Application of statistical tools for data analysis and

interpretation in crops
Sudershan Mishra
Department of Plant Physiology, CBSH, GBPUAT&T, Pantnagar.
Email-tosudershanmishra@gmail.com

Abstract
Statistical methods involved in carrying out agricultural study include planning, designing,
collecting data, analyzing, drawing meaningful interpretation and reporting of the research
findings. The statistical analysis gives meaning to the meaningless numbers, thereby breathing
life into a lifeless data. The results and inferences are precise only if proper statistical tests are
used. A number of graphical user based softwares ranging from proprietary to open source are
available nowadays to test multivariate type of data; which is the most common data type in
agricultural studies. Using these latest softwares the new facets of multivariate analysis have
evolved which include Principal component analysis (PCA), Principal coordinate analysis,,
Correspondence analysis, Multidimensional scaling, Factor analysis (FA), Discriminant
analysis Multiple logistic regression analysis, Multivariate analysis of variance (MANOVA),
Cluster analysis (CA), and Canonical correlation, redundancy, as well as correspondence.

Introduction scale, convey quantitative information and

Statistics is a branch of science that deals
with the collection, organization, analysis of
data and drawing of inferences from the
samples to the whole population. This
requires a proper design of the study, an
appropriate selection of the study sample
and choice of a suitable statistical test. An
adequate knowledge of statistics is
necessary for proper designing of an
epidemiological study or a clinical trial.
Improper statistical methods may result in
erroneous conclusions which may lead to
unethical practice.
Variable is a characteristic that varies from
one individual member of population to
another individual. Variables such as height
and weight are measured by some type of
are called as quantitative variables. Sex and
eye color give qualitative information and
are called as qualitative variables.
Categorical or nominal variables are
unordered. The data are merely classified
into categories and cannot be arranged in
any particular order. If only two categories
exist (as in gender male and female), it is
called as a dichotomous (or binary) data
Ordinal variables have a clear ordering
between the variables. However, the ordered
data may not have equal intervals Interval
variables are similar to an ordinal variable,
except that the intervals between the values
of the interval variable are equally spaced
Ratio scales are similar to interval scales, in
that equal differences between scale values
have equal quantitative meaning. However,
ratio scales also have a true zero point,
which gives them an additional property.
Most of the biological variables usually
cluster around a central value, with
symmetrical positive and negative
deviations about this point The standard
normal distribution curve is a symmetrical
bell-shaped. In a normal distribution curve,
about 68% of the scores are within 1 SD of
the mean. Around 95% of the scores are
within 2 SDs of the mean and 99% within 3
SDs of the mean.

Skewed distribution
It is a distribution with an asymmetry of the
variables about its mean. In a negatively
skewed
Fig1 - Different types of variables distribution figure 3, the mass of the
distribution is concentrated on the right of
STATISTICS: DESCRIPTIVE AND Figure 1. In a positively skewed distribution
INFERENTIAL STATISTICS [Figure 3], the mass of the distribution is
concentrated on the left of the figure leading
Descriptive statistics try to describe the to a longer right tail.
relationship between variables in a sample
or population. Descriptive statistics provide
a summary of data in the form of mean,
median and mode. Inferential statistics use a
random sample of data taken from a
population to describe and make inferences
about the whole population. It is valuable
when it is not possible to examine each
member of an entire population.

Components of descriptive statistics

• Measures of central tendency
• Measures of dispersion
Fig-2 Normal distribution curve
• Skewness
• Kurtosis
• Gaussian distribution
• Skewed distribution

Normal distribution or Gaussian distribution

 whether to reject or retain the null
hypothesis.

Table 1- P Value with intrepretation

Fig3- Negatively and positively skewed

curves

In inferential statistics, data are analyzed

PARAMETRIC AND NON-
from a sample to make inferences in the
PARAMETRIC TESTS
larger collection of the population. The
purpose is to answer or test the hypotheses.
Numerical data (quantitative variables) that
A hypothesis (plural hypotheses) is a
are normally distributed are analysed with
proposed explanation for a phenomenon.
parametric tests.
Hypothesis tests are thus procedures for
making rational decisions about the reality Two most basic prerequisites for parametric
of observed effects. statistical analysis are:

Probability is the measure of the likelihood  The assumption of normality which

that an event will occur. Probability is specifies that the means of the
quantified as a number between 0 and 1 sample group are normally
(where 0 indicates impossibility and 1 distributed
indicates certainty). In inferential statistics,  The assumption of equal variance
the term ‘null hypothesis’ (H0 ‘H-naught,’ which specifies that the variances of
‘H-null’) denotes that there is no the samples and of their
relationship (difference) between the corresponding population are equal.
population variables in question. Alternative
hypothesis (H1 and Ha) denotes that a However, if the distribution of the sample is
statement between the variables is expected skewed towards one side or the distribution
to be true. is unknown due to the small sample size,
non-parametric statistical techniques are
The P value (or the calculated probability) is used. Non-parametric tests are used to
the probability of the event occurring by analyze ordinal and categorical data.
chance if the null hypothesis is true. The P
value is a numerical between 0 and 1 and is
interpreted by researchers in deciding
Parametric tests
The parametric tests assume that the data are
on a quantitative (numerical) scale, with a
normal distribution of the underlying
population. The samples have the same
variance (homogeneity of variances). The
samples are randomly drawn from the
population, and the observations within a
group are independent of each other. The
commonly used parametric tests are the
Student's t-test, analysis of variance
(ANOVA) and repeated measures ANOVA.
Non Parametric tests
When the assumptions of normality are not
met, and the sample means are not normally,
distributed parametric tests can lead to
erroneous results. Non-parametric tests
(distribution-free test) are used in such
situation as they do not require the normality
assumption.[15] Non-parametric tests may
fail to detect a significant difference when
compared with a parametric test. That is,
they usually have less power.
As is done for the parametric tests, the test
statistic is compared with known values for
the sampling distribution of that statistic and
the null hypothesis is accepted or rejected.
The types of non-parametric analysis
techniques and the corresponding parametric
analysis techniques are delineated in Table
2.
Table 2- Analogous parametric and non-
parametric tests
Some basic and advanced application
softwares
SPSS (IBM)
SPSS, (Statistical Package for the Social
Sciences) is perhaps the most widely used
statistics software package within human
behavior research. SPSS offers the ability to
easily compile descriptive statistics,
parametric and non-parametric analyses, as
well as graphical depictions of results
through the graphical user interface (GUI).
It also includes the option to create scripts to
automate analysis, or to carry out more
advanced statistical processing.
R (R Foundation for Statistical
Computing)
R is a free statistical software package that is
widely used across both human behavior
research and in other fields. Toolboxes
(essentially plugins) are available for a great
range of applications, which can simplify
various aspects of data processing. While R
is a very powerful software, it also has a
steep learning curve, requiring a certain
degree of coding. It does however come
with an active community engaged in
building and improving R and the associated
plugins, which ensures that help is never too
far away.
MATLAB (The Mathworks)
MatLab is an analytical platform and
programming language that is widely used
by engineers and scientists. As with R, the
learning path is steep, and you will be
required to create your own code at some
point. A plentiful amount of toolboxes are
also available to help answer your research
questions (such as EEGLab for analysing
EEG data). While MatLab can be difficult to
use for novices, it offers a massive amount
of flexibility in terms of what you want to
do – as long as you can code it (or at least
operate the toolbox you require).
SAS (Statistical Analysis Software)
SAS is a statistical analysis platform that
offers options to use either the GUI, or to
create scripts for more advanced analyses. It
is a premium solution that is widely used in
business, healthcare, and human behavior
research alike. It’s possible to carry out
advanced analyses and produce publication-
worthy graphs and charts, although the
coding can also be a difficult adjustment for
those not used to this approach.
GraphPad Prism
GraphPad Prism is premium software
primarily used within statistics related to
biology, but offers a range of capabilities
that can be used across various fields.
Similar to SPSS, scripting options are
available to automate analyses, or carry out
more complex statistical calculations, but
the majority of the work can be completed
through the GUI.
Minitab
The Minitab software offers a range of both
basic and fairly advanced statistical tools for
data analysis. Similar to GraphPad Prism,
commands can be executed through both the
GUI and scripted commands, making it
accessible to novices as well as users
looking to carry out more complex analyses.
STAR- Statistical Tool for Agricultural
Research
STAR is developed using Eclipse Rich
Client Platform (RCP) and R language for
crop scientists and has a user-friendly
graphical user interface (GUI). Its current
version provides modules for generating
randomization and layout of experimental
designs commonly used in crop research,
data management, and basic statistical
analysis, including descriptive statistics,
hypothesis testing, and ANOVA of designed
experiments. In the future, modules for
mixed models, combined analysis, general
linear models and multivariate analysis will
also be included.
CropStat
CropStat is a computer program for data
management and basic statistical analysis of
experimental data. It can be run in any 32-
bit Windows operating system. It has been
developed primarily for the analysis of data
from agricultural field trials, but many of the
features can be used for analysis of data
from other sources.
  The main modules and facilities are  Manages trait to measured
 Data management with a spreadsheet  Manages images and audio captured
 Text editor
 Descriptive statistics and Scatterplot Various statistical analysis powered by
Graphics the new application softwares
 Balanced analysis of variance
 Unbalanced analysis (generalized Multivariate statistical methods are available
linear models) for analysis of data comprising of multiple
 Linear Mixed Models variables encompass, including Ordination:
 Combined analysis of variance Comprising of principal component analysis
 Analysis of repeated measures (PCA), principal coordinate analysis,
 Regression and correlation analysis discriminant analysis, correspondence
 Single-site analysis for variety trials analysis, multidimensional scaling, and
 Spatial Analysis factor analysis (FA); Discrimination/
 Genotype × environment interaction Classification: Comprising of discriminant
analysis analysis, multiple logistic regression
 Pattern Analysis analysis, multivariate analysis of variance
 Quantitative trait loci analysis (MANOVA), and cluster analysis (CA); and
 Graphics Canonical: Comprising of canonical
 Utilities for randomization and correlation, correspondence, and
layout, and orthogonal redundancy. Ordination aims at describing
polynomial17. Analysis of data by identifying a reduced data dimension
Categorical Data of a few variables accounting for the
greatest amount of variability in the data.
FieldLab Discrimination aims at delineating
experimental groups or classifying
FieldLab is an application for Android tablet observations into experimental groups based
that used for data collection in the field. on a set of variables. Canonical aims at
IRRI’s researchers and technicians are using describing and predicting the relationship
this application to go paperless and thus, between two sets of variables.
promote digital revolution.

Features The MVA usually involves PCA, CA, FA

 Import ICIS workbook as a study
 Export observation data collected to
an ICIS workbook format
 With validation, range entry and
look-up values on data entry form.
 Integration with wireless bar-code
reader (Baracoda brand)
and pattern analysis. PCA is a multivariate
statistical technique which reduces the
dimension of a p-dimensional array by
introducing a set of linear combinations of
the original variables. It has been suggested
that PCA can be used in studying plant
disease epidemics because it provides a
means to quantitatively evaluate the relative
importance of curve element which are level
of effect of a factor curve, the rate of yield
increase, and the variation in shape or
skewness from the mean curve. CA is an
exploratory data analysis tool which aims at
sorting different objects into groups in a
way that the degree of association between
two objects is maximal if they belong to the
same group and minimal otherwise. FA, as a
branch of multivariate analysis, is useful to
explain the inter-correlations of variables. It
helps to find out the number and nature of
causative influences on which more
intensive investigations can be concentrated.
MANOVA
MANOVA is a procedure for assessing
differences among several nonmetric
dependent variables based on the linear
combination of several metric dependent
variables. This procedure enables the
simultaneous examination of several
dependent variables. MANOVA was first
used by Golinski et al (2002) to assess the
effect two pathogens (Fusarium avenaceum
and F. culmorum) on three yield
components (1000-grain weight, and weight
and number of kernels per winter wheat
head) of 14 winter wheat cultivars in a two
year study.
Correspondence analysis
Correspondence analysis describes the
relationships among two or more cross-
tabulated categorical variables (contingency
table). The frequencies in the contingency
table are transformed into Chi-square
distances, which are used to establish a
perpetual map of the relation among
variables In one of the first studies using this
method the genomic variability of 66
isolates of Xanthomonas arboricola pv.
juglandis from different geographic origins
is investigated by analyzing the proximities
among amplified fragment length
polymorphic (AFLP) banding patterns using
correspondence analysis (Loreti et al, 2001).
Canonical correlation analysis
Canonical correlation analysis describes the
association between two sets of variables.
Canonical correlation analysis was first
employed by Schlosser et al (2000) to
characterize the relationship between plant
morphological variables such as plant
height, leaf length, leaf area, and plant
growth rates and rice blast disease variables
like lesion densities, and lesion types in six
upland rice cultivars
Redundancy analysis
Redundancy analysis, which aims at
measuring the percentage of variation in a
set of variables (considered singly) that is
accounted for by the other set of variables
(considered collectively) This determination
is achieved by regressing each variable from
one set on all variables in the other set.
Redundancy analysis was first used by
Folman et al (2003) to describe the
relationship of carbon source utilization
profiles of 20 clusters of rhizobacteria to 9
root tissue types consisting of 3 root regions
(tip, intermediate and base of root) sampled
at three developmental stages (seedling,
vegetative and generative)
GGE Biplot
The concept of biplot was first developed by
Gabriel (1971). It is a scatter plot that
graphically displays both the entries (e.g.,
cultivars) and the testers (e.g.,
environments) of a two-way data. In
breeding and genetics data, testers can also
be traits, genetic markers, etc. When the
two-way data is subjected to singular value
decomposition, it is decomposed into three
matrices: the singular value matrix, the entry
eigenvector matrix, and the tester
eigenvector matrix. The singular value
matrix is a diagonal matrix, and can be
somehow partitioned into the entry and
tester eigenvector matrices. After singular
values are partitioned, the positions of the
entries in the biplot is defined by the entry
eigenvector matrix and those of the testers
by the tester eigenvector matrix.
two-way data. Entry is the factor to be
tested, and tester is the factor used to test.
An entry is a level of the entry factor, and a
tester is a level of the tester factor. In
genotype by environment data, genotypes
are entries and environments are testers. In
genotype by trait data, genotypes are entries
and traits are testers. In genotype by genetic
marker data, genotypes are entries and
markers are testers. In convention, entries
are presented as rows, and testers as
columns in a data matrix.

Properties of a biplot
A biplot graphically displays the two-way
data and allows visualization of:
the interrelationship among the entries (e.g.,
genotypes),
the interrelationship among testers (e.g.,
environments), and
the interaction between entries and testers.

GGE stands for genotype main effect (G) Fig 4- Sample GGE Biplot
plus genotype by environment interaction
(GE), which is the only source of variation Additive main effects and
that is relevant to cultivar evaluation. multiplicative interaction analysis
Mathematically, GGE is the genotype by
AMMI biplot is a graphical
environment data matrix after the
representation in which genotypes,
environment means are subtracted. A GGE
environments or pathogen strains and
biplot is a biplot that displays the GGE of a
host genotypes are displayed
genotype by environment two-way data. The
simultaneously in four sectors depending
GGE biplot methodology originates from
upon the positive or negative signs of the
graphical analysis of multi-environment
scores on the first two principal
variety trials (MET) data, but is equally
components. For simple interpretation of
applicable to all other types of two-way
the biplot, the genotypes with vector end
data. Entry and tester are the two factors in a
points far from the origin contribute
relatively more to the interaction than
those with vector end points close to the
origin. Sector-1 represents host
genotypes pathogen strains or
environments with positive IPCA1 as
well as IPCA2 scores, while sector-2
represents positive IPCA1 and negative
IPCA2 scores. Sector-3 represents
negative IPCA1 as well as IPCA2 scores
and sector-4 represents negative IPCA1
and positive IPCA2 scores.
Fig 5- Biplot of 52 isolates of rice
bacterial blight strains and 16 host
genotypes (Nayak et al, 2008). A, The
mean lesion length and the first
interaction principal component (IPCA1);
B, IPCA1 and IPCA2 scores. IG, Isolate
group; HG, Host genotype group.
Modeling approaches
• Generalized linear model (GLM)-
it assumes one fixed factor and
multinomial distribution for the
variable
• Linear mixed model (LMM)-
with at least one fixed effect
factor and one random effect
factor excluding residual
• Generalized linear mixed
model(GLMM)- it is an extension
to LMM, which contains more
than one random effect in
addition to the usual fixed effects
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