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Automatically imports all the pts files containing landmark coordinates exported from landmark editor or Stratovan checkpoint in your working directory storing everything in a 3D array ready for Procrustes superimposition.

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importpts

import.pts() Narimane Chatar 23/05/2021

Automatically imports all the pts files containing landmark coordinates exported from landmark editor or Stratovan checkpoint in your working directory storing everything in a 3D array ready for Procrustes superimposition using gpagen.

MOST COMMON ERROR MESSAGE

      # Error in ptsarray[, , i] <- as.matrix(read.table(file = ptslist[i],  : 
      # number of items to replace is not a multiple of replacement length

      MEANING:  - some of your pts files do not have the same number of landmarks or 
                - you introduced a number of landmarks that does not correspond to your data. 
      Check all the files in a notepad

Example

Working directory containing 45 pts files, each of them containing 37 points. Data from Chatar & al 2021

Chatar, N., Fischer, V., Siliceo, G. et al. Morphometric Analysis of the Mandible of Primitive Sabertoothed Felids from the late Miocene of Spain. J Mammal Evol 28, 753–771 (2021). https://doi.org/10.1007/s10914-021-09541-0

image image

      import.pts(Landmark = 37)

or

      import.pts(37)

Returns two objetcs:

  1. 'ptslist', a list of all the pts files stored in your working directory:

       > ptslist
        [1] "Acinonyx_j_MNCN_COMP_3438.pts"        "Amphimachairodus_G_BC_102.pts"        "Caracal_c_MAV_1518.pts"              
        [4] "Dinofelis_b_DNMNH_BF_55_23.pts"       "Felis_l_MAV-965.pts"                  "Homotherium_c_CB_06.pts"             
        [7] "Lynx_r_OUVC_9576.pts"                 "Machairodus_a_B 2230.pts"             "Machairodus_a_B_382.pts"             
       [10] "Machairodus_a_B_3974.pts"             "Machairodus_a_BAT_1_01_E7_82.pts"     "Machairodus_a_BAT_1_04_F6_130.pts"   
       [13] "Machairodus_a_BAT_1_05_E6_42.pts"     "Machairodus_a_BAT_1_05_F6_265.pts"    "Machairodus_a_BAT_1_06_E4_52.pts"    
       [16] "Machairodus_a_BAT_3_07_672.pts"       "Machairodus_a_BAT_3_07_698.pts"       "Machairodus_a_BAT_3_09_1017.pts"     
       [19] "Machairodus_a_BAT_3_09_1344.pts"      "Machairodus_a_BAT_3_13_1916b.pts"     "Megantereon_CB_20.pts"               
       [22] "Neofelis_n_BC_005.pts"                "Panthera_l_MNCN_COMP_255.pts"         "Panthera_o_MAV_2415.pts"             
       [25] "Panthera_p_AMNH_113745.pts"           "Panthera_t_MNCN_COMP_999.pts"         "Panthera_u_BC_56.pts"                
       [28] "Promegantereon_o_B_3109.pts"          "Promegantereon_o_B_4708.pts"          "Promegantereon_o_B_5198.pts"         
       [31] "Promegantereon_o_B_5264.pts"          "Promegantereon_o_B_7042.pts"          "Promegantereon_o_BAT_1_01_E5_17.pts" 
       [34] "Promegantereon_o_BAT_1_02_E7_66.pts"  "Promegantereon_o_BAT_1_07_E5_102.pts" "Promegantereon_o_BAT_1_07_E5_97.pts" 
       [37] "Promegantereon_o_BAT_3_05_D8_755.pts" "Promegantereon_o_BAT_3_09_779.pts"    "Promegantereon_o_BAT_3_10_1773.pts"  
       [40] "Promegantereon_o_BAT_3_11_132.pts"    "Promegantereon_o_BAT_3_11_2020.pts"   "Promegantereon_o_BAT_3_13_1596.pts"  
       [43] "Promegantereon_o_BAT_3_14_94.pts"     "Puma_c_ISM_ZOO_693928.pts"            "Smilodon_f_F_AM_14349_M7786_9732.pts"
       [46] "Xenosmilus_h_BC_113.pts"
    
  2. 'ptsarray', a 3D array containing all your landmark coordinates, the name of each specimen is defined as the name of the pts file and the name of each landmark is the same as in the pts file in the same exact order:

       > ptsarray
       , , Acinonyx_j_MNCN_COMP_3438
    
                      [,1]        [,2]       [,3]
       S000     -11.376827  57.2202220 -15.773093
       S001     -13.640221  73.2300720 -12.420223
       S002     -11.688808  74.7713320 -16.106327
       S003     -14.047218  89.9048840 -13.204573
       S004     -12.686813  89.9321060 -15.610176
       S005     -11.890251 105.6621900 -15.602662
       S006     -12.268312 118.7793700 -17.511642
       S007     -30.907965  -2.4989805 -20.663963
       S008     -11.600607  -3.7545605  -6.870319
       S009     -16.444607   1.1018786 -30.346312
       S010      -9.563807   1.6150244 -27.567286
       C000-000  -6.543262   5.0352483 -18.094845
       C000-001   2.637705   5.6062112 -17.486429
       C000-002  16.592236   0.3645229 -11.960574
       C000-003  23.731102   1.9855715  -9.499072
       C000-004  24.605648   5.6825037  -9.990653
       C000-005  23.648840  11.4155610 -10.043732
       C000-006  19.503929  19.4183120 -10.673919
       C000-007   8.296625  29.4243580 -14.277111
       C000-008  -3.601878  42.9294850 -16.499638
       C001-000 -12.264740 101.4087800 -15.946574
       C001-001 -12.610980 101.9130300 -16.154688
       C001-002 -12.701469 102.6044500 -16.263075
       C001-003 -12.645191 103.2161300 -16.231903
       C001-004 -12.523882 103.6936000 -16.101622
       C001-005 -12.397614 104.1010400 -15.955075
       C001-006 -12.259256 104.4817900 -15.807917
       C001-007 -12.108695 104.8627500 -15.674864
       C001-008 -11.992175 105.2774400 -15.621201
       C002-001 -17.854759 117.0316400 -19.819857
       C002-002 -22.519316 113.7537800 -21.052217
       C002-003 -28.057238 108.0118900 -21.574669
       C002-004 -31.865355  98.0132370 -22.160757
       C002-005 -33.163811  84.4842380 -22.574013
       C002-006 -32.679577  68.2203140 -22.551060
       C002-007 -30.297029  50.4204250 -21.864897
       C002-008 -30.803972  28.2110750 -20.945692
    

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Automatically imports all the pts files containing landmark coordinates exported from landmark editor or Stratovan checkpoint in your working directory storing everything in a 3D array ready for Procrustes superimposition.

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