freq_graph: Frequency graph

In Tan-Furukawa/MCMCfreq: Bayesian Gaussian Process regression with Stan: computation of frequency by MCMC

Description

Drawing frequency graph (density plot) and analyzing the out put of cmpt_auto_freq or cmpt_freq.

Usage

freq_graph(data, x_min = NA, x_max = NA, y_max = NA,
  uncertainty = TRUE, rug_plot = 1, graphic_theme = 1, grid = 1,
  xlab = "Age (Ma)", ylab = "frequency", grid_color = "grey30",
  area_color = "grey80", line_color = "black",
  rug_plot_color = rgb(0, 0, 0, alpha = 0.6), hist = FALSE,
  hist_bin = as.integer(50), hist_height = 0.2, hist_color = rgb(1,
  0.62, 0, alpha = 0.6), analyze = FALSE)

Arguments

data	list data of the result of functions; auto_cmpt_freq() or cmpt_freq().
x_min	numeric; the smallest end point of x axis.
x_max	numeric; the largest end point of x axis.
y_max	numeric; the largest end point of y axis.
uncertainty	logical; if TRUE (default), drawing 95 percent confident interval of the estimate line.
rug_plot	apply data points' shape of rug plot. 0: no plot 1: thin line plot (default) 2: thin square plot. This plot should be used for discrete data, such as integer data. 3: thick square plot. Also used for discrete data
graphic_theme	one of either: 1: default theme, with y axis label, graph frame, and grid. 2: simple theme, only with x axis in plot area.
grid	one of either (only used if graphic_theme = 1): 0: no grid 1: dotted grid (default)
xlab	a text style title for the x axis. Defaults to "Age (Ma)".
ylab	a text style title for the y axis, only used if graphic_theme = 1.
grid_color	the color to be used for grid, only used if graphic_theme = 1. Defaults to "grey30".
area_color	the color to be used for 95 percent confident interval area, only used if uncertainty = 1. Defaults to "grey80".
line_color	the color to be used for estimate line. Defaults to "black".
rug_plot_color	the color to be used for rug plot. Defaults to rgb(0, 0, 0, alpha = .6).
hist	logical; if TRUE, drawing histogram in plot area. Defaults to FALSE.
hist_bin	integer, larger than 0. Number of histogram bins. Only used if hist = TRUE.
hist_height	numeric, between 0 and 1. If hist_height = 1, then the height of largest bin is that of plot area. Generally, the height is hist_height times. Only used if hist = TRUE.
hist_color	the color to be used for histgrams. Defaults to rgb(1, 0.62, 0, alpha = .6). Only used if hist = TRUE.
analyze	logical; if TRUE, drawing the peak x-coordinate, largest and smallest data, and number of data. Defaults to FALSE.

Value

data.frame of the x-coordinats and height of peaks. Only returned if analyze =TRUE.

Examples

d <- Osayama
e <- cmpt_freq(d,rho=3,sigma=2)
freq_graph(e)

Tan-Furukawa/MCMCfreq documentation built on Feb. 7, 2020, 10:25 a.m.