Publications by Roeland KINDT
Using the BiodiversityR::treegoer.score() function and the Tree Globally Observed Environmental Ranges and ClimateForecasts databases to Filter GlobalUsefulNativeTrees outputs
1 Packages needed library(data.table) library(readxl) library(dplyr) library(BiodiversityR) # to get the treegoer.score() function 2 Introduction The Tree Globally Observed Environmental Ranges (TreeGOER) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topograph...
10442 sym R (79080 sym/262 pcs)
Using WorldFlora to match GlobalTreeSearch version 1.7 with the latest database versions of World Flora Online and the World Checklist of Vascular Plants
1 Packages needed library(WorldFlora) library(data.table) library(stringr) 2 Introduction In previous posts (see here, here and here), I showed how the WorldFlora package Kindt 2020) can be used to standardize names from GlobalTreeSearch with the taxonomic backbone data from World Flora Online (WFO) or the World Checklist of Vascular Plants...
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Using the Tree Globally Observed Environmental Ranges and CitiesGOER databases to Filter GlobalUsefulNativeTrees Species Lists
1 Packages needed library(data.table) library(readxl) library(dplyr) 2 Introduction The Tree Globally Observed Environmental Ranges (TreeGOER) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. In this document, I show how outputs generated by...
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Standardizing tree species names of GlobalTreeSearch with WorldFlora while testing the faster matching function of WFO.match.fuzzyjoin
1 Packages needed library(WorldFlora) library(data.table) library(stringr) 2 Introduction In previous posts (see here and here), I showed how the WorldFlora package can be used to standardize names from GlobalTreeSearch with the taxonomic backbone data from World Flora Online or the World Checklist of Vascular Plants. (My original inspirat...
7238 sym R (87630 sym/295 pcs)
Analysis of Molecular Variance (AMOVA) with vegan and BiodiversityR, including a graphical method to identify potential migrants
1 Packages needed library(BiodiversityR) # also loads vegan library(poppr) library(ggplot2) library(ggsci) library(ggforce) library(dplyr) library(ggrepel) 2 Introduction Over a decade ago, while working on a manual for statistical analysis of dominant markers (this manual was partially inspired by a previous manual on the statistical ana...
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Cluster diagrams with pvclust and ggraph
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 generating dendrograms via the ggraph package for results that were obtained via pvclust. I expect that similar pathways ca...
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Renyi Diversity Profiles with vegan, BiodiversityR and ggplot2
1 Packages needed library(BiodiversityR) # also loads vegan library(ggplot2) library(ggsci) library(readxl) 2 Introduction The main objective of this document is to give some examples of how data on Renyi diversity profiles, obtained via vegan and BiodiversityR, can be plotted via ggplot2. I expect that researchers and students will modify th...
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Species Accumulation Curves with vegan, BiodiversityR and ggplot2
1 Packages needed library(BiodiversityR) # also loads vegan library(ggplot2) library(ggsci) library(readxl) 2 Introduction The main objective of this document is to give some examples of how data on species accumulation curves, obtained via vegan and BiodiversityR, can be plotted via ggplot2. I expect that researchers and students will modify...
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Ordination graphs with vegan, BiodiversityR and ggplot2
1 Packages needed library(BiodiversityR) # also loads vegan library(ggplot2) library(readxl) library(ggsci) library(ggrepel) library(ggforce) 2 Introduction The main objective of this document is to give some examples of how data from ordination, such non metric multidimensional scaling or redundancy analysis that were obtained via vegan an...
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"Calculating Distance Matrices with Weighted Combinations of Functional Traits and Taxonomic Distinctness
1 Packages needed library(BiodiversityR) # also loads vegan library(FD) library(readxl) 2 Introduction The FD package includes methods for calculating the weighted Gower dissimilarity index, through methods described in A distance‐based framework for measuring functional diversity from multiple traits. The vegan package includes methods for ...
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