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I. INTRODUCTION
collection of individuals based on the set characteristics that are categorical in nature, the
same way that statistical variance is used to provide measure of variability for
stands out because it provides more information about community composition. This
index was originally proposed as a measure of information content of a code. Later on, it
was widely used to determine the diversity of sample of individual from an ecological
community, treating species as symbols and their relative population sizes as the
probability.
Moreover, it has been one of the most commonly used indices because of its
population in which a random sample can be drawn. This classification is the most
the of community’s diversity, it has been proven to be biased especially when all the
Several studies have adopted the index to measure other types of diversity. The
index also measures the variation of genetic, morphologic and phenotypic characteristics.
Analogous to components of biological collection, the properties and condition of
Likewise, the Shannon index used for these diversities is biased and more often
underestimate the true population diversity, especially when the number of not sampled
may not be observed in the sample. Thus, the statistical properties of the index are still in
question since the sample was not able to capture the vital properties of the parameter,
restricting one to proceed on estimation of the index by means of confidence interval and
hypothesis testing based on sampling imposed by field condition. As Peet (1975) had
elaborated, the use of diversity index without a significance test can be quite misleading.
What is required for the solution of these inference problems is the sampling
distribution of the estimate of the Shannon index. Several methods have been done to
develop and obtain improved estimates considering its distribution and other statistical
properties.
Zahl (1977) applied the resampling method called jackknife method to the
estimation of the diversity index and showed the advantages of the method when the
random sampling of the species or subject is not satisfied. This method provided good
improved estimate for Shannon index. Bootstrapping as a technique that allows one to
knowing the distribution of the population. Also, the bootstrap provides a way to
good selection in calculating the Shannon diversity index and its properties.
interval methods, normal approximation method, standard percentile method, and bias-
corrected method seem to be the ones that best take advantage of bootstrapping’s
benefits. They are automatic and relatively simple to program, easy to understand
conceptually, and applicable, perhaps, to any statistics developed from a simple random
sample. For these reasons, these methods are the leading candidate for application in
Over the past decade, substantial attention has been paid to the development of
various population parameters. This study presents a bootstrap simulation for determining
the Shannon index using the four most general and practical method for biological
sciences namely: the normal approximation method, the standard percentile method, and
the bias-corrected method. It also explores the sampling mean coverage of the confidence
intervals for the index when the number of species or subject in the sample itself is
In general the study aims to utilize the bootstrap confidence interval methods for
1. examine the behavior of Shannon index using bootstrapping method when the
as the normal approximation method, the standard percentile method, and the
bias-corrected method;
4. assess the interval based on its statistical properties such as mean coverage,
5. compare the interval obtained using the different interval construction method.
Shannon index, similar to other indices for different field simplifies the
collections and to know which collection exhibits stable and productive community
monitoring the diversity condition of an ecological space through time, reflecting the
represent diversity of the collection could help if not maintain healthy community. Since
it is important to account uncertainty when diversity indices are calculated in making
policies this study may be beneficial to the user of Shannon index. In addition,
identifying the bootstrap method that will give a best coverage of an interval will improve
the analysis of the index. Furthermore, the problem of interpreting this diversity
by ecologist since the late 1950s. However, with the different types of collection, Pielou
(1966) recommended the use of Shannon index for a large collection where a random
sample can be drawn and the number of species is known. Since the basis is only a
portion of the whole collection, one cannot determine the true population diversity or
preferably estimate the average diversity from a sample. The estimated value of Shannon
index is from the incomplete knowledge yielded by a sample and thus has sampling error.
The Shannon index of diversity is obtained as H p
ilnp
i , where pi is the
i
1
proportion of the ith species of a population with s species. The value of H is estimated
the sample. However, this method yields a biased estimator with expected mean
s
s 1
E ( Hˆ ) pi ln pi ...
i 0 2N
and variance
s s
p
il
npi
2
( p
il
np)
i
2
s1
v
a
rˆ
(
H)
i0
i0
.
.
N 2
N
(Hutchenson 1970). The bias may only be insignificant when all of the species are
Several methods had been employed to obtain improved estimates for the
Shannon index. Pielou repeatedly computed the index of a sample, adding new quadrants
in random order at a time, until the index showed no significant difference. Using
Pielou’s method, Heyer and Berven (1973) repeated the procedure for different random
orderings of the quadrant. This method provided an improved or smaller standard error.
However, these methods failed to provide significance tests or confidence intervals for
sampling done when the number of species in the sample is subject to variation.
Shannon index. The method was employed by systematically dropping out quadrants one
at a time and assessing the variation in the resulted index. It automatically took into
account the restriction on filed sampling and showed approximately normally distributed
procedure as a tool to correct the bias of the usual estimation procedure for species
diversity. She compared the relative reduction in bias of the jackknife estimates from the
computed values using sample based procedure of the three diversity indices, including
nonparametric estimates of the standard error of an estimator. It showed that the bootstrap
performs notably better than the jackknife in estimating several parameters like the
standard error of correlation coefficient from a bivariate normal model. He showed that
bootstrap can exhaust all the possible nonempty subsets or at most 2 1 nonempty
n
subset of the data set of size n, while the jackknife utilize only n of them. Hall (1989)
generalized that bootstrap methods are simulation methods for assessing sampling
Several studies extended the index to evaluate other types of diversity. Genetic
Morphologic and agronomic variety of plants implemented the index to characterize the
Jain et al. (1975) adopted the Shannon index to examine the geographical
patterns of the phenotypic diversity in the world collection of the durum wheats (Triticum
turgidum). In the study, durum wheats were classified for different observable
characteristics, each in different number of classes. The Shannon index, Hpi lnpi ,
i
1
was employed, where n is the number phenotypic classes for a character and pi is the
proportion of total number of entries in the ith class. Moreover, Jain et al, used the
diversity in the Ethiopian noug germplasm collections across a wide range of characters
phenotypic frequencies of the characters were analyzed by the Shannon diversity index
(H’) in order to estimate the diversity of each character within each province. The result
supported the assertion of Yang et al. (1991) that the value of the index increases with the
increase in polymorphism and reaches the maximum value when all phenotypic classes
have equal frequencies. Also the variance of H’ has not been characterized. However,
assuming that the eight characters used in the study represent a random sample of all
possible characters of noug plant, an empirical variance was computed from the eight
estimates of Shannon’s diversity index. It was concluded that the utility of germplasm
sampling procedures.
Korean germplasm of rice with different levels of resistance to blast in the Philippines.
the leaves of each Korean germplasm. The bootstrap values was generalized and come in
percentages which can be considered as statistical tests (confidence limits) on the validity
of the various groups. She discussed further that the higher the percentage, the greater the
compared theoretically the three confidence interval method and highlighted the
parametric assumption about the distribution of the estimator but demands the least
Bootstrap Procedure
Efron and Tibshani (1993) simplified the steps of the generic bootstrapping
procedure. This was followed to bootstrap the Shannon diversity index. Suppose a
random sample of x1, x2,.. xN with unspecified probability distribution F, so that xi~indF,
for which the parameter of interest is to estimated. The basic steps in the procedure are as
follows:
observed values xi, assigning 1/n at each data point. This is the empirical
ˆb* .
probability 1/B at each point, ˆ1 , ˆ2 ,…, ˆB . This distribution is the
* * *
interval for Shannon diversity index namely: normal approximation method, standard
constructing confidence intervals. The method assumes that the statistics follow a normal
distribution; however no analytic standard error formula for it exists. The bootstrapped
sampling distribution can be surrogated to estimate the standard error. This estimation is
samples.
( )
The percentile method, on the other hand, takes literally the notion that
percentiles of the distribution. The values will be sorted so that the value
of at the 2.5th and 97.5th percentile of can easily be determined. Thus, given
that B =1000, the lowest 25th value of will be the lower limit and the 25th highest
center of the point estimate. This allows finding asymmetric intervals. The confidence
( )
bootstrap estimates that are larger than the original sample estimate or the bootstrap
population. If the distribution is already centered, that is, if p* is 0.50, then it will turn out
Equivalently, the endpoints can also be obtained using the cumulative probability
lower limit.
Thus the bias corrected percentile limits are the 100 % and 100 % percentile
the IRRI germplasm bank was used in the study. Each phenotypic character, denoted by
Yi, of each rice accession was scored or measured in accordance with the procedure
describe in descriptors for Rice provided by IBPGR – IRRI (1980). For agronomic
characteristics which involve quantitative data, the accessions were categorized into 10
mean and is the variance of the values collected for the variable.
The behavior of bootstrap was examined when (A) the number of original
samples and (B) the number of bootstrap resamples vary. Samples consisting of 3000,
1000, 500, 100, and 50 rice accessions were drawn randomly from the rice collection.
These sample sizes were denoted as the original sample. The (1) Shannon index ( Ĥ ) and
where n is the number phenotypic states for a descriptor and p i is the proportion of the
each original sample. Simple random sample with replacement was used from the
For each original sample, 200, 500, 1000, 1500, 2000, 5000 and 10000 bootstrap
resamples were generated to make bootstrap estimation and examine the performance of
the index in modifying the number of resamples. Then, for each bootstrap resample, the
(1) Shannon index and (2) number of states observed was estimated and compared to the
measures obtained from the original sample. Likewise, the (3) normal approximation
confidence interval, (6) bias, and (7) standard error of Shannon index were estimated.
The empirical coverage of nominal 0.95 confidence will be used for each confidence
interval.
To estimate the magnitude of the bias, the percent bias was calculated as the
difference between the true and estimated Shannon index divided by the true value for all
of each conditions.
different conditions, the number of classes or states of a descriptor was set in varying
number. Given the specified number of states, the Shannon index was then determined.
The performance of Shannon index for each condition was then assessed.
bootstrap confidence intervals were constructed for each of the method. Then, the
Shannon index. The efficiency of the method was amounted based on the Average Range
(AR) of set of estimated confidence interval. The measure of coverage sufficiency was
provided by Realized Coverage Rate (RCR), defined as a percentage by which a set of
estimated intervals actually cover the population index given a prescribed level of
confidence. The RCR of the methods was compared to determine the most efficient
Statistical Analysis Software (SAS) and STATA Software was used for the
analysis.
III. RESULTS AND DISCUSSION
Partial data of rice accessions was composed of 36 rice descriptors with 31 pre-
coded and classified descriptors and five descriptors with actual value. Table 1 shows the
computed Shannon Diversity Index of each of the descriptors of the rice collection.
Some of the accessions that contain rice descriptors with no recorded observation were
Table 1. Shannon Diversity Indices of the rice descriptors of the population of rice
collection and the number of state observed.
*Quantitative Variables
The descriptor with the highest Shannon index was the Culm Length with the
index of 1.723441 with seven states observed, followed by Panicle Threshability with the
index of 1.509179 with nine states. On the other hand, the descriptor with the lowest
Shannon index was found to be the Endosperm Type with the index of only 0.228995
It was also detected that all five quantitative variables acquired an index larger
than one. The Grain Length had the highest Shannon diversity index of 1.464131 with the
complete 10 states observed. This was followed by 100-Grain Weight with the index of
1.442009 with also the complete 10 states observed. Grain Width, Main Heading, and
Ligule Length had indices higher than 1 with detected states of nine, seven, and eight,
respectively.
The Lemma Palea Color had the highest number of states detected with 11 states
observed, providing a Shannon diversity index of 1.418971. On the other hand, the
Endosperm Type and the Culm Diameter had only two states, providing an index of
Analysis of Shannon Index using Bootstrap Method when the Number of Original
Sample and Bootstrap Resamples Vary
For this analysis, only the diversity of the descriptor Blade Color was used to
examine the behavior of the Shannon index when the original samples are 3,000, 1000,
500, 100, and 50 and when the number of resamples are 200, 500, 1000, 1500, 2000,
Out of 9,105 rice accessions with the recorded Blade Color, 5,602 entries had the
color of Pale Green with the registered proportion of 0.61527 among all colors, as shown
Figure 1. It is followed by Dark Green state with 0.28160. However, there were only 13
rice entries with the Purple Tip state, which accounted for 0.00143 of the collection. This
proportional distribution of descriptor Blade Color produced an index for the population
of 1.009778.
Figure 1. Pie graph of the proportional distribution of the Blade Color’s states on
the population of rice collection.
Sample of 3,000
Using the 3000 original sample from the population of the Blade Colors of the
rice collections, the Shannon diversity index estimate of the Blade Color was found to be
1.0091. This estimate had a small bias of -0.0007 which can be attributed to the same
proportional distribution of sample among each descriptor’s states in the sample of 3000
rice accessions and in the rice population collection as presented in Figure 1 and Figure 2.
The two graphs exhibited almost the same proportional distribution of samples among the
Similar to the population collection, rice having Pale Green on Blade Color
showed the highest proportion of 0.62167 in the sample of 3,000 rice entries. Also, there
were only 3 entries or 0.00100 of the sample with the Purple Tip state.
Table 2. Frequency distribution of the Blade Color on the
Population and on the sample of 3000
Figure 2. Pie graph of the proportional distribution of the Blade Color’s states
on sample of 3,000.
All of the bootstrap estimates in different resamples had the value of the index
close to the original sample estimate index of 1.0091 as indicated by the small bias on
each resamples. All the bootstrap estimates underestimated the original sample index.
The most accurate estimate was produced by the bootstrap with 1,000 resamples with
value of index equal to 1.00893. On the other hand, the bootstrap with 200 resamples had
the least accurate estimate with the value of index equal to 1.00718. The standard errors
of the estimates using different number of resamples were found to be reliable with value
The 95% Confidence Intervals constructed using the three methods did not vary
significantly and covered the original sample estimate and the population index. Also, for
all of the bootstrap resamples, it was tested and verified that the distribution of the
Table 3. The Bootstrap estimates and statistical properties of the Shannon Index of the
Blade Color on the 3,000 original samples with different bootstrap resamples.
Bootstrap Bootstrap Standard Normality 95% Confidence Interval Bootstrap
Resample Estimates Bias Error Test Lower Limit Upper Limit Method
0.97582 1.04242 NA
200 1.00718 -0.0019 0.01689 Normal 0.97317 1.04099 P
0.97855 1.04308 BC
0.97396 1.04428 NA
500 1.00817 -0.001 0.01789 Normal 0.97295 1.04224 P
0.97808 1.0458 BC
0.97605 1.04219 NA
1000 1.00893 -0.0002 0.01685 Normal 0.97542 1.04214 P
0.97425 1.04137 BC
0.97622 1.04203 NA
1500 1.00827 -0.0009 0.01677 Normal 0.97554 1.04035 P
0.97662 1.0413 BC
0.97533 1.04291 NA
2000 1.0077 -0.0014 0.01723 Normal 0.97303 1.04107 P
0.97733 1.04474 BC
0.97600 1.04225 NA
5000 1.00825 -0.0009 0.0169 Normal 0.97545 1.04159 P
0.97744 1.04365 BC
0.97625 1.042 NA
10000 1.00806 -0.0011 0.01677 Normal 0.97462 1.04091 P
0.97721 1.04284 BC
NA = Normal Approximation P = Percentile BC = Bias Corrected
Sample of 1,000
Taking a sample of 1,000 from the population of the Blade Colors of the rice
collections, the Shannon diversity index estimate of the Blade Color was found to be
0.9971. This index estimate was smaller than the index estimated from 3,000 samples.
observed that the proportional distribution of samples on the different blade color’s states
was as closed as in the Blade Color’s population and in the sample of 1,000 observations,
Descriptor's Frequency
State Population Sample
Pale Green 5602 621
Green 361 32
Dark Green 2564 285
Purple Tips 13 3
Purple Margins 423 40
Purple Blotch 40 7
Purple 102 12
Total 9105 1000
The sample of 1,000 rice entries was dominated by the state of having Pale Green
with the number of 621 or a proportion of 0.62100; followed by Dark Green with the
0.28500. On the other hand two states had samples with less than ten observations. There
were 3 and 7 rice accessions with Blade Color of Purple Tips and Purple Blotch,
respectively.
Figure 3. Pie graph of the proportional distribution of the Blade Color’s
states on sample of 1,000.
Given the original sample index estimate of 0.99774, all the bootstrap estimates
produced from the sample of 1,000, underestimated the original sample estimate and even
of bootstrap resamples were found to be accurate based on its bias. The bootstrap
resample of 1,000 provided the most accurate estimate with the index of 0.99523 and the
value of bias of -0.00251. On the other hand, the least accurate bootstrap estimate was
found in the resamples of 200 with the index of 0.99378 and bias of -0.00397.
At 95% level of confidence, all the confidence intervals constructed using the
three methods did not vary significantly and covered the original sample estimate and the
population index. Also, for all of the bootstrap resamples, the distribution of the bootstrap
0.93994 1.05555 NA
200 0.99378 -0.00397 0.02931 Normal 0.93442 1.05091 P
0.94232 1.05863 BC
0.94016 1.05533 NA
500 0.99409 -0.00366 0.02931 Normal 0.93577 1.04949 P
0.94395 1.05243 BC
0.93744 1.05805 NA
1000 0.99523 -0.00251 0.03073 Normal 0.93435 1.05586 P
0.93744 1.05965 BC
0.93948 1.05601 NA
1500 0.99515 -0.00259 0.0297 Normal 0.93736 1.0535 P
0.94145 1.06104 BC
0.93943 1.05606 NA
2000 0.99504 -0.0027 0.02973 Normal 0.93695 1.05256 P
0.94003 1.05683 BC
0.93979 1.0557 NA
5000 0.99442 -0.00333 0.02956 Normal 0.93593 1.0521 P
0.94374 1.05933 BC
0.93949 1.056 NA
10000 0.99483 -0.00291 0.02972 Normal 0.93653 1.05255 P
0.94231 1.05799 BC
NA = Normal Approximation P = Percentile BC = Bias Corrected
Sample of 500
Taking an original sample of 500 rice accessions from the population of the Blade
Colors, the Shannon Index estimate of the Blade Color was found to be 0.9971. This
estimate had a bias of -0.101839. Moreover, this index estimate was smaller than the
index estimated from 3,000 and 1,000 as original samples. Furthermore, it can be stated
that the proportional distribution of the rice collection on most of the blade color’s states
was closely the same in the population and in the sample with 500 rice accessions, as
presented in Figure 1 and Figure 4. However, no observation was collected for the state
Descriptor's Frequency
State Population Sample
Pale Green 5602 324
Green 361 14
Dark Green 2564 137
Purple Tips 13 1
Purple Margins 423 22
Purple Blotch 40 0
Purple 102 2
Total 9105 500
Shannon Index 1.0098 0.907940
Similar to the sample of 3,000 and 1,000 entries, the Blade Color state of Pale
Green had the highest sampled entries with 324 in numbers or 0.64800 in proportion.
There were only one and two entries in the sample that are classified as Purple Tips and
Purple, respectively. Moreover, no entry was found in the state of Purple Blotch.
However, all the bootstrap estimates in different number of resamples were accurate
based on its bias. The bootstrap resample of 1,000 provided the most accurate estimate
with the index of 0.90398 and bias of -0.00396. On the other hand, the least accurate
estimate was found in the resamples of 2,000 and 5,000 with the bias of the estimate of -
0.00582.
Table 7. The Bootstrap estimates and statistical properties of the Shannon Index of the
Blade Color on the 500 original samples with different bootstrap resamples.
0.83087 0.98501 NA
200 0.90247 -0.0055 0.03908 Normal 0.82192 0.96784 P
0.82561 0.97421 BC
0.83296 0.98292 NA
500 0.90357 -0.0044 0.03816 Normal 0.83003 0.9749 P
0.83688 0.97805 BC
0.82837 0.98751 NA
1000 0.90398 -0.004 0.04055 Normal 0.8256 0.98381 P
0.83113 0.99359 BC
0.8317 0.98418 NA
1500 0.90266 -0.0053 0.03887 Normal 0.82615 0.98075 P
0.83683 0.99094 BC
0.8331 0.98278 NA
2000 0.90212 -0.0058 0.03816 Normal 0.82438 0.97535 P
0.83727 0.98772 BC
0.83213 0.98375 NA
5000 0.90212 -0.0058 0.03867 Normal 0.82589 0.97596 P
0.8378 0.988 BC
0.83231 0.98356 NA
10000 0.90213 -0.0058 0.03858 Normal 0.82548 0.97671 P
0.83648 0.98662 BC
NA = Normal Approximation P = Percentile BC = Bias Corrected
The standard errors of the bootstrap estimates using different number of
resamples did not vary significantly which ranges from 0.03816 to 0.04055. The most
precise estimate was given by the bootstrap estimate with 500 and 2,000 resamples
In the same way with the intervals in the 3,000 and 1,000 original sample, the
95% confidence intervals in the 500 original sample produced using the three methods
did not vary significantly and covered the original sample estimate. The distribution of
the estimates for all the bootstrap resamples followed the normal distribution.
Sample of 100
three states observed. No accession entries were found on Purple, Purple Tips, and Purple
Blotch in the sample. This sample collection produced a value Shannon index of 0.89913,
Descriptor's Frequency
State Population Sample
Pale Green (60) 5602 59
Green (61) 361 3
Dark Green (63) 2564 35
Purple Tips (80) 13 0
Purple Margins (85) 423 3
Purple Blotch (86) 40 0
Purple (89) 102 0
Total 9105 100
Shannon Index 1.0098 0.88913
Figure 5. Pie Graph of the proportional distribution of the Blade Color’s states on sample
of 100.
In Table 9, all the Bootstrap estimates on the original sample of 100 using the
the Blade color’s Shannon index. The most accurate index was provided by the bootstrap
estimate with 1000 resamples having a bias of only -0.01317. However, trend on the
Non-normality of the distribution of the bootstrap estimates were found for the
resamples of 2,000 and higher. Moreover, the confidence interval using these resamples
0.74643 1.03184 NA
200 0.87139 -0.01771 0.07482 normal 0.74757 1.01639 P
0.7615 1.06629 BC
0.74744 1.03083 NA
500 0.87449 -0.01461 0.07212 normal 0.73066 1.01065 P
0.75628 1.03345 BC
0.74888 1.02939 NA
1000 0.87593 -0.01317 0.07147 normal 0.72907 1.01195 P
0.7615 1.0287 BC
0.74728 1.03099 NA
1500 0.87497 -0.01413 0.07232 normal 0.73066 1.01474 P
0.75628 1.03547 BC
0.7515 1.02677 NA
2000 0.87207 -0.01703 0.07018 not normal 0.72755 1.00192 P
0.7607 1.01877 BC
0.74688 1.03139 NA
5000 0.87342 -0.01568 0.07256 not normal 0.72411 1.008 P
0.75677 1.03474 BC
0.74761 1.03066 NA
10000 0.87256 -0.01654 0.0722 not normal 0.73066 1.01058 P
0.7616 1.03986 BC
NA = Normal Approximation P = Percentile BC = Bias Corrected
Sample of 50
Shannon index estimate of 0.87317 with bias of -0.1366. Sample of rice accessions
registered only on the three Blade color’s states namely Pale Green, Green, and Dark
Green.
Similar to the previous number of original samples, all the bootstrap estimates on
the sample of 100 using the different number of bootstrap resamples underestimated the
original sample estimate of the Blade color’s Shannon index. The most accurate index
was provided by the bootstrap resamples of 1000 having a bias of only -0.01431.
However, the standard errors of the bootstrap estimate in this sample indicated relatively
Descriptor's Frequency
State Population Sample
Pale Green (60) 5602 30
Green (61) 361 4
Dark Green (63) 2564 16
Purple Tips (80) 13 0
Purple Margins (85) 423 0
Purple Blotch (86) 40 0
Purple (89) 102 0
Total 9105 50
Shannon Index 1.0098 0.87317
For all bootstrap resamples, it can be noticed that the upper bound of the interval
using percentile method failed to reach and cover the population index of 1.0098. Bias-
corrected method for 1000 resamples had an upper bound less than the population index.
Table 11. The Bootstrap estimates and statistical properties of the Shannon Index of the
Blade Color on the 50 original samples with different bootstrap resamples.
0.72604 1.02031 NA
200 0.85569 -0.0175 0.07461 normal 0.70276 0.99841 P
0.76099 1.03758 BC
0.71375 1.03259 NA
500 0.85518 -0.018 0.08114 normal 0.68434 0.99787 P
0.7171 1.0181 BC
0.71548 1.03086 NA
1000 0.85886 -0.0143 0.08036 normal 0.68434 0.99783 P
0.70168 1.00487 BC
0.71051 1.03584 NA
1500 0.8539 -0.0193 0.08293 not normal 0.665 0.99787 P
0.70779 1.0181 BC
0.71046 1.03588 NA
2000 0.85279 -0.0204 0.08297 not normal 0.67939 0.99785 P
0.71351 1.01986 BC
0.711 1.03535 NA
5000 0.85164 -0.0215 0.08272 not normal 0.67301 0.99524 P
0.71351 1.01331 BC
0.71064 1.03571 NA
10000 0.85362 -0.0196 0.08292 not normal 0.67301 0.99785 P
0.71351 1.0181 BC
NA = Normal Approximation P = Percentile BC = Bias Corrected
Comparison of Different Number of Original Samples
original sample and the frequency observed in the Blade color’s states. It shows that the
population index of 1.0098 was estimated using 3,000, 1,000, 500, 100, and 50 with the
value 1.0091, 0.9977, 0.9079, 0.88913 and 0.87317 respectively. Relative to the Shannon
index on the population of the Blade Color in the collection of rice, the Shannon index
estimate decreases as the number of original sample decreases. This shows that gathering
fewer samples from the collection will more likely underestimate the true population
index. This can be attributed by having no observation in some of the state of the Blade
Color sampled. In the sample of 500 observations, no sampled rice accession had a Blade
Color of Purple Blotch. In addition, the sample of 100 and 50 left three and four states
unregistered.
Table 12. Comparison of the distribution of Blade Color’s states and Shannon Index on
the different original samples.
Frequency on Sample
State Population 3000 1000 500 100 50
Pale Green 5602 1865 621 324 59 30
Green 361 114 32 14 3 4
Dark Green 2564 818 285 137 35 16
Purple Tips 13 3 3 1 0 0
Purple Margins 423 147 40 22 3 0
Purple Blotch 40 11 7 0 0 0
Purple 102 42 12 2 0 0
Total 9105 3000 1000 500 100 50
Figure 7 shows the percent bias of the bootstrap estimates for each of the
observed that the estimates using the original sample of 3,000 provided the smallest bias
for all of different bootstrap resamples. The graph also shows the significant difference of
percent bias between the large original samples such as 500 and higher and smaller
original samples such as 50 and 100. Nonetheless, for all of the original samples, the
estimates that provided the most accurate estimate were the estimates generated using
The Shannon Index of the descriptor was also examined when the number of
states or classes varied. Table 8 confirmed that the Shannon diversity index decreases as
the number of the state or class decreases. The amount of decrease also increases as the
number of detected state closes to zero. Furthermore, the Shannon index was observed to
be equal to zero when there is only one state collected in the sample.
Table 13. The frequency distribution on the Blade Color’s State on the sample of 1,000 in
different number of states observed
The Shannon indices of different descriptors with different number of state were
also analyzed. Table 14 presents seven descriptors with increasing population index as
the number of state increases. However, there is no descriptor with six states found in the
rice collection. It can be observed that Blade color with seven states had a Shannon index
of 1.00978. This index was less than the index of Leaf Length with only five states but
with an index of 1.02823. Thus, it can be said that the rice collection’s Leaf Length is
more diverse than Blade color. The same behavior was followed for the sample of 100
and 50.
Table 14. Shannon index of different descriptors with different number of states
The original sample of 100 was used for the analysis of bootstrap confidence
interval since only after this number of original sample variation on the index was
observed. Original samples with large number, from 500 to 3,000 for instance, produced
confidence intervals that always cover the original estimate. Thus, a relatively small
sample was utilized to further investigate the power of bootstrap confidence interval.
The 95% confidence interval using the normal approximation method for different
bootstrap resamples with the original sample of 100 observations was presented in Table
10. It was revealed that the confidence interval using normal approximation with 2,000
resamples had the narrowest length; while the bootstrap estimate with 5,000 resamples
had the widest coverage of interval. Figure 8 illustrated the coverage of the intervals and
it can be noticed that the intervals are closed to one another. All the intervals covered the
population index of Blade color with the value of 1.00978 indicated by the solid vertical
Original Sample
Estiimate
Lower Limit
Upper Limit
5000
2000
Resamples
1500
1000
500
200
Shannon Index
Percentile Method
The 95% confidence interval using the percentile method for different bootstrap
resamples with the original sample of 100 observations was presented in Table 16. It
was revealed that the confidence interval using normal approximation with 200 resamples
had the narrowest length; while the bootstrap estimate with 1,500 resamples produced the
Original Sample
Estimate
Lower Limit
Upper Limit
5000
2000
Resamples
1500
1000
500
200
Shannon Index
confidence intervals in different resamples were not symmetric with respect to the
bootstrap estimate. Notably, the upper bound of all the intervals were lie near the
Bias-Corrected Method
The 95% confidence interval using the bias corrected method for different
bootstrap resamples with the original sample of 100 observations was presented in Table
17. Likewise to Normal approximation methods, the confidence interval 2000 resamples
registered the narrowest length among the different number of resamples implemented;
also the bootstrap estimate with 200 resamples had the widest coverage of interval.
method, the skewness in the intervals were more reflected using the bias corrected
method. The lower bound of all the resamples converged to a certain value; while, the
Lower Limit
Uppwe Limit
5000
2000
Resamples
1500
1000
500
200
Shannon Index
The three methods in bootstrap confidence intervals were further analyzed within
the different number of bootstrap resamples as presented in Figure 10. For all the
different number of resamples specified, the lower and upper bound of the intervals using
Percentile Method reached the lowest index value for the confidence interval of the Blade
Color among the three methods except only for the lower bound of 200 resamples. On
the other hand, all the lower and upper bound of the confidence interval for all the
number of resamples specified using the Normal Approximation arrived with the highest
value of Shannon diversity index of Blade Color except with 2000 number of resamples.
BC
200
NA
3 Original Lower
Sample Limit
500
2 Estimate Upper
Bootstrap Limit
1 Estimate
BC
1000
P
NA
BC
1500
NA
NA
2000
NA
BC
5000
NA
BC
10000
NA
Shannon Index
Figure 10. Comparison of the Confidence Interval using different methods in different
numbers of resamples
100 Confidence Intervals
From the 100 constructed confidence intervals using the Normal Approximation
method, all the intervals covered the original bootstrap estimates. It can also observe on
Figure 9 that the confidence intervals were symmetric with the reference on the bootstrap
estimate.
91
88
85
82
79
76
73
70
67
64
61
58
Interval
55
52
49
46
43
40
37
34
31
28
25
22
19
16
13
10
Shannon index
Figure 11. One Hundred Bootstrap confidence interval using Normal Approximation
Method
Unlike other methods, fifty-five out of 100 confidence intervals using Percentile
method covered the true population parameter. The other forty-five intervals have upper
bound less than the parameter. Moreover, the intervals produced were no longer
Original Sample
estimate
Bootstrap estimate
101
99 Lower limit
97 Upper limit
95
93
91
89
87
85
83
81
79
77
75
73
71
69
67
65
63
61
59
57
55
Interval
53
51
49
47
45
43
41
39
37
35
33
31
29
27
25
23
21
19
17
15
13
11
9
7
5
3
1
Shannon index
Figure 12. One Hundred Bootstrap confidence interval using Percentile Method
The Bias-Corrected method also generated 100 confidence intervals that cover the
original bootstrap estimate like the previous two methods. No interval was found to be
symmetric with regard to bootstrap estimate and it can be observed that intervals are
Original Sample
Estimate
101 Bootstrap Estimate
99
97 Lower Limit
95
93 Upper Limit
91
89
87
85
83
81
79
77
75
73
71
69
67
65
63
61
Case Number
59
57
55
53
51
49
47
45
43
41
39
37
35
33
31
29
27
25
23
21
19
17
15
13
11
9
7
5
3
1
Value
Figure 13. One Hundred Bootstrap confidence intervals using Bias Corrected Method
Confidence Interval Measures
Using the 100 generated confidence intervals on the three methods, the
comparison of the properties of the interval were evaluated and presented on Table 14.
As a measure of the interval’s accuracy, the Average Range of the ranges of the 100
intervals indicated that the Bias-corrected method produced the most accurate interval
with the mean range of 0.26601. It was followed by Bias-Corrected and Normal
The Expected Coverage Rate and Realized Coverage Rate of the Normal and
Bias-corrected methods were the same with the rates equal to 0.95 and 1.00, respectively.
Percentile method, on the other hand, has a realized coverage rate of 0.55. Thus, this
means that the intervals constructed under Normal approximation and Bias-corrected had
the same number of intervals that actually covered the original sample estimate. Also,
only 55 percent of the intervals will expect to contain the parameter index using
Percentile method. Thus, the Normal approximation and Bias-corrected method are more
calibration rate of 0.99646 which implies that the average range of each method needs a
downward adjustment for the estimated confidence intervals to equalize the realized
coverage rate with the expected coverage rate. On the other hand Percentile method had a
calibration rate of 1.03454 which needs an upward adjustment. However, based on the
method’s Calibrated Average Rate, the Bias-corrected method is the most efficient
the number of bootstrap resamples varies. The original sample of 100 was used for this
analysis since it is the sample where the index reached its critical limits on fitting the
distribution for normal. Different levels of significance were set to determine the power
all the resamples’ distribution resemble the curve of the normal distribution.
the distribution of the estimates produced by having 200 and 500 bootstrap resamples
fitted the normal distribution at level of significance ranging from 0.01 to 0.2. For the
significantly from normal distribution only at 0.2 level of significance. Both 2,000 and
5,000 resamples detected that index distribution does not fit the normal distribution on at
least 0.05 level of significance. Thus, as the number of bootstrap resamples increases the
0.18
0.18
0.16
0.16
0.14
0.14
0.12 0.12
0.1
f(x)
f(x)
0.1
0.08 0.08
0.06 0.06
0.04 0.04
0.02 0.02
0 0
0.7 0.8 0.9 1 1.1 0.7 0.8 0.9 1 1.1
x x
0.2
0.18
0.18
0.16
0.16
0.14
0.14
0.12
0.12
f(x)
f(x)
0.1
0.1
0.08
0.08
0.06
0.06
0.04 0.04
0.02 0.02
0 0
0.6 0.7 0.8 0.9 1 0.7 0.8 0.9 1 1.1
x x
0.18 0.18
0.16 0.16
0.14 0.14
0.12 0.12
f(x)
f(x)
0.1 0.1
0.08 0.08
0.06 0.06
0.04 0.04
0.02 0.02
0 0
0.7 0.8 0.9 1 0.6 0.7 0.8 0.9 1 1.1
x x
Figure 14. Comparison of the distribution of the Bootstrap estimates using different
resamples
Table 17. Goodness-of-Fit test for the normality of the different bootstrap resamples
collection. However, the estimate of this index is known to be biased and with no simple
formula for statistical properties exist. Without any requirement for the formula,
bootstrapping was used to estimate the Shannon index and construct confidence interval
around it.
The behavior of the Shannon index using the different conditions under bootstrap
method was analyzed in the study. Using the different number of original sample to be
used for bootstrapping, relatively small number of original sample found to have
significant effect on the variation of the statistical properties of the Shannon diversity
index. From almost 9,000 rice accessions, an original sample of size 100 was found to
detect significant bias and interval coverage for the diversity index of Blade Color and
other descriptors. Also, the number of bootstrap resamples did not present any particular
trend for the properties of index for large original samples. However, resamples indicated
that as the number of resamples increases the distribution of the Shannon index will more
Among the three methods used for the interval construction, Bias-corrected
method produced the most accurate, sufficient, and efficient interval based on average
range, expected and realized coverage rate, and calibration rate. On the other hand
Percentile method has a calibration rate of 1.03454 which needs an upward adjustment.
Normal Approximation method provided significant intervals for the some resamples that
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Riley, K.W. 1998. Phenotypic diversity in the ethiopian noug germplasm. African Crop
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YANG, R.C., JANA, S., CLARKE, J.M. 1991. Phenotypic diversity and associations of
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