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Downloads
S.H. Roxburgh
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* Disclaimer *
The various software products, spreadsheets and data provided below are offered
freely and in good faith. Please do the right thing and, where appropriate,
provide due acknowledgement when using these materials. End-user
licence agreements are included in some of the software products. For all other
downloads no responsibility will be taken by myself or my current employer for any losses, damages or costs
incurred by any person as a result of the use of these materials. Use at you own
risk!
Software
Data
Teaching materials
Hardware Fun
stuff
Software
I use a range of programming tools, such as Visual
Basic for Applications (VBA), R, and Gauss, however most of the software below was
developed within the Borland Delphi Pascal
environment. This is a fast and flexible programming language with excellent
support for creating scientific applications, particularly when combined with
Steema
Software's TeeChart Pro graphics add-on for charting, plotting and
visualisation.
Maxent Randomisation Test (MRT)
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Description |
Software to perform the
randomisation-based statistical test described in Roxburgh & Mokany
(2009). "On testing predictions of species relative abundance from maximum
entropy optimisation". Oikos. DOI: 10.1111/j.1600-0706.2009.17772.x |
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Documentation |
Embedded within software. |
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Developer |
SH
Roxburgh. |
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Language |
Borland Delphi Studio 2006. |
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Requirements |
Windows
95 or greater. |
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Download |
MRT program (zip file;
0.7Mb) |
Markaranka Data Analysis Package
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The Digital Transferscope (TDT)
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Description |
The analysis of aerial photographs
has a long history in environmental management, particularly for vegetation
mapping and for quantifying land cover change. The Digital
Transferscope (TDT) was written as a digital alternative to the mechanical 'Zoom
Transferscope' for the collection of cover data from aerial photographs.
Time-series aerial photographs are first digitally scanned at a high resolution, and are
then co-registered (rectified) relative to one another using a
combination of user-defined control points and photographic analysis
algorithms. A downhill simplex search algorithm is used to automate the
rectification process, through the iterative application of either affine or
projective image transformations. Scanned photos are typically around
350mb per photo, and 10,000 x 10,000 pixels resolution, therefore TDT
required the development of custom algorithms for displaying and
manipulating very large images. Once rectified, a
user-defined sampling-grid overlay is added, allowing vegetation cover to be
sampled interactively using a number of methods, e.g. at a number of points
in the landscape (either on a grid, or located at random), or by recording
grid-cell cover dominance. |
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Documentation |
User guide with tutorial exercises
[DRAFT] [ref] |
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Developer |
SH
Roxburgh |
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Language |
Borland Delphi Studio 2006. |
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Requirements |
Windows
95 or greater / MS Excel |
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Download |
TDT program, user guide & sample data (zip file;
39Mb) |
R code for the analyses in Roxburgh & Mokany
(2007)
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Description |
Supporting
R program for the analyses presented in Roxburgh & Mokany (2007) |
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Documentation |
See reference. |
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Developer |
SH
Roxburgh |
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Language |
R. |
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Requirements |
R
programming & analysis environment |
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Download |
R code |
CASS (Carbon Accounting Simulation Software)
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Description |
CASS is a
MS Excel-based model targeted at tertiary education, and designed to
illustrate major features of the terrestrial carbon cycle and the role of
vegetation as carbon sinks. Processes include vegetation growth and decay,
and the impacts of harvesting, fire & land-clearing. Parameterisations for
17 vegetation (biome) types are provided. Additional features include
animated tree growth and disturbance to give visual feedback on the model
output, access to the user-guide directly from within the spreadsheet, and
descriptions of each of the major biome types. |
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Documentation |
User guide with tutorial exercises [ref] |
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Developer |
SH
Roxburgh |
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Language |
MS Excel
spreadsheet / Visual Basic for Applications. |
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Requirements |
Windows
95 or greater / MS Excel 2003 / 2007 (**new**) |
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Download |
CASS
model + user guide (zip file; 4.73Mb) |
Range-ASSESS [top]
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Description |
Range-ASSESS is a state-and-transition based expert system for assessing the
impact of changing land management practices on soil and biomass carbon
across the Australian rangelands.
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Documentation |
User
Guide (installed) & publication [ref
1] [ref 2]. |
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Developer |
SH
Roxburgh & MJ Hill |
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Language |
Borland
Delphi 7.0 |
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Requirements |
Windows
95 or greater |
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Download |
RASetup.exe (19Mb
setup file --> 125Mb installed) |
COINS (COmparison
& INtegration Shell)
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Description |
COINS is
a software shell for integrating many models within the same software
environment. This allows different models to be combined within the same
simulation, and allows the outputs of different models, sharing the same
input driver data, to be compared on an equal footing. The temporal scaling
options accommodate analyses from days to centuries, and the spatial scaling
is from ‘point’ to GIS-type simulations and cellular automata. Factorial and
Monte Carlo capability is provided to allow sensitivity analysis of model
outputs to uncertainty in model parameters.
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Documentation |
User Guide & Help (installed) & publication [ref]. |
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Developer |
ID Davies
& SH Roxburgh |
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Language |
Borland
Delphi 7.0 |
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Requirements |
Windows
95 or greater |
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Download |
Minimum
installation that includes eight small examples to illustrate the major
features of the software (COINS_MIN.zip;
6Mb).
Full installation that includes an additional nine
examples that make use of the spatial analysis capabilities of the shell,
and includes the required spatial input data (COINS_FULL.zip;
296Mb). |
The Random Patterns
Test for spatial association
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Description |
Many organisms
display patchiness in their distribution patterns over a wide range of
spatial scales. Patchy distribution patterns,
caused by processes such as growth, migration, reproduction and mortality,
result in neighbouring areas being more likely to contain a species than
distant areas, a phenomenon known as positive spatial autocorrelation. When
species are patchily distributed the within-species spatial randomness
assumptions of the standard statistical tests for detecting species
associations are seriously violated. To address this problem we
introduce a new test for detecting species associations - the Random
Patterns test. This test takes into account
spatial autocorrelation by including the characteristics of the spatial
pattern of each species into the null model. This software is the
implementation of the random patterns method as described in
Roxburgh& Chesson (1998).
Brief instructions on the use of the software for performing the random
patterns statistical test are included.
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Documentation |
User Guide (included) & publications [ref
1] [ref 2]. |
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Developer |
SH Roxburgh |
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Language |
Borland
Delphi 3.0 |
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Requirements |
Windows
95 or greater |
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Download |
.RandomPatterns.zip
(0.3Mb) |
Illustration of nonlinear averaging &
ecological scaling
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Description |
“Scaling up”
is a commonly used phrase in carbon accounting and throughout the ecological
sciences. By the term, people usually mean that measurements are made at
local scales (e.g. leaves, plants), but estimates are required at larger
scales, e.g. forests stands, continents, global. This disparity between what
is (traditionally) measured and what is needed (i.e. stand to continental
scale estimates) is often referred to as the “scaling problem”. There is
little doubt that there are significant practical difficulties in making
suitable measurements; however, there are also some theoretical
considerations. This short note and
the associated spreadsheet
describes one of the
significant problems – the problem of averaging in the process of scaling
up. |
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Documentation |
Explanatory note &
Excel spreadsheet. |
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Developer |
SH Roxburgh,
ML Roderick, B Barnes |
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Language |
Microsoft
Excel spreadsheet |
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Requirements |
Windows
95 or greater |
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Download |
Scaling.zip (0.04Mb) |
Illustration of scaling & self-thinning
theory
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Description |
Barnes, Bi
& Roderick (2006) developed a theory for combining the mathematics of scaling and
self-thinning into carbon accounting frameworks. The theory demonstrates how
measurements made on individual trees can be used to predict biomass and
carbon stocks at larger spatial scales. This work has been published in the
scientific literature, but requires mathematical expertise to fully
understand, and hence implement. In order to make this work more accessible,
this small software tool illustrates the major features and implications of
the theory, and to enable users to enter and analyse their own data.
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|
Documentation |
Online
help. The software needs to be used in conjunction with the publication
"Barnes,
Bi & Roderick (2006).
Application of an ecological framework linking scales based on
self-thinning. Ecological Applications,
16, 133-142". |
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Developer |
SH Roxburgh |
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Language |
Borland
Delphi 7.0 |
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Requirements |
Windows
95 or greater |
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Download |
STSetup.zip (5Mb) |
Animated climate viewer
[top]
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Description |
This
climate viewer displays month-by-month and year-by-year animations derived from historical
precipitation and temperature surfaces for the Australian continent, for the
period 1900-2004. The
data on which these animations are based are taken from the CRC for
Greenhouse Accounting monthly climate database - see below under 'Data'. |
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Documentation |
ReadMe file |
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Developer |
SH Roxburgh |
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Language |
Borland
Delphi 7.0 |
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Requirements |
Windows
95 or greater |
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Download |
Animated Climate Viewer.zip (23Mb) |
OptIC (Optimisation Intercomparison Project)
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Description |
This software was written to participate in
the OptIC
project, devised by the
Global Carbon Project
to compare different methods for numerically estimating model parameters
from data (so-called model-data fusion methods). Ten contributors applied
their favourite methods to a set of fiendishly tricky pseudo-observed
datasets, in an attempt to uncover the sets of true but unknown model
parameter values that were used to generate the pseudo-observations. My
method combines two approaches - the downhill simplex, and the genetic
algorithm. |
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Documentation |
The
optimisation method is described in the appendix to
Roxburgh et al. (2006).
The software is undocumented. A paper based on the intercomparison results
is currently in press. |
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Developer |
SH Roxburgh |
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Language |
Borland
Delphi Studio 2006 |
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Requirements |
Windows
95 or greater |
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Download |
Program and input data (7.8Mb);
A summary of my results
(0.5Mb); All my results
(8.8Mb) |
DataGrabber (Beta)
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Description |
Ever been in a position where you have a
published bar chart or scatter plot, but what you really need is the
underlying data? Of course, the easiest thing is to just ask the original
author, but sometimes that's not always possible. One option is to make a
photocopy and then get busy with sharp pencils, rulers and graph paper.
Frustrated by the tediousness of that approach, I sat down and wrote
DataGrabber as a software tool to achieve the same end. After scanning or
otherwise obtaining the figure in digital form, its then a simple and
painless task of setting the axes with the mouse, and then making a few
clicks on the computer screen. Its much faster and more accurate than a
photocopier and ruler, and much more fun!
*warning* This software is still in
development and contains many bugs. It is, however, useable in its current
form. |
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Documentation |
There is
a brief tutorial which
covers basic useage. |
|
Developer |
SH Roxburgh |
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Language |
Borland
Delphi Studio 2006 |
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Requirements |
Windows
95 or greater |
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Download |
Program and tutorial (0.6Mb) |
Create correlated random deviates
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Description |
The method of Iman and Conover (Iman,
R.L., Conover, W.J. 1982. A Distribution-Free Approach To Inducing Rank
Correlation Among Input Variables. Commun. Statist.-Simula. Computa. 11,
311-334) is used to generate sets of
inter-correlated random deviates. A typical use is for Monte-Carlo
sensitivity testing of parameter values in a model, where you know that the
parameters are correlated (either negatively or positively). The user
selects the number of deviates, the distribution to use (from a list of 22
continuous and 6 discrete, see picture left), and the desired correlation
structure (by filling in the off-diagonal elements of a correlation matrix).
Sets of univariate deviates can also be generated. The algorithim underlying
the analysis is that used for the Monte-Carlo analyses in the
COINS software. |
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Documentation |
A small
tutorial is provided. |
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Developer |
SH Roxburgh |
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Language |
Borland
Delphi Studio 2006 |
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Requirements |
Windows
95 or greater |
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Download |
Program and
tutorial (1.5Mb) |
Data
Australian continental Net Primary
Productivity (NPP) estimates
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Description |
GIS data of the twelve
modelled continental estimates of Australian long-term average Net Primary
Productivity (NPP) reviewed by Roxburgh et al. (2004).
The
file format is Arcinfo ascii raster format, in geographic projection. All
model estimates have been resampled to a cell size of 0.05 degrees. The
units are g C m2 yr-1.
The
file header is:
ncols 901
nrows 701
xllcorner
109.975
yllcorner -45.025
cellsize 0.05
NODATA value -100
The
methods of calculation for each estimate are varied, and are summarised in
Table 1of Roxburgh et al. (2004) |
|
Documentation |
Roxburgh et al. (2004) |
|
Download |
Continental NPP data
(8Mb) |
Gridded Australian historical
monthly climate data: January 1990 – December 2004
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Description |
A
collection of continental-scale spatial climate data at a monthly resolution
for the period January 1900 – December 2004. Climate grids were generated
using a combination of data extracted from the Bureau of Meteorology (BoM)
Climate Data Australia (CDA) database and the ANUSPLIN software package.
Climate variables include total monthly precipitation, and minimum, maximum
and mean daily temperature for each month. For each climate variable there
are 1260 continental-scale grids (with an approximately 5km x 5km gridcell
size) for the period January 1900 to December 2004 (105 years x 12 months
per year).
Data
for each decade (with 120 grids per decade =12 months x 10 years) are
provided as a single zip file, with each decadal file ranging in size from
20-50 Mb. Data are provided in two GIS software formats: Idrisi raster (*.rst,
*.rdc) or Arc Info float format (*.hdr, *.flt).
The
data format is
ncols 818
nrows 674
xllcorner 112.825
yllcorner -43.725
cellsize 0.050
NODATA_value -99
BYTEORDER LSBFIRST |
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Documentation |
A technical report by
McBeth & Roxburgh (2005) summarises the methods used to generate and
validate the set of spatially interpolated (splined) historical climate
surfaces for the Australian continent, and the resulting set of
continental-scale gridded maps for monthly total precipitation, and mean
monthly minimum and maximum temperature. View poster. |
|
Download |
Data download page. |
Injune soil survey data
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Description |
Excel spreadsheet data
from soil sampling conducted at the Injune study site, as reported in
Roxburgh et al. (2006).
Soil organic carbon and bulk density depth profile data are given for each
of 42 soil cores collected across 14 study sites, in addition to total soil
carbon stocks for each site. |
|
Documentation |
Readme
file for interpreting the spreadsheet |
|
Download |
Injune soils data.zip |
Experimental data from Hely &
Roxburgh (2004)
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Description |
Excel spreadsheet with
raw data from the experiment reported in
Hely and Roxburgh (2004). This was
a growth cabinet experiment investigating the competitive responses of two
grasses to elevated temperature and CO2. |
|
Documentation |
Readme
file for interpreting the spreadsheet |
|
Download |
Hely_Roxburgh.zip |
Teaching materials
Cellular automata laboratory
exercise
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Description |
Cellular automata are a
class of mathematical model that can be used incorporate spatial information
in the study of complex dynamic systems. In a cellular automaton, space is
represented by an array of cells. The array can be a single line of cells, a
two dimensional grid, or multi-dimensional. The essential features of a
cellular automaton are (1) Space is
represented by an aggregation of cells (the array). (2).
At any given time, each cell is
represented by a state, for example a particular species, or type of
forest cover. (3) There is a
neighbourhood which defines what neighbouring cells interact with the
target cell. I.e., the state of a cell in the next time period depends both
on its current state, and also the state of the cells in its neighbourhood.
(4) There is a program, which is
simply the set of rules which define how the state of a cell changes in
response to its current state, and the states of its neighbours.
These laboratory notes and Excel spreadsheet explore
1- and 2-dimensional cellular automata. Examples include population growth,
including chaotic dynamics, and impacts of disturbance size and frequency
('fire') on biodiversity. |
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Download |
CALabnotes.zip (0.1Mb) |
Carbon modelling laboratory
exercise
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Description |
The
ability to mathematically model the flow of carbon into and out of
ecosystems is a central component in assessing the impacts of Global Change.
The first part of these lab notes gets the students to investigate the
behaviour of the CASS model of terrestrial carbon dynamics.
In the
second part of the
lab students
do some
‘hands-on’ model building, where the Visual
Basic for Applications (VBA) programming language
is used
to write and
run the students
own
terrestrial carbon model within Microsoft Excel.
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Download |
Carbon modelling
labnotes (3.3Mb) |
Global productivity and carbon
modelling GIS laboratory exercise
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Description |
A three week laboratory using
ArcView GIS software to explore global-scale patterns of vegetation growth,
land-use, carbon stocks and national-scale greenhouse accounting.
Co-developed with Prof. Brendan Mackey.
The aims of the
exercise are to:
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Illustrate how climate
influences net primary productivity and carbon accumulation in ecosystems
at the global scale;
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Examine how human land use
activity affects ecosystem carbon stocks; and
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Generate data and information to form the basis
of an assignment on national-scale carbon accounting.
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Download |
Global carbon exercise
(0.7Mb) |
ECOSIM spreadsheet exercise for
modelling population growth
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Description |
The spreadsheet and accompanying notes were co-developed
with Dr. Peter Chesson for use in a post-graduate workshop on ecological
modelling. The exercise is designed to provide an introduction to 10
population growth models and their behaviour.
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Download |
Lecture notes (1.0Mb)
Excel spreadsheet (0.7Mb)
Spreadsheet instructions
(0.4Mb) |
Introductory ecology lecture
notes
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Description |
A set of self-contained coursework
notes designed for three four-hour tutorial sessions covering a range of
introductory ecological concepts. These notes were used for tutorial-style
classroom teaching for masters-level students. Topic covered include: What
are ecological communities? Mechanisms structuring ecological communities.
Methods used to describe ecological communities. What is (bio)diversity?
Introduction to population dynamics. Modelling population growth. Population
Viability Analysis. Landscape Ecology. Environmental variability &
disturbance. Consequences of environmental variability on ecological
systems. Succession. Invasion.
|
|
Download |
Set 1
(1.0Mb; 26pp.)
Set 2
(0.5Mb; 26pp.)
Set 3
(0.3Mb; 18pp.) |
Hardware
Laser point quadrat frame
[top]
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Description |
Description of a laser-based point quadrat sampling
frame, designed for sampling vegetation up to approximately 1.3m height. |
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Documentation |
Goto
description |
Fun Stuff
HVLauncher
[top]
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Description |
HVlauncher is launching & PC shutdown software for arcade
game emulators. |
|
Documentation & Downloads |
Goto HVLauncher web page |
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