Input Format

The RELEVANT FORMAT of an input FILE is like the CLIC format:

  • The first row is a FREE COMMENT, next rows are the DATA.
  • The first row is MANDATORY, and CANNOT BE EMPTY.
  • Data (next rows) are organized as a table (without headers).
  • Columns are separated by a TABULATION, preferably.
  • Empty rows are allowed (except the first one, the comment), but not recommended.
  • It is safe to remove any carriage return at the end of the input file.

IMPORTANT REMARKS

  • The data corresponding to different groups must be arranged sequentially within the input file: each group is followed by another group. For instance, if the input file is about three species, A, B and C, the individuals of A must be grouped in a submatrix A, followed by the submatrix B, followed by the submatrix C. XYOM asks not only for the input file, but also for its subdivision. In the example of three species A, B and C, a subdivision like “20,24,29” means that the 20 first rows are about individuals of species A, the next 24 rows about individuals of species B, and the next 29 rows about species C.

 

  • For the file containing pseudolandmarks (outlines).
    • After the very first row, which is a comment, the outline file contains the data, i.e., the x,y coordinates of successive pseudolandmarks, however the three first columns are special columns:
      – col. 1:
      the number of points of the digitized contour (different contours may contain a different number of points); this number includes the centroid point (geometric center of the configuration)
      – col. 2 and 3:
      the X and Y coordinates of the centroid point
    • Next columns are the pseudolandmarks, i.e., the coordinates of the digitized contour
    • The XYOM pseudolandmarks format is automatically built by XYOM when digitizing contours.
    • Note that the matrix is made rectangular by replacing missing data with NA or NaN – like the R format of an outline file (J. Claude, 2008). To convert XYOM/CLIC format of outlines to the R format as used in Claude (2008), just remove the three first columns (MISCELLANEOUS, WORKING ON FILES, EXTRACTING)

 

  • In the near future:
    • – The MISCELLANEOUS section will offer the possibility to build the XYOM/CLIC format of pseudolandmarks from a table of raw pseudolandmarks: it will compute and adds the three first special columns, and complete rows with NA or NaN symbols where and if necessary.
    • – XYOM will adjust the missing data (NA or Na) when concatenating two outline files with a different number of columns. Note that it is currently not possible to concatenate by rows two files with a different number of columns.