Publications by Roeland KINDT
Adding dendrograms to ordination graphs with pvclust, vegan, BiodiversityR and ggplot2
1 Packages needed library(BiodiversityR) # also loads vegan library(pvclust) library(ggplot2) library(ggsci) library(ggraph) library(tidygraph) 2 Introduction The main objective of this document is to show a pathway of how dendrograms for results that were obtained via pvclust can be added to ordination graphs in ggplot2. This documents bui...
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Redundancy analysis with vegan and BiodiversityR as an alternative to Discriminant Analysis of Principal Components for the analysis of genetically structured populations
1 Packages needed library(BiodiversityR) # also loads vegan library(poppr) # also loads adegenet library(ggplot2) library(ggsci) library(ggforce) library(dplyr) library(ggrepel) 2 Introduction Jombart et al. 2010 described their methodology of Discriminant Analysis of Principal Components(DAPC) for the analysis of genetically structured p...
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Plotting smoothed surface diagrams of allele frequencies obtained from AlleleShift on a baseline map via ggmap
First version: 23-JUL-2021 Updated: 18-JAN-2022 1 Packages needed library(AlleleShift) library(BiodiversityR) # also loads vegan library(ggmap) library(dplyr) library(ggrepel) library(patchwork) 2 Introduction The AlleleShift package (Kindt 2021) predicts changes in allele frequencies from baseline to changed climates. The package include...
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Species suitability modelling with BiodiversityR, raster and terra
1 Packages needed library(BiodiversityR) library(raster) library(rgdal) library(dismo) library(terra) library(ggmap) library(ggspatial) library(ggforce) 2 Introduction The main objectives of this document were to: Showcase new options of BiodiversityR to work with the terra package (these options were introduced in version 14.1 of the pa...
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Standardizing GlobalTreeSearch tree species names with World Flora Online and the World Checklist of Vascular Plants
1 Packages needed library(WorldFlora) library(data.table) library(dplyr) 2 Introduction The WorldFlora package (Kindt 2020) was originally designed to use the taxonomic backbone data of World Flora Online (WFO; Borsch et al. 2020; www.worldfloraonline.org). A new function new.backbone introduced in version 1.8 of the package now allows to use...
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Standardizing mammal species names with the Mammal Species Database via exact and fuzzy matching functions from the WorldFlora package
1 Packages needed library(WorldFlora) library(data.table) library(readxl) 2 Introduction The WorldFlora package (Kindt 2020) was originally designed to use the taxonomic backbone data of World Flora Online (Borsch et al. 2020; www.worldfloraonline.org). A new function new.backbone introduced in version 1.8 of the package now allows to use alt...
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Standardizing GlobalTreeSearch tree species names with the 2021 version of World Flora Online
1 Packages needed library(WorldFlora) library(data.table) library(dplyr) 2 Introduction The WorldFlora package (Kindt 2020) uses the taxonomic backbone data of World Flora Online (WFO; Borsch et al. 2020; www.worldfloraonline.org). In December 2021, a new version of the taxonomic backbone was released. After downloading the new WFO backbone v...
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Analyze survey rankings via the PlackettLuce package
First version: 10-DEC-2021 Updated: 30-JAN-2022 (thanks to Jacob van Etten, Kaue de Sousa and Heather Turner for their suggestions) 1 Packages needed library(readxl) library(PlackettLuce) 2 Introduction The main objective of this document is to show how rankings of our Working paper on Opportunities for implementing impoved tree seed sourcing ...
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Analyzing Importance Value Index (IVI) via ordination analysis and rank-abundance curves
1 Libraries needed library(BiodiversityR) library(ggplot2) library(ggsci) library(ggrepel) 2 Introduction Someone recently asked me for some additional examples of analyzing Importance Value Index (IVI) values besides the examples provided with the documentation of the BiodiversityR::importancevalue function. Here I show how the IVI can be an...
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