AGROBIODIVERSITY & AGROECOLOGY | 01(01) NOVEMBER 2021

Published by The Grassroots Institute (Canada) in partnership with University

"Lucian Blaga" from Sibiu (Romania) and Fondacija Alica Banja Luka
(Bosnia i Herzegovina). Website: http://grassrootsjournals.org/aa
ISSN 2564-4653 | 01(01) Nov 2021
M – 00256 | Review Article

Agrobiodiversity Indicators and Measurement using R for Description, Monitoring,

Comparison, Relatedness, Conservation and Utilization
Bal Krishna Joshi
Nepal Agricultural Research Council, Kathmandu, Nepal. Email: [email protected] | ORCID: https://orcid.org/0000-0002-7848-5824

How to cite this paper: Joshi, Abstract

B.K. (2021). Agrobiodiversity
Indicators and Measurement using
Agrobiodiversity is the most important part of biodiversity. It can be described,
R for Description, Monitoring, quantified, compared, and related by using different statistical tools called
Comparison, Relatedness, agrobiodiversity statistics (agro-statistics). Six components and 25 groups of
Conservation and Utilization. agrobiodiversity should be used for agrobiodiversity analysis. Six types and levels of
Agrobiodiversity & Agroecology, agrobiodiversity can be quantified. Both quantitative and qualitative data are used for
01(01): 47-64. Doi:
https://doi.org/10.33002/aa010103 estimating scores and indices. The measurement objects for describing agrobiodiversity
are community, household, site, crop group, species, landrace, etc. These objects are
called operational agricultural units (OAU). Agromorphological, molecular, and
Received: 19 August 2021 perception data are used in agrobiodiversity studies. Among the many software, RStudio
Reviewed: 15 September 2021
is very good. It is an integrated part of R and includes a console, syntax-highlighting
Accepted: 30 September 2021
Published: 10 November 2021 editor, tools for plotting, history, debugging, and workspace management. Vegan and
Copyright © 2021 by author(s) BiodiversityR packages are commonly used for estimating diversity indices and
multivariate analysis. Richness, Shannon index and Simpson index are very common
means of quantifying agrobiodiversity. Spatial and temporal analysis of agrobiodiversity
Publisher’s Note: We stay neutral
helps monitor the status and plan the programs and activities.
with regard to jurisdictional claims
in published maps, permissions Keywords
taken by authors and institutional
Agrobiodiversity index; Agrobiodiversity statistics; Measurement; Indicators; R package
affiliations.

License: This work is licensed under

the Creative Commons Attribution 1. Introduction
International License (CC BY 4.0).
http://creativecommons.org/licenses/b Agrobiodiversity (also called agricultural genetic resources, AGRs) is a part of
y/4.0/ biodiversity and includes all genetic resources that are economically beneficial. In
majority of the countries, native agrobiodiversity is neglected and underutilized due to
their high priority to monomorphic and high yielding varieties. Many different factors
are contributing to losing the AGRs. Among them the major factor is the rapid expansion
of single improved homogenous varieties and breeds in the world. Such single improved
variety is generally developed through studying a single species or variety or set of
genotypes, and there are limited studies on the whole agrobiodiversity at a particular
site. The general trend is that, rather than evaluating, describing and improving the native
Editor-in-Chief:
agrobiodiversity, improved variety or breed is easily adopted and expanded due to which
Dr. Didier Bazile (France) many indicators are being affected. Indicators are any values, scores or status which
Deputy Editors-in-Chief: explain about the agrobiodiversity of a particular location. Agrobiodiversity indicators
Dr. Habil. Maria-Mihaela Antofie have not been standardized across the world; and even the methodologies to estimate
(Romania); Dr. Gordana Đurić and measure the indicators are not available. Indicators are very important to manage
(Bosnia i Herzegovina)
Technical & Managing Editor:
Dr. Hasrat Arjjumend (Canada)
ISSN 2564-4653 | Agrobiodiversity & Agroecology | vol.01, No.01 (November 2021): 47-64 | Doi: https://doi.org/10.33002/aa010103

the agrobiodiversity better, to plan programs and activities, and to monitor the trends
(Sthapit et al., 2017; PAR, 2018).
For the conservation of forest biodiversity (non-agrobiodiversity), different
indicators and approaches have been used, for example red listing of the species. Many
types of species have been defined and given due attention. Different types of species
include Alien, Charismatic, Dominant, Emblematic, Endangered, Endemic, Exotic,
Flagship, Focal, Foundation, Indicator, Indigenous, Invasive, Keystone, Landscape,
Priority, Rare, Specialty, Substitute, Surrogate, Target, Threatened, Tourism, Umbrella
and Vulnerable species. Similar approaches can be applied at species and landrace level
to support AGRs. Quantification of AGRs is another aspect that identifies such species
or landraces.
Different types of scores and indices along with coefficients can be estimated and
used as indicators (Joshi et al., 2005; Jarvis et al., 2000; Grum and Atieno, 2007)).
Several statistical tools can be applied using computer software to quantify
agrobiodiversity. Quantifications (measurements) of agrobiodiversity are generally done
at different levels e.g., at the agroecosystem, species, varieties, and administrative units.
Agrobiodiversity in any area should be estimated properly that leads to choosing the
conservation approaches effectively. This paper, therefore, describes different
operational agricultural units (OAU) for estimating diversity indices using R packages.
Among the various components under agrobiodiversity statistics, this paper focuses on
the measurement of agrobiodiversity. With the approaches described in this paper, one
can rank any household, community, district, or the country and can locate a center of
the diversity. A hotspot of agrobiodiversity and red zone for agrobiodiversity can be
identified, in addition to identifying the indicator species and landraces.

2. Agrobiodiversity Components and Groups

Agrobiodiversity covers all genetic resources that have value for food, nutrition,
health, and other economic uses to human beings. It has six components, and they are
crops, forages, livestock, insects, microorganisms, and aquatic genetic resources (Joshi
et al., 2020c). Insects and microorganisms include only economic and beneficial species.
Under aquatic genetic resources, only economically important species are included e.g.,
fish. Each of these components can further be divided into four sub-components. They
are cultivated/ domesticated, semi-domesticated, wild relatives, and wild edible species
(Joshi and Shrestha, 2017; Joshi and Shrestha, 2019).
Based on the economic uses, agricultural genetic resources can be grouped into
25 groups. They are 1. cereals, 2. pseudocereals, 3. millets, 4. sugar and starch crops, 5.
grain legumes, 6. oilseed crops, 7. summer vegetables, 8. winter vegetables, 9. roots and
tubers, 10. winter fruits, 11. summer fruits, 12. spices, 13. beverages and narcotics, 14.
fibers, 15. forage trees, 16. forage grasses, 17. ornamental plants, 18. medicinal plants,
19. supportive plants, 20. economic and beneficial (EB) insects, 21. EB microorganisms,
22. fish/aquatic animals, 23. aquatic plants, 24. poultry, and 25. livestock (Joshi and
Shrestha, 2019, Joshi and Shrestha 2017). Supportive plants include green manuring
crops, cover crops, pesticide plants, and other economically important plants that are not
included in the above groups.
These components, sub-components, and economic groups (Joshi et al., 2020c;
Joshi and Shrestha, 2019) are very useful to estimate different types of diversity indexes,
indicators, and scores of a particular site, community, or household over a certain period.
The AGRs may be of exotic and native types and both types can be considered for
agrobiodiversity measurement, but measurement based on only native AGRs would be

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more valuable and important. There are many other grouping systems of AGRs (Joshi
and Shrestha, 2019), and these groups can also be considered to quantify
agrobiodiversity.

3. Agrobiodiversity Levels and Types

Agrobiodiversity can be measured and studied at different levels or hierarchies by

using different traits. Based on levels (coverage of objects), there are six types of
agrobiodiversity (Figure 1) (Joshi et al., 2020b; Bajracharya et al., 2012). Genetic diversity
includes three levels of diversity i.e., varietal diversity, genotypic diversity, and allelic
diversity. Agrobiodiversity can also be described under six types of diversity based on
traits and use-values. These include functional diversity, morphological diversity,
molecular diversity, use-value diversity, nutritional diversity, and food diversity. All these
12 types of diversity should be measured and studied at a particular site in a given period.
Based on the data types, objectives, and objects, different measures are used to estimate
and compare these different types of agrobiodiversity. Diversity can also be assessed based
on cropping patterns, growing season, land type and habitat. at species and varietal levels.
Morpho type is very simple indicator to measure the diversity.

Cultivated, semi domesticated, wild relatives and wild edible genetic resources
Agrobiodiversity
within an area , part of biodiversity
Agrobiodiversity levels

1. Agro-ecosystem Diversity, Variety of different agro-ecosystems within an area, different growing seasons,
Agro-ecozone Diversity cropping pattern, agro-ecology and agro-ecozones

2. Agrobiodiversity All components and sub components and groups of agricultural genetic
components and groups resources within agro-ecozone

3. Species Diversity, Inter and intra level species and sub species and crops diversity within a given
Crop Diversity area

4. Varietal Diversity Intra and inter varietal diversity, landrace or cultivar diversity within a species
Genetic Diversity

Variation of genes, traits and genotypes within, landraces, varieties and

5. Genotypic diversity
population structure and among genotypes

6. Allelic Diversity Variation within genes, traits and among alleles within genotypes
Agrobiodiversity
types

Functional Diversity Morphological Diversity Molecular Diversity Food Diversity

Nutritional
Use Value

Diversity
Diversity

Functional traits Phenotypic variation Variation at DNA, Varied recipe with

among and within among and within protein and other different nutritional
species and varieties species and varieties molecules pack

Figure 1: Types of agrobiodiversity based on levels, traits, and use-values.

Source: Joshi et al. (2020b)

4. Agrobiodiversity Statistics (Agro-statistics)

Agro-statistics is a science of studying agrobiodiversity using different statistical

tools, methods, and principles. Many common statistical tools are useful for
measurement (quantification), characterization (description), classification (grouping),

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evaluation (comparison) and association (relationship) of agrobiodiversity (Figure 2)

(Bajracharya et al., 2012; Grum and Atieno, 2007; Jarvis et al., 2000; Joshi et al., 2005).
With the development of different molecular markers and computing software, genetic
parameters are also commonly estimated. Description of these tools has been described
by Joshi et al. (2005). Both parametric and non-parametric tests are also commonly used
to compare agrobiodiversity. Appropriate test statistics are given in figure 3 based on
data types and the number of objects (factors) used. Both temporal and spatial analysis
(called trend analysis) can be carried out to see the status and changes in
agrobiodiversity.
Agrobiodiversity Statistics Genetic parameters

Agrobiodiversity Characterization Classification Evaluation Relationship

measurement (description) (comparison)
(quantification)

• Frequency, • t-test • Correlation

• Cluster analysis • ANOVA, MANOVA
• Diversity indices Percentage • Regression
• PCA • F test
(richness, • Mean, Variance • Chi square
• Discriminant • LSD
evenness, • Max and Min • Scatter plot
analysis • CV
Shannon index, • Range • Box plot, graph
• D2 statistics • Mean, SE
Simpson index) • Rank
• Factor analysis • Max and Min
• Similarity/ • SD, CV
• Principal • Score and rank
dissimilarity • Areas/ HHs/ land
coordinate • Non parametric test
coefficients parcels
analysis • Stability analysis
• Score • Box plot , graph
• Box plot, graph

Figure 2: Different statistical tools for agrobiodiversity study.

Chi square Fisher’s exact

Paired 1 way 2 way Expected count 5 Expected count 5

t test t-test ANOVA ANOVA Mcnemar’s
in >80% of cells in <80% of cells
or Cochran Q

Paired Unpaired 1 factor 2 factors Paired Unpaired Chi square

2 groups > 2 groups 2 groups > 2 groups

Continuous Nominal
Data Type

Ordinal or skewed continuous

2 groups > 2 groups

Paired Unpaired Paired Unpaired

Wilcoxin signed rank Mann Whitney U Friedman Kruskal Wallis

Figure 3: Statistical testing tools (parametric and non-parametric) for comparing
agrobiodiversity based on data types

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5. Agrobiodiversity Measurement (Quantification)

Agrobiodiversity measurement includes the quantification of AGRs at different

levels. Based on the quantification, AGRs can be grouped at the level of different strata
e.g., red list, endangered, rare, common, etc. (Joshi and Shrestha, 2019). The main
measures of agrobiodiversity are richness, evenness, diversity indices (Shannon,
Simpson indices), similarity coefficients, dissimilarity coefficients, scores (Joshi et al.,
2005; Kindt and Coe, 2005; Joshi et al., 2018; Jarvis et al., 2000; Grum and Atieno,
2007). Another measure is species density, which takes into account the number of
species in an area. Similarly, landrace density can also be estimated. These measures
should be measured at six different levels and types of agrobiodiversity (Figure 1) e.g.,
household, community, ward, municipality, district, province, and country. Such
estimates are generally calculated based on native agrobiodiversity and are, therefore,
useful for identifying the hotspot areas for agrobiodiversity. Quantification helps locate
the center of diversity, identify the hotspot and red zone areas for agrobiodiversity.
Hotspot areas are those areas that have the higher diversity score and indices, high
diversity on wild relatives, endemic species, many rare and unique landraces, and
species, and different types of land and cropping patterns.
Measurement (quantification) may be based on phenotypic, genotypic,
perception, and survey data. Such data can be collected and measured through
community biodiversity register and community seed bank, diversity block, diversity
collection, diversity fair, field/transect walk, focus group discussions, food fair,
household survey, key informant interviews, online survey, lab experiment, literature
review, local market, on-farm, and on-station trials. Diversity changes over time and
space are also estimated using different diversity measures, which are important for
monitoring and applying appropriate methods for conservation and utilization.
For the index calculation at different levels, one can count the number of species
within-group, or several landraces within species as well as group (PAR, 2018;
Pudasaini et al., 2016; Borcard, Gillet and Legendre, 2011; Grum and Atieno, 2007;
Joshi and Baniya, 2006). Taking the natural logarithms of species richness or landrace
richness, an index can be calculated. The proportion of each group, species, or landraces
can be calculated by dividing the number of that groups, species, or landraces by the
total number of all groups, species, or landraces in a given area. The formula for
calculating the Shannon diversity index, Simpson index, evenness, and other indices can
be applied on these data. Agrobiodiversity index (ABDI) can be of household (HH),
village or community, district, province, agroecozone, and country. A weighted index
using either agrobiodiversity components or groups can be estimated as described in the
literature1. In some cases, microorganisms, insects, ornamental plants, and the medicinal
plant may be excluded from the calculation due to data unavailability.
The percentage of species or landraces in each group or species can be calculated
considering the total number of species or landraces in the country or studied areas
(Pudasaini et al., 2016; Joshi et al., 2018; Joshi et al., 2007). Based on the data obtained,
each household or area or district can be ranked. For example, ABDI (based on
landraces) for each household is equal to the number of landraces in each species or
group divided by the total number of landraces in a community or district.

6. Agrobiodiversity Indicators (Score and Index)

1 https://news.mongabay.com/2016/05/top-10-biodiverse-countries/

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Agrobiodiversity indicators are any scores, indices, signs, symptoms, values,

drivers, or marks that speak about the status of total diversity, trends on diversity, the
status of intra- and inter-level diversity of species, and landraces in a particular area. It
indicates that the agrobiodiversity is increasing, remaining constant, or decreasing.
There is a wide range of methods of measuring various dimensions of agrobiodiversity,
which is often referred to as the agrobiodiversity indicators, scores, and indices
(Boversity International, 2017; Sthapit et al., 2017; PAR, 2018; Kindt and Coe, 2005;
Joshi et al., 2020b). Diversity indicators, indices, and scores can be used to compare
within and between different populations at species, landraces, and genetic levels over
locations and years.
Agrobiodiversity indicators can be assessed at three different systems, namely, in
consumption and market system, in production system, and in genetic resource
management system (Sthapit et al., 2017). Some indicators include the red zone, red list,
landraces coverage (based on five cell analysis), cropping pattern, mixture, monocrop
vs. multicrops, land type, food items, native products in the market, the richness of
species and landraces, population size, etc. A red list is the list of names of genetic
resources (at genotype, landrace, variety, strain, and breed levels) under different groups
based on the analysis of distribution and population size (also called five cell analysis),
and trait distribution. Among these indicators, scores and indices are more commonly
estimated and used.
Diversity indices and scores are calculated using both qualitative and quantitative
data. In case of quantitative data, it needs to be converted into qualitative groups. The
proportion of entries in ith class can be calculated using morphological data considering
the different phenotypic classes of traits. Similarly, frequency data on genebank
collection can be used to estimate different indices. Many ways can be used to estimate
several types of household scores and indices. Household-level diversity can be of
household diversity score and index as given below.

6.1 A1. Household Agrobiodiversity Score (HHABDS)

1. Number of species (species richness, n) in each of 6 agrobiodiversity
components (crops, forages, livestock, economical insects, economically
important microorganisms, aquatic agricultural species) over a year
2. Number of landraces (landrace richness, n) per species for each of 6 components
in a year
3. Land type, n (marshy/ wetland, pond/aquatic, slopy upland, terrace upland,
slopy low land, terrace low land, riverside, agroforestry land, grassland)
4. Functional diversity (number of special functions using special landraces) in a year
5. Unique diversity value (the number of specialty/ unique landraces divided by
the total number of landraces)
6. Agrobiodiversity group score (or agrobiodiversity group richness) (based on 25
agrobiodiversity groups i.e., cereals, pseudocereals, millets, sugar and starch
crops, grain legumes, oilseed crops, summer vegetables, winter vegetables, roots
and tubers, winter fruits, summer fruits, spices, beverages and narcotics, fibers,
forage trees, forage grasses, ornamental plants, medicinal plants, supportive
plants, economical and beneficial (EB) insects, EB microorganisms, fish and
aquatic animals, aquatic plants, poultry, and livestock), at 0 or 1 scale over a
year with maximum 25 score
7. Dietary diversity score (based on 15 groups: cereals, pseudocereals, millets, roots
and tubers, vegetables, fruits, nuts, meat and poultry, eggs, fish and aquatic animals,

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pulses and legumes, milk and milk products, oil/fat and ghee2, sugar and honey, and
miscellaneous) at 0 or 1 scale on half-year basis with maximum 15 score
8. Social agrobiodiversity score (number of religious or culturally associated
landraces, considering all 6 agrobiodiversity components)
9. Food diversity score (number of food items/recipes eaten per meal, average of
morning, day, and evening foods)
10. Food component score (number of species in food per meal, average of morning,
day, and evening foods)
11. The average area per species (crops and forages) in square meter
12. HH agrobiodiversity score: sum from above 1 to 10 scores.

6.2 A2. Household Agrobiodiversity Index (HHABDI)

A. Based on species within agrobiodiversity group
▪ HH agrobiodiversity group richness, n
1. HH Shannon diversity index (based on number of species within a group)
2. HH Simpson index (based on number of species within a group)
3. HH species evenness (specie within a group)
B. Based on landraces within the agrobiodiversity group
▪ HH agrobiodiversity group richness, n
4. HH Shannon diversity index (based on number of landraces within a group)
5. HH Simpson index (based on number of landraces within a group)
6. HH landraces evenness (specie within a group)
C. Based on landraces within species
▪ HH agrobiodiversity species richness, n
7. HH Shannon diversity index (based on number of landraces within a species)
8. HH Simpson index (based on number of landraces within a species)
9. HH species evenness (specie within a group)
HH agrobiodiversity index (HHABDI): sum of above 1 to 9 index values.
In the similar way of household scores and indices, one can estimate village or
community agrobiodiversity scores and indices as follows.

6.3 B.1. Village Agrobiodiversity Score (VABDS)

1. Number of species (species richness, n) in each of 6 agrobiodiversity
components (crops, forages, livestock, economical insects, economical
microorganisms, aquatic agricultural species) over a year
2. Number of landraces (landrace richness, n) per species for each of 6
agrobiodiversity components over a year
3. Land type, n (marshy/ wetland, pond/aquatic, sloppy upland, terrace upland,
sloppy low land, terrace low land, riverside, agroforestry land, grassland)
4. Functional diversity (number of special functions using special landraces) in a year
5. Unique diversity value (number of specialty/ unique landraces, functional trait-
specific genotypes divided by total number of species)
6. Village agrobiodiversity score (based on 25 agrobiodiversity groups, i.e.
cereals, pseudocereals, millets, sugar and starch crops, grain legumes, oilseed
crops, summer vegetables, winter vegetables, roots and tubers, winter fruits,
summer fruits, spices, beverages and narcotics, fibers, forage trees, forage
grasses, ornamental plants, medicinal plants, supportive plants, economical and
beneficial (EB) insects, EB microorganisms, fish and aquatic animals, aquatic
plants, poultry, and livestock) at 0 or 1 scale over a year with maximum 25 score

2
It is made by melting butter.
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7. Village dietary diversity score (based on 15 groups: cereals, pseudocereals,

millets, roots and tubers, vegetables, fruits, nuts., meat and poultry, eggs, fish
and aquatic animals, pulses and legumes, milk and milk products, oil/ fat and
ghee, sugar and honey, and miscellaneous) at 0 or 1 scale on half-year basis with
maximum 15 score
8. Social agrobiodiversity score (number of religious or culturally associated
landraces, considering all 6 agrobiodiversity components)
9. Food diversity score (number of food items/recipes eaten per meal, average of
morning, day, and evening foods)
10. Food component score (number of species in food per meal, average of morning,
day, and evening foods)
11. Village agrobiodiversity score: sum of above 1 to 10 values
12. The average area per species (crops and forages) in square meter
13. Average agrobiodiversity HH score
14. Average social agrobiodiversity HH score
15. The average number of species per HH
16. The average number of landraces per HH
17. Average areas per HH.

6.4 B.2. Village Agrobiodiversity Index (VABDI)

A. Based on species within agrobiodiversity group
▪ Agrobiodiversity group richness, n
1. Village Shannon diversity index (based on number of species within a group)
2. Village species evenness (specie within a group)
3. Village Simpson’s index
B. Based on landraces within the agrobiodiversity group
▪ Agrobiodiversity group richness, n
4. Village Shannon diversity index (based on number of landraces within a group)
5. Village landraces evenness (specie within a group)
6. Village Simpson’s index
C. Based on landraces within species
▪ Agrobiodiversity species richness, n
7. Village Shannon diversity index (based on number of landraces within a species)
8. Village species evenness (specie within a group)
9. Village Simpson’s index
Village agrobiodiversity index (VABDI): Sum of above 1 to 9 values

Similarly, we can estimate agrobiodiversity indices and scores at district,

province/ state levels or any defined specific areas. OAUs can be further ranked based
on these scores and indices. The followings are additional measures of agrobiodiversity.
• Agrobiodiversity index at HH, community, district, province, ward levels using
the number of species or landraces divided by the total number of species or
landraces in a country
• Analog site index of a particular landrace or species, calculated from climate
analog tool based on reference site of a particular landrace or species
• Driver index can be estimated for each of different drivers (factors) in a
particular area over the particular time frame, using the formula, lost landraces
divided by the total number of landraces available before the effect of this driver.

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7. Data Types and Collections

Different types of data are generated and collected for the measurement and other
studies of agrobiodiversity. Different data types for agrobiodiversity study are given in
figure 4. Data could be agro-morphological, molecular, and perception, which can be
generally collected from on-station research, on-farm trial, surveys, and lab research.
Several methods and techniques can be used to collect data and information (see Joshi
et al., 2005 for detail).
Apps and software are available for collecting data and information electronically
both online as well offline. FieldLab is an application for Android tablets that are used
for data collection in the field. It is developed by IRRI3 and is available freely. Field
Book is a simple app for taking phenotypic notes. It is an open-source application for
field data collection on Android4 and is available from Google Play5. The Fieldbook2020
software developed by CIMMYT6 provides offline capabilities for managing pedigrees,
phenotypic data, seed stocks, and field books for a breeding program. It provides
integrated management of global information on genetic resources, crop improvement,
and evaluation for individual crops. R Package7 included in this software is useful for
statistical analyses. Biologer8 is a simple and free software designed for collecting data
on biological diversity.

Observation = Variable = Data

Quantitative Perception Qualitative Binary

Variables, Numerical Attributes, categorical

Interval scale Non-interval scale

Continuous Discrete (discontinuous) Groupable w/t rank Rankable
Fractional
measurement Nominal scale Ordinal scale
Measurement data Attribute data

Primary Secondary Primary Secondary

Raw data Descriptive Statistics and Inferential Statistics

Figure 4: Data types for measuring on-farm agrobiodiversity at ecosystem, species, and
cultivar levels

Perception data is generally collected from a survey. Along with the advancement
of information technology, many data collections survey tools are available. These

3 http://bbi.irri.org/products/fieldlab
4 http://dx.doi.org/10.2135/cropsci2013.08.0579
5 https://play.google.com/store/apps/details?id=com.fieldbook.tracker&hl=en&gl=US
6 https://www.cimmyt.org/
7 https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10548370
8 https://biologer.org/

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online tools are very useful to minimize errors and speed up data processing. Some
electronic media-based survey tools are given below.
▪ Surveymonkey9: A cloud-based survey tool that helps users create, share, collect
and analyze surveys.
▪ Google forms10: It is used to create online forms and surveys.
▪ SoGoSurvey11: A cloud-based platform that enables creation, distribution, and
multilingual analysis of surveys, forms, polls, quizzes, and assessments.
▪ mWater Portal12: Free platform for data collection, data visualizations, and data-
driven management of infrastructure in emerging economies.
▪ ODK13: It is an Open Data Kit, open-source software for collecting, managing,
and using data in resource-constrained environments.

8. Measurement Objects

The information for measuring agrobiodiversity comes from different levels.

These levels are alleles, genes, genotypes, cultivars (varieties and landraces), crops,
species, components and groups, agroecosystems or agroecozones, parcels or plots,
households (farmers), villages, communities, ethnicities, wards, municipalities,
landscapes, regions, districts, provinces/ states, countries, and continents. These levels
are measurement objects, called OAU (operational agricultural unit).
In addition, there are several crop groups that are OAU based on different criteria
e.g., use-value base, economic importance base, national list base, habitat base, red list
base, growing season base, national priority base, etc. Examples are cereals, vegetable
fruits, released variety, registered variety, major, minor, primary, secondary, staple,
commodity, high value, commercial, industrial, food crops, feed crops, manuring crops,
pesticidal plants, cash crops, cover crops, trap crops, catch crop, cultivated, semi-
domesticated, wild edible, field crops, garden crops, aquatic plants, common, rare,
endangered, extinct, localized, vulnerable, winter crops, summer crops, and off-season
(Joshi and Shrestha, 2019).
Object or OAU refers to the things being analyzed, interpreted, evaluated, or
described. Variable or character refers to the properties used to describe the objects under
study. Variables may be both qualitative and quantitative, and include
agromorphological, genotypic, and perception data. These are measured or observed
from an individual, representative samples, or population. In some cases,
agromorphological markers, traits, and molecular markers can be treated as OAU.

9. Software for Agrobiodiversity Statistics

Many software are available for agrobiodiversity statistics. The general and
molecular software are given below.

I. General Statistical Software

▪ AGROBASE14: For data management, experiment management, and statistical
analysis.

9 https://www.surveymonkey.com/
10 https://www.google.com/forms/about/
11 https://experience.sogosurvey.com/
12 https://portal.mwater.co/#/
13 https://opendatakit.org/
14 https://www.agronomix.com/AGROBASE.aspx

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▪ CropStat15: For data management and basic statistical analysis of experimental

data.
▪ DIPVEIW: For genebank data management and analysis.
▪ DIVA-GIS16: For mapping and geographic data analysis (a geographic
information system (GIS).
▪ Genstat17: For data analysis, particularly in the field of agriculture.
▪ GGEbiplot18: For biplot analysis, conventional statistical analysis, and decision
making based on univariate and multivariate data.
▪ Instat+19: A general statistical package.
▪ Minitab20: Simple and general statistical package.
▪ MS Excel21: Spreadsheet software program, a powerful data visualization, and
analysis tool.
▪ MSTAT-C22: For the design, management, and analysis of agronomic research
experiments.
▪ NTSYSpc23: Commonly used package for numerical taxonomy and multivariate
analysis system.
▪ Past24: For scientific data analysis, with functions for data manipulation,
plotting, univariate, multivariate statistics, ecological analysis, time series, and
spatial analysis.
▪ R25 and RStudio26: For statistical computing and graphics.
▪ SAS27: For data management, advanced analytics, and multivariate analysis.
▪ SPSS28: A software platform that offers advanced statistical analysis, a vast
library of machine learning algorithms, and text analysis.
▪ STAR29: Statistical tool for agricultural research.
▪ Statistica30: A data analysis and visualization program.
▪ Statistix31: Statistical analysis program.
▪ PDA32: For biodiversity analysis and conservation prioritization problems.
▪ BioDiversity Pro33: A free statistical package program enabling many measures
of diversity to be calculated for a dataset of taxa by samples.

II. Molecular Data Analysis Software

▪ Arlequin34: Powerful genetic analysis packages performing a wide variety of
tests, including hierarchical analysis of variance.

15 http://bbi.irri.org/products
16 https://www.diva-gis.org/
17 https://www.vsni.co.uk/software/genstat
18 http://ggebiplot.com/
19 https://instat.software.informer.com/3.3/
20 https://www.minitab.com/en-us/
21 https://www.microsoft.com/en-ww/microsoft-365/excel
22 https://www.canr.msu.edu/afre/projects/microcomputer_statistical_package_mstat._1983_1985
23 http://www.appliedbiostat.com/ntsyspc/ntsyspc.html
24 https://www.nhm.uio.no/english/research/infrastructure/past/index.html
25 https://www.r-project.org/
26 https://www.rstudio.com/
27 https://www.sas.com/en_us/home.html
28 https://www.ibm.com/analytics/spss-statistics-software
29 http://bbi.irri.org/products
30 https://www.statistica.com/en/
31 https://www.statistix.com/
32 http://www.cibiv.at/software/pda/
33 https://www.sams.ac.uk/science/outputs/
34 http://cmpg.unibe.ch/software/arlequin35/

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▪ GDA35: For the analysis of discrete genetic data.

▪ GenAlEx36: Excel Add-In for the analysis of genetic data, particularly useful for
dominant data such as RAPD and AFLP data.
▪ MEGA37: For reconstructing phylogenies using distance matrices and maximum
parsimony methods, and includes neighbor-joining, branch-and-bound
parsimony methods and bootstrapping.
▪ PHYLIP38: Extensive package of programs for inferring phylogenies.
▪ POPGENE39: For the analysis of genetic variation among and within
populations using co-dominant and dominant markers, and quantitative data.
▪ PowerMarker40: A comprehensive set of statistical methods for genetic marker
data analysis, designed especially for SSR/SNP data analysis.
▪ STRUCTURE41: Uses a clustering method to identify population structure and
assigns individuals to those populations.

10. R Packages for Agrobiodiversity Measurement and Study

Most of the software and R packages used in biodiversity analysis can be used for
agrobiodiversity analysis. Past is simple and free software that can be used for
agrobiodiversity data. It is good for generating a graph, doing multivariate analysis,
estimating different diversity indices, and analyzing time-series data. Some of the R
packages useful for analysis of agrobiodiversity data are:
▪ adiv42: Analysis of Diversity, with functions, data sets, and examples for the
calculation of various indices of biodiversity including species, functional and
phylogenetic diversity.
▪ agricolae43: Statistical Procedures for Agricultural Research, offers extensive
functionality on experimental design especially for agricultural and plant
breeding experiments and other statistical analysis.
▪ analogues44: To calculate the climatic similarity between a reference site and a
prescribed area, helps identifying locations with similar climates.
▪ BAT45: Biodiversity assessment tools, assess alpha and beta diversity in all their
dimensions (taxonomic, phylogenetic and functional).
▪ BiodiversityR46: For statistical analysis of biodiversity and ecological
communities.
▪ BioFTF47: To study biodiversity with the functional data analysis.
▪ BIO-R48: Biodiversity analysis using molecular data.
▪ GGEBiplotGUI49: A graphical user interface for the construction of, interaction
with, and manipulation of GGE biplots.

35 https://phylogeny.uconn.edu/software/
36 https://biology-assets.anu.edu.au/GenAlEx/Welcome.html
37 https://www.megasoftware.net/
38 https://evolution.genetics.washington.edu/phylip.html
39 https://sites.ualberta.ca/~fyeh/popgene.html
40 https://brcwebportal.cos.ncsu.edu/powermarker/
41 https://web.stanford.edu/group/pritchardlab/structure.html
42 https://cran.r-project.org/web/packages/adiv/index.html
43 https://cran.r-project.org/web/packages/agricolae/index.html
44 https://github.com/CIAT-DAPA/analogues
45 https://biodiversityresearch.org/software/
46 https://www.worldagroforestry.org/output/tree-diversity-analysis
47 https://cran.r-project.org/web/packages/BioFTF/index.html
48 https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10820
49 https://cran.r-project.org/web/packages/GGEBiplotGUI/index.html

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▪ hclust50: Hierarchical cluster analysis on a set of dissimilarities and methods for

analyzing it.
▪ prcomp51: Performs a principal components analysis on the given data matrix
and returns the results as an object of class prcomp.
▪ pscyh52: Procedures for psychological, psychometric, and personality research.
▪ rich53: For the analysis of species richness.
▪ vegan54: For community ecologists with multivariate and diversity analysis and
other functions.

11. Data Preparation, Import and Analysis in R

A very common data frame in agrobiodiversity study is a data matrix that contains
information about the properties, traits, characters, variables of several OAU
(individuals, samples, specimens and population). For example, data is a household data
matrix (household by several landraces within a species) and it is a count data set. The
first column is household name or number, and it may be a community, site, household,
species, agrobiodiversity component, agrobiodiversity group, or any other OAU. Other
columns are the number of landraces under different crop species, and it may be species,
cultivars, or any other variables. Data is generally prepared in MS Excel, and it is good
to cross-check and verify the data before importing it into the R environment. The useful
commands in Excel for data check are freezing or splitting panes, filter, sort, text to a
column, data validation, exploratory data analysis, scatter plot, etc.
RStudio is more user-friendly, and the following analysis and process are based
on RStudio. RStudio has four windows, script/editor window, data import/workspace
window, console/ command window, and file/plot/package window. Among many R
packages, vegan and BiodiversityR are more useful for estimating agrobiodiversity
indices (Kindt and Coe, 2005), and, therefore, methods including R script are described
below. To import data, the import dataset menu under environment is used. Here
example data file is hhdata. The followings are the R scripts to import, view data, and
converting imported data into a data frame.
library(readxl)#loading readxl package
hhdata <- read_excel("C:/Users/BK Joshi/Downloads/canada
training/ram/hhdata.xlsx")#importing data from given drive and saving this data
into hhdata
View(hhdata)#to see the data
hhdata<- as.data.frame (hhdata)#converting imported excel data into R data
frame
rownames(hhdata) <- hhdata[,1] #assigning row names from 1st column
hhdata[,1] <- NULL #removing the first column
hhdata #to display data contents

Followings are the R script for installation and estimating diversity indices using
R package, vegan
#install vegan package from a menu, Package then install in RStudio
S=apply(hhdata>0,1,sum)# estimate species richness (S) without loading vegan

50 https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust
51 https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp
52 https://cran.r-project.org/web/packages/psych/index.html
53 https://cran.r-project.org/web/packages/rich/index.html
54 https://cran.r-project.org/web/packages/vegan/index.html

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S # to display a richness
library(vegan) #loading vegan package
H=diversity(hhdata)#estimate Shannon diversity index
help(diversity)# look for description of function diversity
simp=diversity (hhdata, index="simpson") #estimate simpson index
J = diversity (hhdata, index =”simpson”)/log(S) #estimate Pielou’s evenness (J)
diversity(hhdata[-1], index="shannon")#exclude first column in case of data file
with first column as row name
barplot(simp) #plot simpson index
pairs(cbind(H, simp), pch="+", col="blue") #plot all
## Species richness (S) and Pielou's evenness (J):
S <- specnumber(hhdata) #estimate richness
cor(H,simp) #correlation coefficient between the Shannon and Simpson indices
A useful picture of diversity across several units is the function anosim() in the
package, vegan. This analysis ranks all the dissimilarities among accessions and
produces a boxplot of the ranks of dissimilarities within a given unit e.g., household. As
an example, iris data set within this package is given below.
data(iris) #loading data in R memory
distiris<-dist(iris[,1:4]) #distance matrix computed by using the specified
distance measure to compute the distances between the rows of a data matrix
anoiris<-anosim(distiris,iris$Species) #analysis of similarities (anosim)
provides a way to test statistically whether there is a significant difference
between two or more groups of sampling units.
plot(anoiris) #produces a boxplot of the ranks of dissimilarities within a given
unit.
Another useful R package is BiodiversityR, which is a graphical user interface 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 cluster,
constrained and unconstrained ordination analysis. It is menu-driven built within Rcmdr
package. BiodiversityR analyzes two datasets simultaneously as does the vegan
community ecology package. These data sets are the community datasets (rows
correspond to sample units and columns correspond to species) and the environmental
datasets.
It is suggested to install the package in R following the guidelines55 as described
in the installation guide. The manual56 can also be accessed.
Followings are the commands and steps for analysis in BiodiversityR. An analysis
can be carried out either through menu driven or using commands:
library (BiodiversityR) #load BiodiversityR package
library (Rcmdr) #load Rcmdr package
BiodiversityRGUI() #open graphical interface
help("BiodiversityRGUI", help_type="html") #to see details.
These are the steps for doing analyses with the menu options of BiodiversitR. To
select the species and environmental matrices, follow these menu-driven steps:
BiodiversityR > Environmental Matrix > Select environmental matrix
Select the dune.env dataset as an example
Biodiversity > Community Matrix > Select community matrix
Select the dune dataset as an example.

55 https://www.worldagroforestry.org/sites/default/files/users/admin/Installation%20of%20BiodiversityR%202018.pdf
56 http://apps.worldagroforestry.org/downloads/Publications/PDFS/b13695.pdf

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To calculate diversity indices for each site, follow these steps:

BiodiversityR > Analysis of diversity > Diversity indices …
Diversity index: Shannon
Calculation method: separate per site.
To calculate diversity indices for each site using the command options of
BiodiversityR, use the following scripts:
Diversity.1 <- diversityresult(dune, index=”Shannon”,method=”each site”)
Diversity.1
Diversity.2 <- diversityresult(dune, index=”Simpson”,method=”each site”)

11.1 Interpretation
Richness (S) is a number of species, landraces, particular traits in household,
community, sites, or landrace. It quantifies types of the dataset. Shannon index (Shannon
diversity index or Shannon Weaver index, H’) includes both species number and
evenness, where a greater number of species increase diversity, as does a more equitable
distribution of individuals among species. High H’ is representative of a diverse and
equally distributed community. H’ is strongly influenced by species richness and by rare
species. Simpson index (D) is a measure of diversity, which takes into account both
richness and evenness. The value of D ranges from 0 to 1, the greater the value the
greater the diversity. The Simpson index gives more weight to evenness and common
species. Evenness (Pielou’s evenness, E) is a measure of the relative abundance of the
different species making up the richness of an area. A community dominated by one or
two species is considered to be less diverse than one in which several different species
have a similar abundance. Its value ranges from 0 to 1 and 1 is complete equitability.

12. Conclusion

Native agrobiodiversity is generally neglected for conservation, quantification,

evaluation, and monitoring. Different statistical tools can be used under agrobiodiversity
statistics. Many software and R package are now available for agrobiodiversity study
including measurement. Six types and levels of agrobiodiversity need to quantify and
study for better management of agrobiodiversity. An operational agricultural unit is like
a factor in which variables are generated and analyzed. Multivariate analysis and
diversity indices are the major statistical components used in agrobiodiversity
measurement. Estimates help generate the agrobiodiversity indicators that ultimately
drive the program plans and activities. Many different types of scores and indices can be
measured for household, community, any other administrative unit, and other OAUs.
Among the many software and R packages, vegan and BiodiversityR are very useful
packages for estimating diversity indices and multivariate analysis along with many
statistical features. Such estimates should be measured over a certain geo-region and
period to monitor the status, plan the program, and rank the geo-regions.

13. Acknowledgments

The Grassroots Institute organized a Summer Field School on Mountain

Ecosystem and Resource Management in September 2021. Based on the presentation in
this Summer School, this review article was written. A special thank goes to Dr Hasrat
Arjjumend for his initiation and Dr. Lila Khatiwada for valuable suggestions and
grammar correction.

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Author’ Declarations and Essential Ethical Compliances

Author’ Contributions (in accordance with ICMJE criteria for authorship)

This article is 100% contributed by the sole author. She conceived and designed the
research or analysis, collected the data, contributed to data analysis & interpretation,
wrote the article, performed critical revision of the article/paper, edited the article, and
supervised and administered the field work.

Funding
No funding was available for the research conducted for and writing of this paper.

Research involving human bodies (Helsinki Declaration)

Has this research used human subjects for experimentation? No

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Has this research involved animal subjects for experimentation? No

Research involving Plants

During the research, the author followed the principles of the Convention on Biological
Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and
Flora. Yes

Research on Indigenous Peoples and/or Traditional Knowledge

Has this research involved Indigenous Peoples as participants or respondents? No

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Has author complied with PRISMA standards? Yes

Competing Interests/Conflict of Interest

Author has no competing financial, professional, or personal interests from other parties
or in publishing this manuscript.

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