResults[["timeSeriesPlot"]] <- plot
-
-    if (!ready) {
-      return()
-    }
-
-    .tsFillTimeSeriesPlot(
-      plot, dataset, options,
-      type = options$timeSeriesPlotType,
-      distribution = options$timeSeriesPlotDistribution
-    )
-  }
-}
-
-.tslagPlotDescriptives <- function(jaspResults, dataset, options, ready, position, dependencies) {
-  if (!options$lagPlot) {
-    return()
-  }
-
-  if (is.null(jaspResults[["lagPlot"]])) {
-    plot <- createJaspPlot(title = gettext("Lag Plot"))
-    plot$dependOn(dependencies)
-    plot$position <- position
-
-    jaspResults[["lagPlot"]] <- plot
-
-    if (!ready) {
-      return()
-    }
-
-    .tsFillLagPlot(plot, dataset, options)
-  }
-}
-
-.tsFillLagPlot <- function(lagPlot, dataset, options) {
-  # create lag version of y
-  yLag <- c(rep(NA, options$lagPlotLag), dataset$y[1:(length(dataset$y) - options$lagPlotLag)])
-
-  yName <- decodeColNames(options$dependent[1])
-  xName <- as.expression(bquote(.(yName)[t - .(options$lagPlotLag)]))
-  yName <- as.expression(bquote(.(yName)[t]))
-
-  dat <- data.frame(y = dataset$y, yLag)
-  dat <- na.omit(dat)
-
-  breaks <- jaspGraphs::getPrettyAxisBreaks(c(dat$y, dat$yLag))
-
-  p <- jaspGraphs::JASPScatterPlot(
-    dat$yLag, dat$y,
-    xName = xName,
-    yName = yName,
-    addSmooth = options$lagPlotRegressionLine,
-    addSmoothCI = options$lagPlotRegressionCi,
-    smoothCIValue = options$lagPlotRegressionCiLevel,
-    forceLinearSmooth = options$lagPlotRegressionType == "linear",
-    plotAbove = "none", plotRight = "none"
-  )
-
-  # make sure the y-axis and the x-axis have the same breaks
-  p$subplots$mainPlot <- p$subplots$mainPlot +
-    ggplot2::scale_x_continuous(breaks = breaks, limits = range(breaks)) +
-    ggplot2::scale_y_continuous(breaks = breaks, limits = range(breaks)) +
-    jaspGraphs::geom_rangeframe() +
-    jaspGraphs::themeJaspRaw()
-
-  lagPlot$plotObject <- p
-
-  return()
-}
-
-.tsACFDescriptives <- function(jaspResults, dataset, options, ready, position, dependencies) {
-  if (!options$acf) {
-    return()
-  }
-
-  if (is.null(jaspResults[["acfPlot"]])) {
-    plot <- createJaspPlot(title = gettext("Autocorrelation Function"))
-    plot$dependOn(dependencies)
-    plot$position <- position
-
-    jaspResults[["acfPlot"]] <- plot
-
-    if (!ready) {
-      return()
-    }
-
-    .tsFillACF(plot,
-      type = "ACF", dataset, options,
-      zeroLag = options$acfZeroLag,
-      maxLag = options$acfMaxLag,
-      ci = options$acfCi,
-      ciValue = options$acfCiLevel,
-      ciType = options$acfCiType
-    )
-  }
-}
-
-.tsPACFDescriptives <- function(jaspResults, dataset, options, ready, position, dependencies) {
-  if (!options$pacf) {
-    return()
-  }
-
-  if (is.null(jaspResults[["pacfPlot"]])) {
-    plot <- createJaspPlot(title = gettext("Partial Autocorrelation Function"))
-    plot$dependOn(dependencies)
-    plot$position <- position
-
-    jaspResults[["pacfPlot"]] <- plot
-
-    if (!ready) {
-      return()
-    }
-
-    .tsFillACF(plot,
-      type = "PACF", dataset, options,
-      maxLag = options$pacfMaxLag,
-      ci = options$pacfCi,
-      ciValue = options$pacfCiLevel,
-      ciType = options$pacfCiType
-    )
-  }
-}
-
-.tsDescriptivesTable <- function(jaspResults, dataset, options, ready, position, dependencies) {
-  if (!is.null(jaspResults[["descriptivesTable"]])) {
-    return()
-  }
-
-  table <- createJaspTable(gettext("Descriptive Statistics"))
-  table$dependOn(dependencies)
-  table$position <- position
-  table$showSpecifiedColumnsOnly <- TRUE
-  table$transpose <- !options[["descriptivesTableTransposed"]] # the table is transposed by default
-
-  table$addColumnInfo(name = "variable", title = " ", type = "string")
-  table$addColumnInfo(name = "valid", title = gettext("Valid"), type = "integer")
-  table$addColumnInfo(name = "missing", title = gettext("Missing"), type = "integer")
-  table$addColumnInfo(name = "mean", title = gettext("Mean"), type = "number")
-  table$addColumnInfo(name = "sd", title = gettext("Std. Deviation"), type = "number")
-  table$addColumnInfo(name = "var", title = gettext("Variance"), type = "number")
-  table$addColumnInfo(name = "range", title = gettext("Range"), type = "number")
-  table$addColumnInfo(name = "min", title = gettext("Minimum"), type = "number")
-  table$addColumnInfo(name = "max", title = gettext("Maximum"), type = "number")
-  table$addColumnInfo(name = "start", title = gettext("Start"), type = "number")
-  table$addColumnInfo(name = "end", title = gettext("End"), type = "number")
-  table$addColumnInfo(name = "ar", title = gettext("Lag 1 Autocorrelation"), type = "number")
-
-  jaspResults[["descriptivesTable"]] <- table
-
-  if (ready) {
-    na.omitted <- na.omit(dataset$y)
-    yName <- options$dependent[1]
-
-    nY <- length(na.omitted)
-    minY <- min(na.omitted)
-    maxY <- max(na.omitted)
-
-    yLag <- c(NA, dataset$y[1:(length(dataset$y) - 1)])
-    corY <- cor(dataset$y, yLag, use = "complete.obs")
-
-    rows <- data.frame(
-      variable = yName,
-      valid = nY,
-      missing = nrow(dataset) - nY,
-      mean = mean(na.omitted),
-      sd = sd(na.omitted),
-      var = var(na.omitted),
-      range = maxY - minY,
-      min = minY,
-      max = maxY,
-      start = na.omitted[1],
-      end = na.omitted[nY],
-      ar = corY
-    )
-    table$addRows(rows)
-  }
+DescriptivesTimeSeriesInternal <- function(jaspResults, dataset, options) {
+    jaspDescriptives::.DescriptivesTimeSeries(jaspResults, dataset, options)
 }

R/DescriptivesTimeSeriesWrapper.R

@@ -0,0 +1,70 @@
+#
+# Copyright (C) 2013-2022 University of Amsterdam
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+# This is a generated file. Don't change it
+
+DescriptivesTimeSeries <- function(
+          data = NULL,
+          version = "0.18.3",
+          acf = FALSE,
+          acfCi = TRUE,
+          acfCiLevel = 0.95,
+          acfCiType = "whiteNoise",
+          acfMaxLag = 10,
+          acfZeroLag = FALSE,
+          dateEnd = "",
+          dateStart = "",
+          dependent = "",
+          descriptivesTableTransposed = FALSE,
+          filter = FALSE,
+          filterBy = "row",
+          lagPlot = FALSE,
+          lagPlotLag = 1,
+          lagPlotRegressionCi = TRUE,
+          lagPlotRegressionCiLevel = 0.95,
+          lagPlotRegressionLine = TRUE,
+          lagPlotRegressionType = "smooth",
+          pacf = FALSE,
+          pacfCi = TRUE,
+          pacfCiLevel = 0.95,
+          pacfMaxLag = 10,
+          plotHeight = 320,
+          plotWidth = 480,
+          rowEnd = 100,
+          rowStart = 1,
+          time = "",
+          timeEnd = 100,
+          timeSeriesPlot = TRUE,
+          timeSeriesPlotDistribution = "none",
+          timeSeriesPlotType = "both",
+          timeStart = 1) {
+
+   defaultArgCalls <- formals(jaspTimeSeries::DescriptivesTimeSeries)
+   defaultArgs <- lapply(defaultArgCalls, eval)
+   options <- as.list(match.call())[-1L]
+   options <- lapply(options, eval)
+   defaults <- setdiff(names(defaultArgs), names(options))
+   options[defaults] <- defaultArgs[defaults]
+   options[["data"]] <- NULL
+   options[["version"]] <- NULL
+
+   optionsWithFormula <- c("dependent", "time")
+   for (name in optionsWithFormula) {
+      if ((name %in% optionsWithFormula) && inherits(options[[name]], "formula")) options[[name]] = jaspBase::jaspFormula(options[[name]], data)   }
+
+   return(jaspBase::runWrappedAnalysis("jaspTimeSeries::DescriptivesTimeSeries", data, options, version))
+}