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1: Data Preparation

To start with, we need to obtain a set of data with which we can carry out the modelling process. The environmental and species distribution data is provided for the whole of central and southern Africa. However, for the practical, we want to look at distributions within individual countries.

In order to prepare the data for a single country of your choice, follow the instructions in the Arcview data export flash animation.

You will need to select one species of mammal to use in your model. It is important to select a species that is found in the country you have selected to study. The species available for each country are as follows:

Countries in which species is found

Common name

Scientific name

Indicator in DBF file

ALL

African weasel

Poecilogale albinucha

AFR_WEAS

ALL

Giraffe

Giraffa camelopardalis

GIRAFFE

ALL

Blue, sky or diademed monkey

Cercopithecus mitis

SKY_MONK

ALL

Tsessebe

Damaliscus lunatus

TSESSEBE

Botswana

Black-footed or small spotted cat

Felis nigripes

BLACK_FT_C

Burundi

L'Hoest's guenon (monkey)

Cercopithecus lhoesti

LHO_GUENO

DRC

Dryas guenon (monkey)

Cercopithecus dryas

DRYAS_GUEN

DRC

Aquatic or fishing genet

Osbornictis piscivora

FISH_GENET

Kenya

Grant's gazelle

Gazella granti

GRANT_GAZE

Kenya

Plain zebra

Equus grevyi

PLAIN_ZEBR

Kenya

Puku

Kobus vardonii

PUKU

Kenya/Moçambique/Tanzania

Suni

Neotragus moschatus

SUNI

Malawi

Bushy-tailed mongoose

Bdeogale crassicauda

BUSH_MONGO

Malawi

Natal red duiker

Cephalophus natalensis

NATAL_DUIK

Moçambique

Dusky or Peters' short-snouted elephant-shrew

Elephantulus fuscus

DUSK_SHREW

Namibia

Small grey mongoose

Galerella flavescens

GREY_MONGO

Namibia

Mountain zebra

Equus zebra

MOUNT_ZEBR

Namibia/Zimbabwe

Jameson's red rockhare

Pronolagus randensis

JAMES_RHAR

RSA

Cape grysbok

Raphicerus melanotis

CAPE_GRYSB

RSA

Cape or small grey mongoose

Galerella pulverulenta

CAPE_MONGO

RSA

Natal red hare

Pronolagus crassicaudatus

NATAL_HARE

RSA

Vaal or grey rhebok

Pelea capreolus

VAAL_RHEBO

Tanzania

Abbott's duiker

Cephalophus spadix

ABBOT_DUIK

Tanzania

Black-and-rufous elephant-shrew

Rhynchocyon petersi

BL_RUF_SHR

Tanzania

Harvey's red duiker

Cephalophus harvey

HARV_DUIKR

Uganda

Short-nosed or dusky-footed elephant-shrew

Elephantulus fuscipes

SH_N_SHREW

Zimbabwe

Nyala

Tragelaphus angasii

NYALA



Poecilogale albinucha

Giraffa camelopardalis

Cercopithecus mitis

Damaliscus lunatus

Felis nigripes

Cercopithecus lhoesti

Cercopithecus dryas

Osbornictis piscivora

Gazella granti

Equus grevyi

Kobus vardonii

Neotragus moschatus

Bdeogale crassicauda

Cephalophus natalensis

Elephantulus fuscus

Galerella flavescens

Equus zebra

Pronolagus randensis

Raphicerus melanotis

Galerella pulverulenta

Pronolagus crassicaudatus

Pelea capreolus

Cephalophus spadix

Rhynchocyon petersi

Cephalophus harvey

Elephantulus fuscipes

Tragelaphus angasii

Once you have chosen a species, take note of the "Indicator in DBF file" column. This is what the distribution data in your database is signified by, and you will use this tag to tell R to look for the relevant species when you are running the GAM.

To find out more details about the species, have a look at the African Mammal Databank.

Now, go to the C:\climate change course practical folder, and open R by clicking on the "R 2.0.1" shortcut in this folder.

Following the instructions in the first R flash animation, load the Functions.R script. You will load the relevant libraries and then load and run the GAM by highlighting and carrying out the relevant lines from the script.

NB: Here is an animation to show you how to display and move multiple layers in Arcview. You will need to do this for some of the practical answers.