UNIVERSITY OF THE WESTERN CAPE
October 2005
SUBJECT: NISL CONSERVATION FOR CLIMATE CHANGE COURSE
MARKS: 100
TIME: 5 DAYS
Examiner Dr Richard Knight
GENERAL INSTRUCTIONS AND ACCEPTANCE OF CONDITIONS
All STEPS ARE COMPULSORY
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KNIGHT_NISL_PRAC_2005.DOC)
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SURNAME_NISL_PRAC_2005
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Initial_Surname / Please indicate that you have read and understood these instructions by inserting your name and confirming that this is exclusively your work and that you did not consult with any other person(s) other than the designated examiner. You may consult the Internet/library but all text submitted must be your own composition (unless in quotes and referenced) and that you accept that this text may be electronically scanned for plagiarism (On the Hard Copy you must add you signature against your typed name)WHERE IS THE DATA?
File Names – R.exe
R_additional_packages.exe
Climate_Change_Course_Practical.exe
DATA DESCRIPTION
You’ll need to run each of these executables. Install the software in the default directories that these programmes specify.
R.exe – This will install the R statistical package that you will use for running the GAM model and evaluating its accuracy.
R_additional_packages.exe – This will install the additional package Hmisc into the R directory. This package contains a library that is needed in order to run the model.
Climate_Change_Course_Practical.exe – This installs all the data and additional files that you will use in the practical to the C:\Climate Change Practical Folder. When unzipped, this folder should have the following files:
a2_2050.dbf
AMD_DATA.dbf
Climate_Change_practical.doc
Climate_Change_Practical_Template.doc
countries.dbf
countries.sbn
countries.sbx
countries.shp
countries.shx
Functions.R
national_iucn1to6_poly.dbf
national_iucn1to6_poly.sbn
national_iucn1to6_poly.sbx
national_iucn1to6_poly.shp
national_iucn1to6_poly.shx
R 2.0.1 (shortcut)
SACIC_WMS_help.doc
Script.R
All the data for modelling the species are contained within the AMD_DATA.dbf. This database file comprises XY locational data for Central and Southern Africa, at a resolution of 10’ by 10’. For each point, data on the average ecoregion is specified, as well as presence data for 27 species of African mammals, and each of six environmental variables.
The environmental variables are:
Table 1.
VARIABLE / DESCRIPTIONEVTR0112 / Net evapotranspiration (mm)
GDD10_0112 / Growth days over 10ºC (number of days)
MTC / Mean temperature of the warmest month (ºC)
MTW / Mean temperature of the coldest month (ºC)
PREC0112 / Mean annual precipitation (mm)
TMEAN0112 / Mean annual temperature (ºC)
The species for which data are provided are detailed on the following page (Table 2).
Table 2.
Countries in which species is found / Common name / Scientific name / Indicator in DBF fileALL / 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 / Capegrysbok / 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
ANSWER 1- [10 marks]
Question 1Verify that the species you are planning to model does in fact fall within the limits of your selected country. Show the distribution of the species within your study country by changing the legend, (display the presence values over the countries shapefile) and discuss whether the distribution is suitable for modelling from the selected country. If it is not, specify any additional or alternative areas that you will include in the modelling process to ensure an appropriate model.
Use “Print Screen” and paste the screen capture into Windows Paint® to capture the images from ArcView® but save them in an image directory as *.jpg images. From this image directory you should paste the images into your MS Word® document (this will prevent accidental loss of images in the final document).
Insert your picture for Figure 1a here…
Figure. 1 (Caption for distribution of species X in country Y using point data at a resolution of (specify))
Table 1. (insert a suitable caption)
(Mammal species) / Number of cells of (specify country)Present
Absent
Total
Discussion of the results from the above table and image (ensure it is unbolded and normal text)
Start your answer here…
ANSWER 2- [15 marks]
Question 2Write a short description of the species you are modelling, including as many details of the ecology of the species (habitat, diet, breeding habits, rarity) as you can. Include a photograph of a specimen of the species (attribute your sources of information).
Insert your picture for Figure 2 here…
Figure. 2 (Caption for a picture of your chosen study species)
Source: (insert source or URL of webpage from which you obtained the image)
Describe the distribution and ecology of the species
Start your answer here…
ANSWER 3- [20 marks]
Question 3Specify for each of your three models the environmental characteristics you used in the GAM, their p-values, the overall p-value for the model, and the amount of the deviation in distribution the models explain. All of these values should be obtainable from the console once you have run a summary of the GAM. Explain whether these variables are direct or indirect descriptors of the distribution of your species, and what the implications of this might be. For the single variable model, explain why you chose your variable, and whether you think it is a good descriptor of the species’ distribution.
Table 2. (insert a suitable caption - 1 variable model)
Variable name / p-value / Total model Pr (>|t|) / Deviance explainedExplain why you used this variable, and whether you think it is a good descriptor of the species distribution.
Start your answer here…
Table 3. (insert a suitable caption – 3 variable model)
Variable name / p-value / Total model Pr (>|t|) / Deviance explainedTable 4. (insert a suitable caption – 5 variable model)
Variable name / p-value / Total model Pr (>|t|) / Deviance explainedExplain whether the variables are direct determinants of the species distribution, and the implications of this for modelling:
Start your answer here…
ANSWER 4- [5 marks]
Question 4Using one of the variables that is used in at least two of your models, show the plots of its response curves in each model. These should be screenshots from R. If you do not have the response curves available, you can run the command again from the relevant script, in order to capture the curves. Explain why these curves are different in different models, and why the margin of error (dotted lines) is higher at the edges of the distribution than in the middle.
Insert your picture for Figure 3a here…this is just an example pic!
Figure.3a (Insert caption - Insert a plot of the response curve for the first model using the chosen variable.)
Insert your picture for Figure 3b here…
Figure.3b (Insert caption - Insert a plot of the response curve for the second model using the chosen variable.)
Insert your picture for Figure 3c here…
Figure.3c (Insert caption - Insert a plot of the response curve for the third model using the chosen variable. If there is not third model, delete this section.)
Interpret the differences between the curves, and explain why the margin of error is greater at the edges of the distribution:
Start your answer here…
ANSWER 5- [12 Marks]
Question 5By comparing the modelled and actual distributions of your species, as well as by comparing the receiver operating characteristic values of the respective models, describe how you decided on the most appropriate model to use for the determination of the future niche for your species. You should display the modelled distributions in ArcView using each of the models, as well as the actual distribution.
Table 5. (Insert a suitable caption)
Number of variables used in model / AUC (calibration dataset) / AUC (evaluation dataset) / AUC (total1
3
5
Insert your picture for Figure 4 here…
Figure. 4 (The actual distribution of the species within your study area)
Insert your picture for Figure 5 here…
Figure.5 (Insert caption - output of model 1)
Insert your picture for Figure 6 here…
Figure.6 (Insert caption - output of model 2)
Insert your picture for Figure 7 here…
Figure.7 (Insert caption - output of model 3)
Discuss the above results and differences, and explain which model you decided was best and why.
Start your answer here…
ANSWER6- [5 Marks]
Question 6What is the cutoff value determined by the function as appropriate for estimating species presence for your study species (using your final model)? This can be obtained from the R console window. Once again, if you cannot find it, rerun the relevant command from the script:
#Print out cutoff values in Console window
What, if anything, does this cutoff point imply about the model’s accuracy?
Start your answer here…
ANSWER7- [20 Marks]
Question 7 Describe the likely impact of the climate change induced transformation of habitat for the conservation of this species. Where possible, combine your outputs with the IUCNNational Parks and designated conservation areas (national_IUCN1to6_poly.shp) shapefile to illustrate possible complications in terms of conservation areas. Using the attributes table for the IUCN parks shapefile, calculate the extent of conservation areas (in ha) in both present and future scenarios in which the species can be found. This value can be found in the “Gis_ha” column of the database for each park that falls within the distribution area.
Insert your picture for Figure 8 here…
Figure.8 (The modelled future niche for your mammal species for the whole of Africa (binary representation))
Insert your picture for Figure 9 here…
Figure. 9 (The current distribution for your mammal species for the whole of Africa (binary representation) )
Insert your picture for Figure 10 here…
Figure. 10 (A map of conservation areas overlapped by the future species distribution (may be a shapefile or an event layer output). For some species you may need to prepare more than one map. If the species is predicted not to overlap any conservation areas in 2050, overlay the conservation areas layer with your modelled distribution to illustrate this.)
Discuss the implications for the conservation of your chosen mammal species under conditions of climate change by 2050 (under the A2 emissions scenario).
Start your answer here…
ANSWER8- [13 Marks]
Question 8 Prepare a shape file from the modelled future distribution of your species, and post it on the UWC mapserver site:
You will need to set up your own account. You must save the session to the server, and this will give you a response URL that can be used to access the session at any time. Report the URL of your submission, and create a PDF of the distribution. You can either submit ht. The PDF should have an appropriate title, and in the map notes you should include your name, the date, and the model details used for preparing the future distribution of your chosen species. Detailed instructions on this process are available in the South African Coastal Information Centre Web Mapping Service helpfile (SACIC_WMS.doc), which can be found in the practical folder on your C: drive
Mapserver session URL :
PDF output URL:
An electronic copy of this MS WORD® document can be found at