AUTOMATED FLORA ANALYSIS FOR QUADRAT METHOD USING PYTHON

L. G. dela Cruz , N.B. Gatdula , K.R. F.Quinton

Dept. of Geodetic Engineering, University of the Philippines, Diliman, Quezon City, 1101
leizeldelacruz@gmail.com, nerigatdula@gmail.com, krquinton@gmail.com

KEY WORDS: Vegetation Analysis, Quadrat Method, Shannon-Wiener, Shannon-Evenness, Simpsons Index,
Python, Biodiversity Pro Software, Importance Value

ABSTRACT:

Different floral analysis methods were developed to assess plant biodiversity of an area, but one of the most commonly
used method is the use of quadrat. This study is focused on the development of a python program that will aid in the faster
and easier selection of sample sites, management of data and computation of ecological parameters and vegetation index.
Using the program, we could present data in greater detail since it can produce six output text files that contains the
computed and summarized ecological parameters (Dominance, Density, Relative Dominance, Relative Density, Frequency,
Relative Frequency and Importance Value) and biodiversity indices (Shannon-Wiener, Shannon-Evenness and Simpson's
Index). Results show that the program produces vegetation index values that is comparable with the biodiversity pro
software in terms of its accuracy, speed, generated outputs and the capacity to hold data. Wholly, the automated flora
analysis program created is much more convenient to use in the conduct of quadrat method vegetation analysis.

1. INTRODUCTION sizes is the most widely applicable technique in vegetation

Biodiversity refers to communities of flora and fauna
distinctly of diverse species and situated within pristine or
primary habitat nowhere to be duplicated in space and time
(Bucad, 2001). Thus, biodiversity is a measurable entity
having three approaches for measuring: molecular,
phylogenic and taxic measurement. Taxic measurement
refers to the number of higher taxa, which includes phyla,
orders and families of organisms. It provides a practical,
quick and cheap method of measuring biodiversity since
species richness and numbers of higher taxonomic units
tend to be positively related (Labutap, 2005).
One way to measure biodiversity is through the
conduct of flora analysis which is defined as the way to
study species composition and structure of plant
community.It is a modern science with relevant
applications in nature management, particularly on
preservation of biodiversity, sustainable use of natural
resources, and detection of changes in plant cover.
There are important factors to be considered in
studying an vegetation area. One of which is the
community type of vegetation, either heterogeneous or
homogeneous. The other is the sampling vegetation that
may employ either quadrat and line plot methods. Quadrats
vary in shape which could be circular, square and or
rectangular plots. The commonly used sized are 10 x 10m
quadrat for trees, 4m x 4m quadrat for all woody
undergrowth up to 3m height, 1 x 1m quadrat herb
layer.This method of using quadrats or plots with standard
analysis.
Biodiversity Indices that is most commonly use in
vegetation analysis is the Shannon-Wiener, Shannon
Evenness and Simpson’s Index. Simpson Index is actually
an evenness index, meaning that if the value gets higher the
community will be increasingly dominated by fewer species
and diversity will decrease. Meanwhile, Shannon index
actually increases with increasing diversity and is maximum
when all species in a community are present in equal
proportions. Unfortunately, the Shannon index varies with
sample size (it’s an additive measure), so it is difficult to
compare between studies and sometimes even within a
single study
1.1 Background
In the fast development of technology, regardless of
the field of study, it is possible to make manual data
manipulation and computations instant, easier and faster
using programming knowledge. Automation of ecological
parameters and biodiversity indices would greatly help the
ecology and forestry community for assessment. Through
the aid of Python programming language and its modules
such as ogr, math, numpy, etc, automation of vegetation
analysis is possible.
The created program can be use in the step by step
quadrat method vegetation analysis from selection of
sampling sites up to the computation of flora indices. This
program works hand in hand with ArcGIS or any mapping
software that has shape file(.shp).
The six(6) text file outputs of the program will be
the main basis for analysis of the area.
However, the program is designed to compute for
the basal area, thus, it is only applicable to trees with
diameter at breast height (dbh) greater than or equal to ten
(10) centimetres. Lastly, the program input requires that it
should be in shapefile format containing attributes of trees
gathered in the field.

1.2 Statement of the Problem
Estimation of whole vegetation begins by doing a
preliminary survey or reconnaissance followed with
quadrat selection and establishment. Quadrat selection and
establishment are very difficult field activities since almost
all parts of the site should be well represented.
The basis for accuracy assessment was the result
from the biodiversity Pro software (bioPro), a statistical
package program for Windows PC enabling many
measures of diversity. Data used in the test was from an
old study of Miras M.P.

Another constraints on the conduct of vegetation 2. METHODOLOGY

analysis is the very tedious and time consuming manual
data arrangement and manual computation of vegetation
indices that requires group table results . Thus,
quantitative data interpretation and analysis is delayed.
Through the creation of an automated vegetation
indices with quadrat method it is made possible faster and
efficient information outputs essential for analysis. This
ensures speedy recording, processing and presenting of
information especially when on field
2.1 System/Program Requirements
The program requires polygon shapefile for Area
of Interest (AOI) and point shapefile for species list
including its geospatial information. The program should
also involve ArcGIS software since the required inputs for
the script are in ESRI shapefiles format.

1.3 Objectives

The main objective of the study is to develop a

program that will compute for the biodiversity indices in an
area that will facilitate for better assessment and nature
management. Specifically, it aims to:

1. Be familiar on the methods on conducting quadrat

method on the field;
2. To have an easier plot selection method on field
using random sampling design;
3. Identify appropriate ecological parameters and
indices that will be the basis of better analysis; and
4. To generate table output that contains baseline
information on the current vegetation existing in
the area for future monitoring, protection and
conservation.

1.4 Scope and Limitations

The study focused on the development of a

python program that will automate data management and
computation of ecological parameters, importance value
and biodiversity indices (Shannon-Wiener (H’), Shannon
Evenness (E’H) and Simpsons diversity indices (D)).

The flora analysis program uses quadrat

vegetational analysis method limited to 10m x 10m, 15m x
15m, 20m x 20m and 25m x 25m quadrat sizes and is
applicable only to simple random sampling design.
2.2 Flowchart
 Area of Interest (AOI) polygon was used as 3. RESULTS AND DISCUSSION
boundary for the program. The directory was set to access
the inputs and to locate where the outputs will be stored. The efficiency and effectiveness of the program
was done using the Biodiversity Pro software (bioPro), a
The size of the quadrat was determined by statistical package program for Windows PC enabling many
entering the desired grid height/width. Only valid quadrat measures of diversity, as the reference.
sizes can be recognized, else the program will ask you to
enter for a new size. The results of the comparison of the processes
above are presented below:
A fishnet algorithm method was also performed
to create grids based on the boundary input. The extent of Parameter Biodiversity Python Program
the AOI was acquired to get the values for the x- s Pro Software
minimum, x-maximum, y-minimum and y-maximum.
Accuracy Serves as the Little discrepancy
From the assigned grid height/width and from the basis for (3 decimal places)
acquired boundary extent, rows and columns were checking output
obtained. Then the creation of grid cells was done.
Polygons were added from left to right until the whole
Speed Less than 30 1- 10 minutes (for
AOI was occupied.
seconds all processes)
Since this study requires only to get samples
from grids that are completely within the AOI, fishnet Output 1. Computed 1. Computed
Shannon Wiener Ecological
filtering algorithm was done by looping through all the
and Shannon Parameters
features in the fishnet until appropriate grids were sieved.
(Frequency,
Evenness
Dominance,
Sampling intensity (SI%) was entered (minimum computed per Density, Relative
of 10% and maximum of 100%). Then, Simple Random plot (not on the Density, Relative
Sampling Method was done to randomly select the average) Dominance and
samples within the sampling area. Relative
2. Computed Frequency);
Lastly, from the species input and selected Simpson Index
quadrats, ecological parameters, importance values and 2. Computed
per plot
diversity indices were calculated. All computed data were Shannon Wiener
stored in text file format delimited by tab (\t). and Shannon
Evenness for the
Six (6) output text files were generated such as whole
the Sampling Quadrats.txt, Plot Computation.txt, area(average)
Frequency.txt, Ecological Parameters.txt, Importance
Value.txt and Biodiversity Indices.txt. 3. Computed
Simpson Index per
plot
2.3 Modules/Libraries used
Capacity Can compute Unlimited number
and hold 100 of Species
species only

Table 1. Comparative table of the Parameters used to test

OS was imported for setting the file directory,
OGR for vector access, SYS was used for system exit,
MATH was brought for mathematical functions
(logarithms), and TIME for measuring processing/running
length of the program.
Numpy module was also needed in the program
for efficient computation of n-dimensional and multi-
dimensional arrays integrated with Python.
efficiency of the program developed using Python language.
Table above shows that in terms of accuracy, the
results generated from the Python program has a little
discrepancy brought by the number of decimal places used
in the program and the Bio pro software. Bio pro used
three (3) decimal place while in the program, four (4)
decimal place was used.
As for the speed, Bio pro takes only less than 30
seconds to generate result but the input of data for the Bio
pro is very time consuming as it requires encoding of
species per plot. While the program could provide output
within a minute to ten (10) minutes for all the six outputs.
As soon as you have put the shape file of trees in the
program, it will automatically do the computation.
Another thing that makes the program a lot more
comfortable to use is that the program can generate an
output that is used as the input for the bioPro, thus,
problem in data organization is addressed. However, the
speed of generating outputs will be sacrificed as many
species will occur. Speed of the program is also dependent
on the sampling intensity, sampling size and number of
sampling plots.
In regards to the outputs generated, bioPro
limits only to computation of different biodiversity indices
per quadrat, not yet generalized for the whole area.
Meanwhile generated Python program computes indices
including ecological parameters and importance values per
quadrat and in general The program also can facilitate in
the determination of sampling plot unlike in the bioPro
that is solely focused on the computation of indices .
As for the capacity to hold data, bioPro can only
hold one hundred (100) species while the program holds
unlimited number of species.
Wholly, the program produces vegetation index
values that is comparable with the biodiversity pro
software and is really designed to facilitate the conduct of
quadrat method vegetation analysis.
Wholly, the program can serve as valuable tool that
will calculate diversity indices and describe the numerical
structure of an area through different ecological parameters
and importance values.
5. RECOMMENDATIONS
Since, no other programming language or literature
has done the automation of flora analysis, it is
recommended to improve the codes that will facilitate
faster computation of indices. As per its input requirements,
which was a shapefile, it would be better if this program be
made as plug-ins to Qgis or ArcGIS for better visualization
and easier interaction of the user.
It was observed that the output of the program is
very rough ,thus, it is highly recommended that the output
file be presented in xls or csv file format for a better
visualization and understanding. Since the program output
are only values, it is suggested that upon the result of
quantitative values, it will also include the general
implications of the values obtained (eg. 0.5-1.oo means
Moderately diverse area, while 0.0-0.49 means Highly
diverse area). And lastly, it is recommended to include
more sampling techniques to enhance flexibility of the
program.
6. REFERENCES

M.P. Miras, “Vegetational Analysis of Brgy. West

Kalaongan, Caviniti Laguna”, 2012. Unpublished Thesis
4. CONCLUSIONS

Python GDAL/OGR Cookbook. (2013). Retrieved March

After several tests, the results obtained from the 2014 from http://pcjericks.github.io/py-gdalogr-cookbook/.
program is as reliable and comparable with the
Biodiversity pro Software. However, there is a M. Beals, L. Gross, and S. Harrell "Diversity Indices:
discrepancy on the result due to the number of decimal Shannon's H And E". (2000). Retrieved March 2014 from
places use for the algorithm of the program. Using the http://www.tiem.utk.edu/~gross/bioed/bealsmodules/shann
created program, it ensures faster and better data onDI.html.
organization and product of good database since the
program can produce six (6) text file outputs, which are
the following: 1)Sampling Quadrats.txt that contains the
chosen quadrat numbers and the coordinates of the
boundary of the plot and other attributes; 2) Plot
computations. txt that comprises the computed Density,
Dominance, Relative Density and Relative Dominance per
quadrat; 3) Frequency.txt shows the computed frequency
and relative frequency per species, this is also use as an
input for the bioPro software before it can provide
information;4)Ecological Parameters.txt shows the
summarize computation of Density, Relative Density,
Dominance and Relative Dominance for the whole area;
5) Importance Values.txt contains the computed IV per
species of the whole area; and 6) Biodiversity Indices.txt
that shows the result for Shannon-Wiener (H’), Shannon
Evenness (E’H) and Simpsons diversity indices (D).