Characterization

Size and shape computation from your digitization data.

 

Input:

Data for characterization are always RAW COORDINATES.

(raw coordinates are the coordinates as saved after a digitisation session)

Output:

For each individual, characterization analyses provide:

  • A GLOBAL SIZE ESTIMATOR
    • centroid size (CS), if from landmarks,
    • perimeter (PER) or square root area (ARE), if from pseudolandmarks (outlines)
  • A number of SHAPE DESCRIPTORS

 

If Input = raw coordinates of anatomical LANDMARKS (LM)

or

If Input = raw coordinates of LM + SL (semilandmarks)

ANALYSES

  • GPA (Generalized Procrustes Analysis)
  • PCA (Principal component analysis) using (automatically) as input the rotated specimens after orthogonal projection (ORP)
  • DA (Discriminant analysis) using (automatically) as input the principal components (PC) of the ORP.

OUTPUT

  • Reports 
  • Graphics
    • GPA Cuantile boxes for centroid size
    • Raw, Translated, Scaled, and Rotated landmarks
    • Mean objects (rotated landmarks averaged by groups)
    • PCA, DA Factor map of the two first multivariate variables.
  • Files (from folder …_ANALYSES_landmarks_SUBDIVISION_…)
    • Raw coordinates of landmarks (landmarks.txt)
    • Centroid size (…- CS.txt)
    • Rotated (or aligned) specimens (… – ROTATED.txt)
    • Orthogonal Projection of aligned specimens (… – ORP.txt)
    • Principal components of ORP (… – PC.txt)
    • Euclidean distances between PCs (… – ED.txt)
    • Discriminant analysis of PC, discriminant factors (… – DF.txt)
    • Mahalanobis distances (… – Mahalanobis distances – .txt)

 

If Input = raw coordinates of pseudoLANDMARKS (outlines)

ANALYSES

  • EFA (Elliptic Fourier analysis), which generates two important outputs for subsequent analyses:
    • (1) … – EST_OUTL.txt, the estimated coordinates after EFA 
    • (2) …- the Normalized Elliptic Fourier coefficients (… – NEF.txt). 
  • GPA, which is automatically applied on  … – EST_OUTL.txt for graphical outputs
  • PCA, automatically using as input the … – NEF.txt data 
  • DA, automatically using as input the principal components of NEF (… – PCs.txt).

OUTPUT

  • Reports
  • Graphics:
    • Graphical comparison of outlines, using estimated outlines (…_EST_OUTL.txt)
      • Usual graphics after GPA
      • Especially: Mean objects (rotated landmarks averaged by groups)
    • EFA (…_PER.txt): Quantile boxes for perimeter
    • EFA (…PC.txt on NEF)PCA, DA: Factor map of the two first PC.
    • EFA (…DF.txt from …PC.txt): Factor map of the two first DF.
  • Files  (from folder: _ANALYSES_outlines_SUBDIVISION_…)
    • Coordinates of pseudolandmarks (outlines.txt)
    • Perimeter (… – PER.txt)
    • Square Root area (… – ARE.txt)
    • Estimated coordinates after EFA (… – EST_OUTL.txt)
    • (Centroid sizes)
    • (ROTATED)
    • (ORP)
    • Normalized Elliptic Fourier Coefficients (… – NEF.txt)
    • Principal components (of NEF) (… – PCs.txt)
    • Euclidean distances between principal components (… – ED.txt)