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
import.pts(Landmark = 37)
or
import.pts(37)
Returns two objetcs:
-
'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" -
'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