Analysis

Birds

level1a

DD estimations

• 112 Estimated phylo
• 19.858 computing time
• 52 phylogenies with non zero ext rate
• 11.075 computing time
• 6 phylogenies with DDD numerical issues

PD estimations

• 112 Estimated phylo
• 16.193 computing time
• 52 phylogenies with non zero ext rate
• 8.334 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

level1b

DD estimations

• 49 Estimated phylo
• 23.612 computing time
• 49 phylogenies with non zero ext rate
• 23.612 computing time
• 6 phylogenies with DDD numerical issues

PD estimations

• 49 Estimated phylo
• 21.047 computing time
• 49 phylogenies with non zero ext rate
• 21.047 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

level1c

DD estimations

• 50 Estimated phylo
• 29.012 computing time
• 50 phylogenies with non zero ext rate
• 29.012 computing time
• 6 phylogenies with DDD numerical issues

PD estimations

• 50 Estimated phylo
• 260.021 computing time
• 50 phylogenies with non zero ext rate
• 260.021 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

Comments about results

Cacatuidae

load("~/Dropbox/Pancho/05 - SystematicBiology (paper 2)/DEphasis/results/DD/level1/Cacatuidae.RData")
pars2 = c(1000,1,0,1,0,2)


pars_dd = DDD:::dd_ML(brts = input$brts,cond = 0,soc=2)

pars1 = c(pars_dd$lambda,pars_dd$mu,pars_dd$K)
pars1 = c(1.211,0.196,(1.211-0.196)/0.055   )
DDD:::dd_loglik(pars1 = pars1,pars2 = pars2,brts = input$brts,missnumspec = 0)

Cotingidae

In this case, computing times are similar and we could make emphasis way faster if we cut off until iteration 30.

Mammals

level1d

DD estimations

• 61 Estimated phylo
• 34.005 computing time
• 21 phylogenies with non zero ext rate
• 9.469 computing time
• 2 phylogenies with DDD numerical issues

PD estimations

• 61 Estimated phylo
• 35.028 computing time
• 21 phylogenies with non zero ext rate
• 7.521 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

level1b

DD estimations

• 15 Estimated phylo
• 45.31 computing time
• 15 phylogenies with non zero ext rate
• 45.31 computing time
• 2 phylogenies with DDD numerical issues

PD estimations

• 15 Estimated phylo
• 124.456 computing time
• 15 phylogenies with non zero ext rate
• 124.456 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

Amphibia

level1b

     Caecilidae          Hynobiidae       Salamandridae      Plethodontidae 
             42                  60                 103                 440 
       Alytidae      Bombinatoridae             Pipidae Eleutherodactylidae 
             11                  10                  33                 207 
      Alsodidae             Ranidae 
             29                 363 

DD estimations

• 7 Estimated phylo
• 5.483 computing time
• 3 phylogenies with non zero ext rate
• 2.984 computing time
• 2 phylogenies with DDD numerical issues

PD estimations

• 7 Estimated phylo
• 9.272 computing time
• 3 phylogenies with non zero ext rate
• 3.896 computing time

level1b

DD estimations

• 7 Estimated phylo
• 5.483 computing time
• 3 phylogenies with non zero ext rate
• 2.984 computing time
• 2 phylogenies with DDD numerical issues

PD estimations

• 7 Estimated phylo
• 9.272 computing time
• 3 phylogenies with non zero ext rate
• 3.896 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]

Squamate

level1a

Xantusiidae  Gerrhosauridae      Cordylidae       Varanidae  Chamaeleonidae 
         34              35              64              73             198 
  Iguanidae   Crotaphytidae Phrynosomatidae      Pythonidae       Viperidae 
         38              12             144              40             321 
 Colubridae 
        825 

DD estimations

• 8 Estimated phylo
• 3.1 computing time
• 1 phylogenies with non zero ext rate
• 0.52 computing time
• 0 phylogenies with DDD numerical issues

PD estimations

• 8 Estimated phylo
• 1.702 computing time
• 1 phylogenies with non zero ext rate
• 0.186 computing time

CrocoTurtle

level1a

DD estimations

• 1 Estimated phylo
• 21.954 computing time
• 1 phylogenies with non zero ext rate
• 21.954 computing time
• 0 phylogenies with DDD numerical issues

PD estimations

• 1 Estimated phylo
• 33.874 computing time
• 1 phylogenies with non zero ext rate
• 33.874 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]]

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

[[3]] [[4]] [[5]]

All

level1a

DD estimations

• 67 Estimated phylo
• 75.02 computing time
• 67 phylogenies with non zero ext rate
• 75.02 computing time
• 10 phylogenies with DDD numerical issues

PD estimations

• 67 Estimated phylo
• 84.647 computing time
• 67 phylogenies with non zero ext rate
• 84.647 computing time

[[1]]

## `geom_smooth()` using formula 'y ~ x'

[[2]] [[3]] [[4]] [[5]]