In [5]:

    

require(evolqg)
require(ggplot2)
require(geomorph)
require(shapes)
require(magrittr)

load('../data/Primates/06_grouped.RData')


    

In [6]:

    

primates %>% str


    

    




List of 4
 $ extinct:List of 2
  ..$ coord: num [1:36, 1:3, 1:2, 1:31] -48.09 -37.06 -19.41 9.22 37.11 ...
  .. ..- attr(*, "dimnames")=List of 4
  .. .. ..$ : chr [1:36] "IS" "NSL" "NA" "BR" ...
  .. .. ..$ : chr [1:3] "X" "Y" "Z"
  .. .. ..$ : NULL
  .. .. ..$ : NULL
  ..$ info :'data.frame':	31 obs. of  15 variables:
  .. ..$ ID    : Factor w/ 1840 levels "AMNH100503","AMNH100504",..: 98 271 101 99 94 270 426 412 428 429 ...
  .. ..$ GEN   : Factor w/ 32 levels "","Allocebus",..: 19 3 3 25 18 18 3 3 3 3 ...
  .. ..$ SPE   : Factor w/ 76 levels "","adipicaudatus",..: 55 42 56 43 40 25 NA NA NA NA ...
  .. ..$ SUB   : Factor w/ 19 levels "bengalensis",..: NA NA NA NA NA NA NA NA NA NA ...
  .. ..$ GROUP : logi [1:31] NA NA NA NA NA NA ...
  .. ..$ MSM   : Factor w/ 9 levels "AMNH","FMNH",..: 1 1 1 1 1 1 3 3 3 3 ...
  .. ..$ IDORI : Factor w/ 130 levels ""," majori"," Propithecus edwardsi?",..: 74 2 5 93 72 71 6 6 6 6 ...
  .. ..$ SEX   : Factor w/ 2 levels "F","M": NA NA NA NA NA NA NA NA NA NA ...
  .. ..$ LOC   : Factor w/ 337 levels "","0","Eminiminy",..: 49 50 49 49 NA NA 1 71 70 70 ...
  .. ..$ DIET  : logi [1:31] NA NA NA NA NA NA ...
  .. ..$ REP   : logi [1:31] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. ..$ MISS  : logi [1:31] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. ..$ FOSSIL: logi [1:31] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. ..$ MAJOR : Factor w/ 1 level "Prosimian": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ FILE  : Factor w/ 268 levels "AMNH_NewYork/Madagascar/Avahi/Avahi_A_ok.xlsx",..: 41 41 41 41 41 41 78 78 78 78 ...
 $ info   :'data.frame':	10084 obs. of  17 variables:
  ..$ ID    : Factor w/ 10068 levels "_A100014","_A100018",..: 9159 9160 9161 9166 9167 9168 9169 9170 9171 9174 ...
  ..$ GEN   : Factor w/ 68 levels "Allenopithecus",..: 6 3 3 6 6 6 6 6 6 3 ...
  ..$ SPE   : Factor w/ 286 levels "adipicaudatus",..: 105 202 202 105 105 105 105 105 105 46 ...
  ..$ SUB   : Factor w/ 262 levels "abbotti","aequatorialis",..: 90 150 150 90 90 90 90 90 90 42 ...
  ..$ GROUP : Factor w/ 19 levels "","argentata",..: 8 1 1 8 8 8 8 8 8 1 ...
  ..$ MSM   : Factor w/ 26 levels "","AIMZU","AMNH",..: 25 25 25 25 25 25 25 25 25 25 ...
  ..$ IDORI : Factor w/ 235 levels "","?","?, se for Co",..: 6 12 12 6 6 6 6 6 6 56 ...
  ..$ SEX   : Factor w/ 2 levels "F","M": 1 1 1 1 1 2 2 1 1 2 ...
  ..$ LOC   : Factor w/ 1272 levels "","0.5 mi de Ju",..: 899 571 571 64 684 684 684 684 684 201 ...
  ..$ DIET  : Factor w/ 4 levels "FruitLeaves",..: 1 1 1 1 1 1 1 1 1 1 ...
  ..$ REP   : logi [1:10084] FALSE FALSE FALSE FALSE FALSE FALSE ...
  ..$ MISS  : logi [1:10084] FALSE TRUE FALSE FALSE FALSE FALSE ...
  ..$ MAJOR : Factor w/ 4 levels "Catarrhini","Homo",..: 3 3 3 3 3 3 3 3 3 3 ...
  ..$ FILE  : Factor w/ 507 levels "AIMZU Hylobates 01",..: NA NA NA NA NA NA NA NA NA NA ...
  ..$ HALF  : logi [1:10084] NA NA NA NA NA NA ...
  ..$ RIGHT : logi [1:10084] NA NA NA NA NA NA ...
  ..$ FOSSIL: logi [1:10084] NA NA NA NA NA NA ...
 $ coord  : num [1:36, 1:3, 1:10084] 1.87 3.07 3.17 2.27 -2.15 ...
  ..- attr(*, "dimnames")=List of 3
  .. ..$ : chr [1:36] "IS" "NSL" "NA" "BR" ...
  .. ..$ : chr [1:3] "X" "Y" "Z"
  .. ..$ : chr [1:10084] "USNM_100517" "USNM_100519" "USNM_100521" "USNM_108275" ...
 $ rep    : num [1:36, 1:3, 1:2, 1:5990] -0.4111 0.1889 0.0889 0.4889 0.9116 ...
  ..- attr(*, "dimnames")=List of 4
  .. ..$ : chr [1:36] "IS" "NSL" "NA" "BR" ...
  .. ..$ : chr [1:3] "X" "Y" "Z"
  .. ..$ : chr [1:2] "R1" "R2"
  .. ..$ : chr [1:5990] "AMNH_133694" "AMNH_133695" "AMNH_183290" "USNM_194355" ...