Roeland Kindt

Roeland Kindt
Consultative Group on International Agricultural Research | CGIAR · World Agroforestry Centre (ICRAF)

dr. ir. (Google Scholar: https://scholar.google.com/citations?user=A2NaTjoAAAAJ)

About

984
Publications
238,965
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39,807
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Additional affiliations
May 1993 - present
Consultative Group on International Agricultural Research
Position
  • senior ecologist

Publications

Publications (984)
Article
Full-text available
Planetary health brings together intrinsically linked issues of human health and natural systems. This paper reviews evidence of how agrobiodiversity underpins dietary diversity for current human populations in the context of fruits and vegetables, and ways to maintain and improve these for future generations. Both the conservation and sustainable...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clust...
Book
Full-text available
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well. The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for th...
Article
Full-text available
A main question in restoration of degraded forests and forest landscapes recovering from logging and fire is what to expect from natural regeneration through surviving propagules in the soil or seed sources and associated dispersal agents from the surrounding landscape mosaic, as alternative to tree planting. Tree diversity in secondary forests may...
Book
Full-text available
The main objectives of the publication were to: (i) Showcase new options of BiodiversityR to work with the terra package (these options were introduced in version 14.1 of the package). (ii) Showcase some of the more recent methods for species distribution modelling pipelines that were introduced in newer versions of BiodiversityR than the version t...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Article
Current tree-planting initiatives are not always successful in achieving their stated targets of biodiversity conservation, climate change mitigation and human livelihood improvement. This is in part due to a lack of attention to the proper sourcing of the tree seeds and seedlings that are used. In this working paper, we explore these sourcing issu...
Article
Full-text available
The publication shows how rankings of our Working paper on 'Opportunities for implementing impoved tree seed sourcing for forest landscape restoration, agroforestry and wider tree planting at the project design stage: Findings of a survey of planters, researchers and funders' (https://worldagroforestry.org/publication/opportunities-implementing-imp...
Book
Full-text available
World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website....
Book
Full-text available
The work of the CGIAR Research Program on Forests, Trees and Agroforestry (FTA) on tree seed systems — the authors’ shorthand for the means through which growers obtain access to tree-planting materials, either seeds or seedlings — has sought to address significant constraints in the diversity and genetic quality of the tree seeds and seedlings tha...
Article
Full-text available
The Ethiopian government has set ambitious landscape restoration targets to achieve by 2030. Here, we describe a novel approach to identify landscapes to prioritize for tree-planting-based restoration interventions in the country. Our approach, which has several advantages compared to existing prioritization methods, starts with current land use pa...
Presentation
Full-text available
Presentation on a climate change atlas for Africa of tree species prioritized for forest landscape restoration in Ethiopia. The atlas is available from https://atlas.worldagroforestry.org/.
Article
Full-text available
The document shows how the function of WorldFlora::new.backbone can create a backbone data set from the World Checklist of Vascular Plants that can consequently be used by matching functions of the WorldFlora package. An application is shown of checking tree species names from the GlobalTreeSearch list.
Article
Full-text available
In a previous publication (<https://rpubs.com/Roeland-KINDT/812716>), species names from GlobalTreeSearch were standardized with the World Checklist of Vascular Plants. Here I re-check names that could not be matched directly with the latest version (December 2021) of the World Flora Online taxonomic backbone. This document was generated from a R m...
Book
Full-text available
Methods (Kindt, R. 2021. <doi:10.7717/peerj.11534>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon....
Book
Full-text available
World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website....
Article
Full-text available
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 alternative taxonomic backbone data sets. What is required is that the new backbone data includes...
Article
Full-text available
The AlleleShift package (Kindt 2021; https://doi.org/10.7717/peerj.11534) predicts changes in allele frequencies from baseline to changed climates. The package includes the shift.surf.ggplot function that generates and plots smoothed regression surfaces, internally via vegan::ordisurf and BiodiversityR::ordisurfgrid.long (see Kindt 2021 Figure 5)....
Article
Full-text available
Background At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of...
Article
Full-text available
Agroforestry (AF)-based adaptation to global climate change can consist of (1) reversal of negative trends in diverse tree cover as generic portfolio risk management strategy; (2) targeted, strategic, shift in resource capture (e.g. light, water) to adjust to changing conditions (e.g. lower or more variable rainfall, higher temperatures); (3) veget...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Conference Paper
Full-text available
Fruit and vegetable species and varieties, their wild relatives, and pollinators and other associated organisms underpin diverse food production systems and contribute to worldwide health and nutrition. This biodiversity, however, is threatened, remains poorly conserved, and is largely undocumented. Its loss leads to a narrowing of new crop options...
Article
A systematic approach to tree planting and management globally is hindered by the limited synthesis of information sources on tree uses and species priorities. To help address this, the authors ‘mined’ information from 23 online global and regional databases to assemble a list of the most frequent tree species deemed useful for planting according t...
Article
Full-text available
(Full document can be obtained via: http://www.fao.org/documents/card/en/c/cb2488en) EXECUTIVE SUMMARY Products and services derived from trees in forests, on farmland and within other landscapes provide benefits to hundreds of millions of people in the tropics, but these benefits from the trees and their genetic resources have not been well quan...
Presentation
Full-text available
Forestry, agroforestry and forest landscape restoration are about more than planting trees. ICRAF’s (now CIFOR-ICRAF’s) global tree knowledge platform (https://worldagroforestry.org/tree-knowledge) comprises a wide range of interlinked databases, maps, R open-source software packages, guidelines and other decision-support tools to guide the plantin...
Article
Full-text available
The primary challenge of the contemporary world is to meet accelerating requirements for food. Limited land, competition between crop and livestock farming and climate change are major challenges. Agroforestry offer a form of sustainable agriculture through the direct provision of food by raising farmers’ incomes and through various ecosystem servi...
Article
Brazil nut (Bertholletia excelsa) is one of the most important non-timber forest producing tree species in the Amazon. One aspect related to the sustainability of Brazil nut that has so far received very limited attention in literature is how the species’ distribution has changed through time and will continue to do so in light of anthropogenic cli...
Preprint
Full-text available
Natural regeneration depends on surviving propagules in the soil, seed sources from a surrounding landscape mosaic, and dispersal agents. We compiled and analyzed four sets of case studies varying in degree of disturbance, for secondary forests recovering from logging, fire, and conversion to agroforest in Sumatra or Kalimantan (Indonesia) on miner...
Article
Full-text available
Aim: Traditional African vegetables have high potential to contribute to healthy diets and climate resilience in sub-Saharan African food systems. However, their genetic resources are likely at threat because they are underutilized and under the radar of agricultural research. This paper aims to contribute to a conservation agenda for traditional A...
Book
Full-text available
Methods (Kindt, R. 2021. <doi:10.1101/2021.01.15.426775>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift...
Preprint
Full-text available
Background At any particular location, frequencies of alleles in organisms that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline f...
Article
Full-text available
Jombart et al. 2010 described their methodology of Discriminant Analysis of Principal Components(DAPC) for the analysis of genetically structured populations as a new methodological approach that retained all the assets of Discriminant Analysis, whereas not being burdened by its limitation of requiring the number of variables (alleles) to be less t...
Book
Full-text available
This document has several objectives. One objective was to show how Sums-of-Squares that are calculated in the AMOVA procedure can also be obtained from Multivariate Analysis of Variance Using Distance Matrices and from (distance-based) redundancy analysis. I show how distances among centroids of populations and subpopulations correspond to Sums-of...
Article
Full-text available
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 builds on previous documents where I showed how to generate ordination graphs with vegan, BiodiversityR and ggplot2 and how to create dendrograms for pvclust results with...
Article
Full-text available
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 can be used to generate dendrograms (especially those of the 'hclust' object type) with ggraph. The document was generated as a R markdown file in preparation of https:/...
Book
Full-text available
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well. # The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for t...
Article
Full-text available
The FD package includes methods for calculating the weighted Gower dissimilarity index, through methods described by Laliberte and Legendre 2010 (https://doi.org/10.1890/08-2244.1). The vegan package includes methods for calculating taxonomic distances, through methods described by Clarke and Warwick 2003 (https://doi.org/10.1046/j.1365-2664.1998.3...
Article
Full-text available
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 the scripts given here to create their own graphs. This obviously requires some working knowledge of the ggplot2 package, for which...
Article
Full-text available
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 and BiodiversityR, can be plotted via ggplot2. The key intermediate steps to allow plotting with ggplot2 is to get data in the ‘long’ (tidy) format that is used in ggp...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Article
Full-text available
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 the scripts given here to create their own graphs. This obviously requires some working knowledge of the ggplot2 package, for wh...
Article
Full-text available
Premise: The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an on...
Presentation
Full-text available
This presentation discusses results obtained towards a climate change atlas for Africa for 150+ species. The research was funded through the PATSO project (Provision of Adequate Tree Seed Portfolios project; supported by Norway’s International Climate and Forest Initiative through the Royal Norwegian Embassy in Ethiopia) and FTA (the CGIAR Research...
Presentation
Full-text available
World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. R package WorldFlora (<https://cran.r-project.org/package=WorldFlora>) provides methods of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbon...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (of-ten based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clu...
Book
Full-text available
This document provides a worked example with the RcmdrPlugin.WorldFlora package of standardizing plant names with a downloaded copy of the Taxonomic Backbone data set of World Flora Online. RcmdrPlugin.WorldFlora provides a graphical user interface (GUI) that is integrated in the R Commander GUI for the WorldFlora package The suggested citation o...
Book
Full-text available
WorldFlora is an R package that is available from <https://cran.r-project.org/package=WorldFlora>. World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided in the package of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static c...
Article
Full-text available
Understanding the vulnerability of tree species to anthropogenic threats is important for the efficient planning of restoration and conservation efforts. We quantified and compared the effects of future climate change and four current threats (fire, habitat conversion, overgrazing, and overexploitation) on the 50 most common tree species of the tro...
Preprint
Full-text available
Premise of the study: Standardization of plant names is a critical step in various fields of biology including biodiversity, biogeography and vegetation research. WorldFlora matches lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort of completing an online flora of all known vascular plants and bryophyte...
Article
Full-text available
Human activities change the structure and function of the environment with cascading impacts on human health, a concept known as “planetary health.” Agroforestry—the management of trees with crops and livestock—alters microclimates, hydrology, biogeochemistry, and biodiversity. Besides the nutritional benefits of increased fruit consumption, howeve...
Article
Full-text available
Climate change threatens coffee production and the livelihoods of thousands of families in Mesoamerica that depend on it. Replacing coffee with cocoa and integrating trees in combined agroforestry systems to ameliorate abiotic stress are among the proposed alternatives to overcome this challenge. These two alternatives do not consider the vulnerabi...
Article
Full-text available
The Agroforestry Species Switchboard is a "one-stop-shop" to retrieve data about a particular plant species across a wide range of information sources. Its particular objective is to provide information that supports research on trees and tree-based development activities such as agroforestry plantings and wider restoration initiatives, but it also...
Data
Harvard Dataverse <https://doi.org/10.7910/DVN/0O1GW1>. We performed an ensemble method for Species Distribution Modelling (SDM) using a subset of 17 SDM algorithms. The area cover the current Mesoamerica, comprised by Panama to central Mexico (coordinates-101 to-77 W, 7 to 22 N). All analyses were done in R (version 3.3.3) using a consensus method...
Article
Full-text available
Especially in low income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low input conditions. The evolving space for these crops in production systems pre...
Article
Biodiversity supports sustainable food production, although recognition of its roles has been relatively neglected in the sustainable intensification literature. In the current study, the roles of biodiversity in sustainable food production are considered, assessing how these roles can be measured, the current state of knowledge and opportunities...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Chapter
Supporting the diversification of African agricultural systems by the further integration of nutritious, perennial ‘new and orphan crops’ (NOC) is seen as an important means to address malnutrition in Africa. The approach may be of particular relevance in the context of climate change, with the diversification of food systems possibly supporting mo...
Preprint
Full-text available
In this report, results of climate change analysis are presented for villages located in the Goz Beida region of eastern Chad. These results were obtained for villages that are targeted by a BRACED project on ‘Improving resilience of 280,000 settled and nomadic marginalised communities to climate and conflict-related shocks and stresses in Eastern...
Poster
Full-text available
The BiodiversityR package (https://cran.r-project.org/package=BiodiversityR) is an open-source R package for species distribution modelling, biodiversity and community ecology analysis. It offers powerful methods for ensemble suitability modelling and has been used in several studies investigating the potential effects of climate change on the dist...
Preprint
Full-text available
In this report, results of climate change analysis are presented for villages located in the Goz Beida region of eastern Chad. These results were obtained for villages that are targeted by a BRACED project on ‘Improving resilience of 280,000 settled and nomadic marginalised communities to climate and conflict-related shocks and stresses in Eastern...
Poster
Full-text available
The vegetationmap4africa is an interactive vegetation map (available as web-based, Google Earth and smart phone versions) designed as a decision support tool for the selection of suitable indigenous tree species for restoration, forestry, agroforestry and landscape diversification projects. The map currently covers eight African countries (Burundi,...
Preprint
Full-text available
In this report, results of climate change analysis are presented for villages located in the Goz Beida region of eastern Chad. These results were obtained for villages that are targeted by a BRACED project on ‘Improving resilience of 280,000 settled and nomadic marginalised communities to climate and conflict-related shocks and stresses in Eastern...
Preprint
Full-text available
In this report, results of climate change analysis are presented for villages located in the Goz Beida region of eastern Chad. These results were obtained for villages that are targeted by a BRACED project on ‘Improving resilience of 280,000 settled and nomadic marginalised communities to climate and conflict-related shocks and stresses in Eastern...
Article
Full-text available
This is a quick guide to install BiodiversityR on your computer and to start using the package. Step 1: Download the installation file for the R statistical environment (e.g. R-3.5.1-win.exe) from the CRAN website (URL http://cran.r-project.org/bin/windows/base/), preferably via a mirror site (URL http://cran.r-project.org/mirrors.html; e.g. https:...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Book
Full-text available
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well. The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for th...
Book
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Article
Species distribution modelling (SDM) was integrated in version 2.0 of the BiodiversityR package released in 2012. Ensemble habitat suitability is calculated as the weighted average of suitabilities predicted by different algorithms. Advanced options for SDM in the current version (2.8–4) of the package include tuning the best combination of the num...
Article
Full-text available
Rethinking the logic of institutional environments aiming to facilitate agroforestry smallholders in economic development, this article compares smallholder input supply systems for crop and tree seeds in sub‐Saharan Africa and reflects on two basic challenges: (1) how to develop a large number of relevant tree crops for different agroecologies, (2...
Article
Full-text available
Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities , including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and clus...
Presentation
Full-text available
Launch of ”Suitability of key Central American agroforestry species under future climates: an atlas”. The atlas itself is available from: http://www.worldagroforestry.org/atlas-central-america
Book
Full-text available
For the full information on this publication, please look at < http://www.worldagroforestry.org/atlas-central-america >. This atlas provides habitat suitability maps for 54 species that are widely used in Central America for shade in coffee or cocoa agroforestry systems. The 54 species represent 24 fruit species, 24 timber species and 6 species use...
Book
Full-text available
The Agroforestry Species Switchboard (http://www.worldagroforestry.org/products/switchboard/) is a “one-stop-shop” to retrieve data about a particular plant species across a wide range of information sources. Its particular objective is to provide information that supports research on trees and tree-based development activities such as agroforestry...
Book
Full-text available
Para acceder a todos los productos de esta publicación vea URL < http://www.worldagroforestry.org/atlas-central-america >. Las prácticas agroforestales como los sistemas silvopastoriles,café y cacao bajo sombra, cercas vivas, barreras rompevientos y barbechos son una de las estrategias clave para el desarrollo de una agricultura adaptada al clima e...
Article
Full-text available
Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for p...
Data
Annona senegalensis. Threat magnitude levels of (A) ‘Overexploitation’, (B) ‘Overgrazing’, (C) ‘Fire’, (D) ‘Climate change’, (E) ‘Cotton production’, (F) ‘Mining’ and (G) ‘Combined threat’. (TIF)