Compute Phases

Source: R/AllGenerics.R, R/phases.R

Constructs the minimum and maximum for a group of events (phase).

phases(x, groups, ...)

# S4 method for class 'EventsMCMC,missing'
phases(x)

# S4 method for class 'EventsMCMC,list'
phases(x, groups)

Arguments

x

An EventsMCMC.

groups

A list of (named) vector of names or indexes of columns in x (see phases()).

...

Currently not used.

Value

A PhasesMCMC object.

Note

The default value of start or end corresponds to a CSV file exported from ChronoModel.

See also

Other phase tools: duration()

Author

A. Philippe, M.-A. Vibet, N. Frerebeau

Examples

## Coerce to phases
(pha <- as_phases(mcmc_phases, start = c(1, 3), calendar = CE(), iteration = 1))
#> <PhasesMCMC>
#> - Number of phases: 2
#> - Number of MCMC samples: 30000
summary(pha, calendar = CE())
#> $P1
#>           mad mean  sd   min   q1 median   q3  max start  end
#> start    -708 -773 148 -1349 -890   -749 -671 -207 -1059 -501
#> end      -690 -521 169 -1050 -670   -537 -384   -5  -776 -214
#> duration  278  253 138     1  151    249  345  880     1  487
#> 
#> $P2
#>            mad  mean  sd   min    q1 median    q3   max start   end
#> start    -1766 -1785 100 -2000 -1857  -1785 -1719 -1223 -1981 -1611
#> end      -1240 -1235  87 -1833 -1289  -1235 -1181  -719 -1404 -1067
#> duration   561   551 132     5   464    552   639  1157   297   806
#> 

## Plot phases
plot(pha)

plot(pha, succession = "hiatus")

plot(pha, succession = "transition")


## Compute phases from events
(eve <- as_events(mcmc_events, calendar = CE(), iteration = 1))
#> <EventsMCMC>
#> - Number of events: 4
#> - Number of MCMC samples: 30000

## Compute min-max range for all chains
pha1 <- phases(eve)
summary(pha1, calendar = CE())
#> $P1
#>            mad  mean  sd   min    q1 median    q3   max start   end
#> start    -1766 -1785 100 -2000 -1857  -1785 -1719 -1223 -1981 -1611
#> end       -690  -521 169 -1050  -670   -537  -384    -5  -776  -214
#> duration  1167  1265 196   483  1116   1253  1411  1947   915  1637
#> 

## Compute min-max range by group
pha2 <- phases(eve, groups = list(phase_1 = c(1, 3), phase_2 = c(2, 4)))
summary(pha2, calendar = CE())
#> $phase_1
#>           mad mean  sd   min   q1 median   q3  max start  end
#> start    -708 -773 148 -1349 -890   -749 -671 -207 -1059 -501
#> end      -690 -521 169 -1050 -670   -537 -384   -5  -776 -214
#> duration  278  253 138     1  151    249  345  880     1  487
#> 
#> $phase_2
#>            mad  mean  sd   min    q1 median    q3   max start   end
#> start    -1766 -1785 100 -2000 -1857  -1785 -1719 -1223 -1981 -1611
#> end      -1240 -1235  87 -1833 -1289  -1235 -1181  -719 -1404 -1067
#> duration   561   551 132     5   464    552   639  1157   297   806
#> 


zz <- pha@.Data
head(zz)
#> , , start
#> 
#>             P1        P2
#> [1,] -319045.0 -625448.0
#> [2,] -273570.0 -629970.0
#> [3,] -335555.9 -604871.0
#> [4,] -319169.8 -609557.0
#> [5,] -323497.0 -706432.8
#> [6,] -355422.6 -677593.3
#> 
#> , , end
#> 
#>             P1        P2
#> [1,] -267769.1 -399848.8
#> [2,] -270327.0 -435810.7
#> [3,] -231655.0 -431449.5
#> [4,] -255757.0 -448294.4
#> [5,] -300265.5 -478087.0
#> [6,] -263102.0 -444912.5
#> 

head(zz[, 1, ])
#>          start       end
#> [1,] -319045.0 -267769.1
#> [2,] -273570.0 -270327.0
#> [3,] -335555.9 -231655.0
#> [4,] -319169.8 -255757.0
#> [5,] -323497.0 -300265.5
#> [6,] -355422.6 -263102.0

head(pha)
#> <PhasesMCMC>
#> - Number of phases: 2
#> - Number of MCMC samples: 6