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Plot

Source: R/AllGenerics.R, R/plot.R
plot.Rd

Plot

Usage

multiplot(...)

# S4 method for MCMC
autoplot(
  object,
  ...,
  select = NULL,
  groups = NULL,
  density = TRUE,
  interval = NULL,
  level = 0.95,
  decreasing = TRUE
)

# S4 method for MCMC,missing
plot(
  x,
  select = NULL,
  groups = NULL,
  density = TRUE,
  interval = NULL,
  level = 0.95,
  decreasing = TRUE,
  ...
)

# S4 method for PhasesMCMC
autoplot(
  object,
  ...,
  select = NULL,
  level = 0.95,
  range = NULL,
  decreasing = TRUE,
  facet = TRUE
)

# S4 method for PhasesMCMC,missing
plot(
  x,
  select = NULL,
  level = 0.95,
  range = NULL,
  decreasing = TRUE,
  facet = TRUE,
  ...
)

Arguments

...

Extra parameters to be passed to stats::density().

object, x

An MCMC or a PhasesMCMC object.

select

An integer vector specifying the index of the MCMC samples to be drawn.

groups

A character vector used for mapping colours.

density

A logical scalar: should estimated density be plotted?

interval

A character string specifying the confidence interval to be drawn. It must be one of "credible" (credible interval) or "hpdi" (highest posterior density interval). Any unambiguous substring can be given. If NULL (the default) no interval is computed.

level

A length-one numeric vector giving the confidence level.

decreasing

A logical scalar: should the sort order be decreasing?

range

A character string specifying the additional time range to be displayed. It must be one of "hiatus" or "transition". If NULL (the default), no additional time ranges are displayed.

facet

A logical scalar: should a matrix of panels defined by phase be drawn?

Value

  • autoplot() returns a ggplot object.

  • plot() is called it for its side-effects: it results in a graphic being displayed (invisibly returns x).

Methods (by class)

  • plot(x = MCMC, y = missing): Plots of credible intervals or HPD regions of a series of events.

  • plot(x = PhasesMCMC, y = missing): Plots the characteristics of a group of events (phase).

See also

stats::density()

Author

A. Philippe, M.-A. Vibet, T. S. Dye, N. Frerebeau

Examples

## Coerce to MCMC
eve <- as_events(events, calendar = "CE", iteration = 1)

## BP
eve_BP <- CE_to_BP(eve)
summary(eve_BP)
#>     mad mean  sd  min   q1 median   q3  max lower upper
#> E1 2849 2587 271 1954 2335   2607 2838 3298  2995  2151
#> E2 3715 3734  99 2920 3668   3734 3806 3949  3930  3560
#> E3 2651 2605  91 2016 2560   2621 2666 3178  2752  2399
#> E4 3190 3185  86 2668 3130   3184 3238 3813  3350  3013

## CE
eve_CE <- BP_to_CE(eve_BP)
summary(eve_CE)
#>      mad  mean  sd   min    q1 median    q3  max lower upper
#> E1  -900  -638 271 -1349  -889   -658  -386   -5 -1046  -202
#> E2 -1766 -1785  99 -2000 -1857  -1785 -1719 -971 -1981 -1611
#> E3  -702  -656  91 -1229  -717   -672  -611  -67  -803  -450
#> E4 -1241 -1236  86 -1864 -1289  -1235 -1181 -719 -1401 -1064

## Plot events
plot(eve_CE, interval = "credible", level = 0.68)
#> Picking joint bandwidth of 15.1

plot(eve_BP, interval = "hpdi", level = 0.68)
#> Picking joint bandwidth of 15.1


## Compute phases
pha <- phase(eve, groups = list(B = c(2, 4), A = c(1, 3)))
summary(pha)
#> $B
#>            mad  mean  sd   min    q1 median    q3   max lower upper
#> start    -1766 -1785  99 -2000 -1857  -1785 -1719 -1223 -1981 -1611
#> end      -1240 -1235  86 -1833 -1289  -1235 -1181  -719 -1404 -1067
#> duration   560   550 131     4   463    551   638  1156   296   805
#> 
#> $A
#>           mad mean  sd   min   q1 median   q3  max lower upper
#> start    -708 -773 147 -1349 -890   -749 -671 -207 -1059  -501
#> end      -690 -521 168 -1050 -670   -537 -384   -5  -776  -214
#> duration  277  252 137     0  150    248  344  879     0   486
#> 

## Plot phases
plot(pha)

plot(pha, range = "hiatus")

plot(pha, range = "transition")