sephora-methods: Plot methods for 'sephora'
In sephora: Statistical Estimation of Phenological Parameters

plot.sephora

R Documentation

Plot methods for `sephora`

Description

Methods associated with sephora-class.

Usage

## S3 method for class 'sephora'
plot(
  x,
  y,
  startYear,
  endYear,
  frequency,
  type = NULL,
  sizeLine = 1,
  sizePoint = 2,
  position_legend = "none",
  title_legend = NULL,
  xLab = "Time",
  yLab = "Index",
  xLim,
  msTitle = "Cluster",
  pointShape = 16,
  pointSize = 2,
  pointStroke = 3,
  textFontface = 2,
  textSize = 5,
  text_hjust = 0.5,
  text_vjust = -0.5,
  ...
)

Arguments

`x`	a numeric vector or a `sephora` object.
`y`	ignored.
`startYear`	integer, time series initial year.
`endYear`	integer, time series final year.
`frequency`	integer giving number of observations per season.
`type`	character specifying type of plot. By default, `NULL`; "profiles", "ms" and "derivatives" are also allowed. See Details.
`sizeLine`	integer giving line size
`sizePoint`	integer giving point size
`position_legend`	character. Should a legend be added? Where? See `theme`.
`title_legend`	character. Should a legend be added? What would it be? See `theme` and Details.
`xLab`	character, label to display in x-axis.
`yLab`	character, label to display in y-axis. See Details.
`xLim`	date vector of length 2 indicating limits of x-axis. When no supplied, `x` will be displayed in the period of time defined by `startYear`, `endYear` and `frequency`.
`msTitle`	character. Default "Cluster". See Details.
`pointShape`	`shape` parameter used in `geom_point`. Default 16. See Details.
`pointSize`	`size` parameter used in `geom_point`. Default 2. See Details.
`pointStroke`	`stroke` parameter used in `geom_point`. Default 3. See Details.
`textFontface`	`fontface` parameter used in `geom_text`. Default 2. See Details.
`textSize`	`size` parameters used in `geom_text`. Default 5. See Details.
`text_hjust`	`hjust` parameter used in `geom_text`. Default 0.5. See Details.
`text_vjust`	`vjust` parameter used in `geom_text`. Default -0.5. See Details.
`...`	additional `ggplot` parameters.

Details

By default, type=NULL and this option allows for plotting numeric vectors and sephora objects; argument title_legend is only pertinent in this case. Other allowed options for type are "profiles", "ms" and "derivatives". When type="profiles" all the arguments used in the default case are allowed except for title_legend. When type="ms", arguments msTitle, pointShape, pointSize, pointStroke, textFontface, textSize, text_hjust and text_vjust are pertinent. When type="derivatives", the default value of argument yLab will be used.

Value

A gg object (or NULL (invisible) when type="derivatives").

Plotting

This function draws either a graphic based on a ggplot or a plot object.

The default is intended for numeric vectors and sephora-class objects. This method employs the ggplot2 system and returns a sort of time series plot.

The method profiles, selected when type="profiles", is also intended for numeric vectors and sephora-class objects. This method is based on the ggplot2 system and draws p curves, one for each period (p=length(startYear:endYear)), on the same time scale (days of the year).

The method ms, selected when type="ms", is intended for sephora-class objects only. Using the ggplot2 system this method draws the result of a multidimensional scaling analysis performed on the smoothed version of the p curves described above.

The method derivative, selected when type="derivatives", is intended for sephora-class objects only. A 5-panel plot is drawn showing (from top to bottom):

FPCA estimate: the fpca entry of sephora-class object. See phenopar.
First, second, third and fourht derivative of FPCA estimate: curve obtained by applying ndvi_derivatives to FPCA estimate.