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MorphoTools is a set of R functions for the convenient handling of morphometric analysis. No previous knowledge of R is required. The functions includes data import from Excel or tab-delimited text files, descriptive statistics for populations and taxa, histograms of characters, correlation matrices of characters, cluster analysis, principal component analysis (PCA), linear discriminant analysis (LDA) with permutation tests, classificatory discriminant analysis and k-nearest neighbour classification. For testing of the functions, a sample data set is provided.
Experienced R users are welcome to modify the functions according to their specific needs. I would also be grateful for any comments, improvements of the functions or suggestions for additions in future versions.
Citation
Koutecký P. (2015): MorphoTools: a set of R functions for morphometric analysis. - Plant Systematics and Evolution 301: 1115-1121, DOI 10.1007/s00606-014-1153-2
Download
- Manual to the functions, version 1.1 (21 Dec 2016)
- Function definitions (version 1.1) in .R format, to be used as a source file (24 Apr 2016; minor corrections 17 Dec 2019)
- Sample data, MS Excel 2003 format (6 Dec 2016)
- Working protocol of sample data analysis (16 Mar 2016) in .R format (to be opened in the software such as R Studio or similar, but can also be opened as a plain .txt in any text editor)
- Download all files as .zip , version 1.1 (21 Dec 2016; minor corrections 17 Dec 2019)
Contact
Petr Koutecký
University of South Bohemia
Faculty of Science, Department of Botany
Branišovská 1760, České Budějovice, 37005, Czech Republic
E-mail: kouta@prf.jcu.cz
Updates
Dec 2019 Minor corrections in function definitions.
Dec 2016 Minor corrections in the PDF Manual (esp. correct form of quotes to allow direct copying to R).
Mar 2016 Compared to the previous version (1.01), several function were modified and new graphical functions were introduced; several minor corrections were done.
- In cases there were several similar functions differing only in one or two parameters (such as reading the data with dot or comma as decimal separator) only one function is retained with additional parameters. This leads to fewer function at all and applies for: read.morphodata, charhist, cormat, clust, classif.da, knn.select, knn.classif.
- New functions were introduced to make graphical outputs from PCA and discriminant analysis: (a) scatterplots of ordination scores, (b) “arrow” diagram for characters, (c) biplots, (d) function adding labels to individual objects, (e) histograms of ordination scores for two-group discriminant analysis. For classificatory discriminant analysis, (f) a barplot of posterior probabilities is added. These functions replace or much shortens the original graphic scripts.
- In read.morphodata the spelling has been changed (from “morfodata”). The function now also prints the structure str(x) of the imported data frame.
- charhist prints a taxon code as a part of the x-axis label.
Nov 2014. Minor corrections were done in the Manual. In the source .R file, the function cluster.ward has been updated (in the function hclust, the parameter method= has been changed in the current version of R; now method="ward.D" is used).
On some computers, warning appears after reading the source file "Error in source...unexpected end of input". This is caused by some text editors (including Notepad in Win7), which introduce some hidden character to the end of the file. If you open and save the .R file in such editor, the problem may appear. The solution is to open the .R file in RStudio or in R script editor (File - Open script) or in some other text editor (but which one is the good one?) and add one enter (one line) at the end.
