Birds Survey

Landscape Ecology SLE322. Major Project. Urban Birds; detection and occupancy.
Report instructions
Your major landscape ecology project uses new skills in data collection and analysis that you will learn in
the practical sessions. You will learn how to perform a sophisticated occupancy and detection analysis
using the computer program R. You will learn how to create spatial covariates in GIS software ARCmap; a
critical tool for enabling you to ask landscape-scale questions. You will also learn how to identify birds and
conduct bird surveys. This exciting project gives you the suite of tools and skills that you will need to
understand landscape concepts, and to put those concepts into practice in real-world case studies.
Key Dates
Week 2 Prac 1. Analysis training in R. Learn how to do these analysis now because you have to do it on
your own for real in Prac 4!
Week 3 Prac 2. Bird identification training and field site allocation (10 sites/person)
24th March. Week 3. Begin field surveys.
Week 4 Prac 3. Create spatial variables for your sites using GIS software
2nd April. Mid-day (12pm). All your data must be loaded to the shared file and all your surveys
submitted to Birdata by midday on Sunday 2nd April. Data will be extracted at midday on Sunday to
prepare for pracs on Monday 3rd April. No extensions possible as data must be prepared for analysis.
Week 5. Prac 4. Analysis of your field data.
4th May, 12pm mid-day. Week 8, Full draft of your report submitted. Reports submitted after this date will
not undergo peer-review or be eligible for a second submission, losing 8.5 marks out of 35. Submit your
reports to
10th May, 12pm mid-day, Week 9. All comments on other people’s projects must be submitted.
17th May, 12pm mid-day, Week 10. Final draft with comments and track changes submitted.
Which sites to go to?
There are 24 groups of sites, with each group having five sites. Your job is to survey all five sites in two of
the groups. You have been allocated to specific groups for the survey. The sites are grouped to be close to
each other so that it will be possible to do all five sites in a group in one morning.
Step 1. Find the “students allocated to survey groups of sites.xlsx” excel file. Find your name or username,
and read across to see the two groups you have been allocated
Step 2. Download the KMZ files for those two groups of sites. Find these under Resources > Bird
Occupancy and Detection Major Project > Bird Survey Groups of Sites KMZ files. The files are named, for
example for group 12 Bird_Points_120_12. So use the last number in the file name to find the right groups
for you.
Step 3. See How to use your KMZ file to get to your sites below.
AMAZING OPPORTUNITY!!! Note that due to a slight mismatch in sites and student numbers, groups 1,
2, 3, 4, 21, 22, 23, and 24 are only scheduled for nine surveys. If you are enjoying your bird surveys and
want to do some extra groups of sites, please contact me and you will be able to survey some of these
additional groups.
How to get to your sites?
Go to this web page for instructions on how to create a map.
https://support.google.com/mymaps/answer/3024836?hl=en
In a nutshell, you upload your two KMZ files into your MyMaps (part of google maps), and the points will
then appear in Google Maps. Use your smart-phone with google maps to navigate to the point. Start your
survey exactly on the point (except where that might endanger your life).
Step by step instructions that worked for me:
Open google MyMaps
https://www.google.com/maps/d/u/0/
click menu (three lines on top left)
select create a new map
Rename the layer (eg. Bird Group 1)
click import
Drag the correct kml file (eg. for bird group 1 drag Bird_Points_120_1.kmz)
That’s it!
Then when you want to go to these sites
Open google maps
Click menu in top left
Select Your Places
Select Maps tab
click SEE ALL YOUR MAPS
Your map should appear; click on it.
Click on the site you want to go to first
In the bottom left of that box is the ‘directions to here’ button!!
Indicate where you are starting from in the A box and your route is drawn on the map. How cool is that!
Field Surveys
In a nutshell:
 Complete surveys at the 10 sites you were allocated, between 24 March and 2nd April
 Submit bird surveys using the birdata app; include name in comments section
 Complete the site and survey covariates spreadsheet at the same time as each survey
 Submit your site and covariate data as a CSV file in the appropriate assignment folder before midday
12pm 2nd April.
Students visit allocated sites between 24 March and 2nd April (make your own travel arrangements; walk,
bike, public transport, car (ok, car is definitely going to be best)). All data must be loaded up by Mid-day
12pm on Sunday 2nd April.
We will be collecting data that will be used by Birdlife and other organisations to understand risks to
Melbourne’s bird community. It is really important that everyone does their absolute best to ensure the data
we collect in the field is of the upmost integrity. If for any reason you cannot provide quality data, DO NOT
MAKE UP THE DATA. If for whatever reason you did not go to your designated sites to survey birds,
please submit no data (data submission is worth 3.5% of your overall mark).
Survey protocols. Your tutor for prac 2 in week 3 will be Kerryn Herman from BirdLife Australia. She will
teach you how to implement the 20 minute 2 ha active bird survey and to enter data in the birdata app
(http://birdata.birdlife.org.au/).
Your survey must be completely independent of anyone else also surveying that site. If your visit happens to
coincide with someone else, wait until they finish before you start. Never walk together with someone else
because your survey will not be independent.
When you submit your survey using the app, YOU MUST INCLUDE YOUR NAME IN THE
COMMENTS SECTION. If you don’t include your name, you cannot be allocated marks for
collecting the data. Do not include any other comments there. It is critical that you enter the correct site
name in each survey before submitting to birdata.
If, for any reason, you cannot use the app (eg, you dropped your phone in the river while looking through
binoculars), always have a notebook, your bird ID sheets from the prac, and a watch so that you can
complete your 20 minute survey and record the birds you saw. Transfer your paper-survey to an on-line
survey when you get home.
If you see birds other than the species targeted in the prac and you can identify them, please add them to
your survey. Record all birds that you can identify.
In addition to the bird data, you will need to collect environmental data. You need to download the
spreadsheet from CloudDeakin under Resources > Bird Occupancy and Detection Major Project > site and
survey covariates data entry sheet.xls. For each variable in the spreadsheet you need to estimate appropriate
values for each response. Do not change the spreadsheet headings or columns, just add your results. These
data need to be uploaded to the appropriate assignment page as a comma-delimited text file (.csv). That is,
you must save the data page of your excel file in the .csv format before you upload the results. Details of
what to collect are described on the instructions tab of the spreadsheet.
Surveying the right area. Use google maps or other tool to get to the survey point. We want everyone to
survey the same place, so it is important that you go to the designated point to begin. If the area is mostly
forested, survey a circular area that is approximately 80m in diameter, which is approximately 2ha. Most
sites have linear vegetation: see below. If the site has massive walls of near-impenetrable vegetation you
should make sure you are surveying within the 2ha area, but you might choose not to go the exact point.
However, for all sites, you will need to be walking off designated tracks to cover the 2ha area.
Many sites have linear vegetation. You should survey in the linear vegetation rather than the adjacent
oval/open spaces (don’t stick to a circular area if the vegetation is not in the circle). Adjust the length of
linear vegetation you search based on the width of the vegetation to ensure your area remains at 2 hectares,
with the gps point in the middle. There are 10,000m2 in one ha, so you want to survey 20,000 m2. For
example, if your linear vegetation is approximately 30m wide you will need to survey the linear vegetation
for 20,000/30 = 667m.
A few sites have very few trees. In those cases, survey the areas with trees but include open areas as well to
make up the 2ha.
ANALYSIS AND WRITE UP
Select a species and do the analysis
 Select a species from the group data set to analyse.
 The species MUST have been observed on between 25% and 75% of sites. DO NOT use species
that occurred on less than 25% or more than 75% of sites because you need enough data in both the
present and absent categories for your analysis to be meaningful.
 If your species is potentially an invasive or expanding species, your introduction will need to be
tailored to include ideas about urbanization promoting undesirable species. If your species is a
native species, your introduction should focus on the risk of decline of native species. This is
particularly relevant to the second paragraph.
 Analysis will be completed in Prac 4, week 5.
Write up.
You are provided with a strict structure for your report. This reflects the kind of structure (and in some
cases, word limits) that are encouraged by leading international scientific journals.
There are very strict word counts that must be adhered to in both the draft and final versions of your report.
There are three phases to the write up
1. Complete draft (23/35 marks)
1. Comment on drafts written by your peers (2.5 marks)
2. Update your first draft based on peer comments and submit for assessment. (6 marks)
Phase 1. Complete Draft
Each paragraph, except the results and conclusions, must refer to the scientific literature, putting your work
into an international context as appropriate. Find appropriate references using the data-bases Web of
Science (nice consistent flow of citations into endnote), and/or Google-scholar (less consistent flow into
endnote, but ok).
ONLY peer-reviewed journal articles can be cited (no web citations or grey literature allowed).
You must use EndNote or similar software to organize your references.
The report must be a Microsoft Word document and must be submitted on CloudDeakin for assessment.
WORD LIMITS. Each numbered section has the word limits for that section in (). Longer paragraphs will
not be marked (score of zero).
The report MUST be structured as shown below. Each numbered point refers to a separate paragraph (except
6 which are the graphs of results).
REPORT STRUCTURE
Introduction
1. (Less than 100 words) The big problem. Urbanisation impacts on wildlife. Global perspective. This
provides readers with broadest context of why your research is very important.
2. (less than 150 words) Why changes associated with urban development impacts on wildlife. This goes
into additional detail to explain the mechanisms through which urbanization cause environmental problems;
how it reduces biodiversity and/or how it promotes exotic species.
3. (less than 100 words) How the general problems in the paragraph 1 and 2 are relevant to your study
species in greater Melbourne.
4. (less than 100 words) The specific aims/questions/hypotheses (however you want to frame it) of thisstudy. There should be three of these, the first about landscape properties (e.g. road cover within 1km), thesecond about patch-level properties (e.g. percentage weed cover, vegetation type), the third aboutinteractions of landscape and patch-level properties (e.g. does the effect of road cover depend on thepercentage weed cover?).Methods.5. (less than 150 words) Field survey methods: in your own words.6. (less than 150 words) Describe your analysis, which should be an adaptation of Prac 1. Your analysis forthis project will be completed during Prac 4. An additional table or appendix may be used if many differentmodels need to be documented.Results.7. Graph significant relationships and present plots as numbered figures. Present only those figures relatedto your three aims and that you will discuss as either the first, second or third most important finding. Givenstrict word limits, you might not be able to include everything. Each graph should have a caption thatenables readers to fully understand the graph without referring to the text. Captions must not exceed 30words each.8. (less than 150 words) Write very brief text to describe the key patterns in each plot, referring to theappropriate figure. The idea is to draw the reader’s attention to the most important trend in each graph.Discussion9. (less than 75 words) Overview paragraph: were landscape variables, patch variables, or interactions mostimportant? And therefore, what is the likely importance of your discovery (a taster sentence highlighting themain point of the discussion to come).10. (less than 150 words) Discuss the most important finding in the context of the international literature.You could: reiterate discovery, explain what it means and how that discovery sheds light on, or is informedby, the international literature about factors influencing birds in urban landscapes.11. (less than 150 words) Discuss the second most important finding in the context of the internationalliterature. You could: reiterate discovery, explain what it means and how that discovery sheds light on, or isinformed by, the international literature about factors influencing birds in urban landscapes.12. (less than 150 words) Discuss the third most important finding in the context of the internationalliterature. You could: reiterate discovery, explain what it means and how that discovery sheds light on, or isinformed by, the international literature about factors influencing birds in urban landscapes. (if there is nothird most important finding that warrants discussion, you may add a paragraph after paragraph 10 to expandon the most-important finding.)13. (less than 75 words) Conclusion. References can be used in the conclusions, but may not always beneeded.14. References (not included in word count, use Endnote to produce your bibliography).Submit your report to the assessments folder Bird detection and occupancy Groups for commentingon Draft. These groups include three people: you will comment on the two other reports in yourgroup.Phase 2. Comments Your draft will be read by the other two members of your group (students are randomly assigned togroups) You will read the two other reports in your group and provide comments on both. Feedback consists of constructive comments and is given in the margins as comments. Providefeedback on sentences or paragraphs that are poorly constructed, content that could be changed tostrengthen an argument, statements that could be better supported by citations to the literature etc. Comments should be long enough to explain the problem and suggest solutions, but must also be asbrief as possible. 10-20 words will typically be enough for a simple problem. 75 words is the upperlimit. Comments must be added in a way that includes your name (find out how to do this herehttps://support.office.com/en-us/article/Change-the-author-name-for-review-comments-cdd4b8acfbca-438d-a5b5-a99fb1c750e3), otherwise you will not get any marks for your comments. Comments cannot be submitted anonymously; all comments must be polite and professional (even ifyou are close friends with the author). If a paragraph is perfect already, the comment may indicate that it is perfect, and explain why. Notethat if the paragraph has flaws that are obvious, a comment that a paragraph is perfect will not scorehighly. The number of comments you provide will depend on the project you are reviewing: a perfect projectreport will only need one comment per paragraph to explain why it is perfect. Realistically, morecomments than that will be required. Submit the reports that you have reviewed and which include your comments to the samegroup folder that you share with two other students: Bird detection and occupancy Groups forcommenting on Draft.Phase 3. Final version Respond to comments in the way shown connected to this paragraph using MS Word’s in-builtcomment facility. If a comment will make the text worse in the view of the author of that paragraph, the author mustexplain why they have not made the suggested change in responding to the comment.Commented [DD1]: Use MS Word’s comment tool to addyour feedback. Be as succinct as possible. No extra marks forlong essays in comments.Commented [DD2]: The comment tool can be found on theinsert tab.Commented [DD3R2]: you can respond to a commentusing that little box in the top right corner of this box.Commented [DD4R2]: But make sure your name appearsassociated with each comment. You need your full name hereso that you can be allocated marks for your comments andresponses. In this case, whoever did this comment would beallocated zero marks because they haven’t shown their fullname. If a comment makes a good point, you may alter your original text to improve the report. TrackChanges MUST be turned on when you make changes to the text. You can make other changes to the text using track-changes in addition to changes in response tosuggestions provided in comments.DO NOT SUBMIT THIS BACK TO THE GROUP FOLDER. Submit your final version into theassessments folder Bird Detection and Occupancy Final Report.ASSESSMENTTotal Marks for bird occupancy project 35Major categories that marks are allocated to MarksData of adequate quality submitted on time 3.5Complete Draft 23.0Constructive comments provided 2.5Submitted final draft with comments responded to appropriately 6Allocation of marks to components of your complete draft, prior to the comments phasetopic and task of each paragraph/sectiontotalmarks forthissectionIntroduction1 Urbanisation as a threat to biodiversity 1.52 Mechanisms of impact on wildlife 23 Relevance of 1 and 2 to birds in Melbourne 1.54 Aims 1Methods.5 Field survey methods: in your own words. 16 Describe your analysis 3Results.7 Graph significant relationships and present plots as numbered figures. 4.58 Describe the key patterns in each plot, referring to the appropriate figure. 1Discussion9 Overview: were landscape variables, patch variables, or interactions mostimportant?.1.510 Most important finding. 1.511 Second most important finding 1.512 Third most important finding 1.513 Conclusion. 114 References 0.5Plagiarism. If there is strong evidence of copying in any section, 0 marks will be allocated to that section.Word Count. If a section exceeds the designated word count, 0 marks will be allocated to that sectionLate Reports. Draft reports submitted after the deadline will not be eligible for review by the two othergroup members, or for submitting a final draft. Late reports will therefore not be assessed for 8.5 marks outof 35 (24%).Using References. 3-6 references to peer-reviewed literature will be needed in most paragraphs to justifyyour arguments. You will be assessed on the number of references, their relevance and appropriate use.Paragraph and sentence structure. You will be assessed on clarity of writing. Is there a clear topicsentence in each paragraph of intro and discussion, is the argument logically developed through theparagraph (e.g. no non-sequiturs), are sentences concise, to the point, and clear?Paragraph content. Each paragraph or section (numbered 1-14 in report description above) has beenallocated a task in your overall story. You will be assessed on how well each section performs its allocatedtask.Methods. You will be assessed on whether you have described your methods correctly, demonstrating anunderstanding of techniques and analyses used.Results. Presenting your results demonstrates that you have completed the analysis correctly. You will beassessed on whether the analysis was completed (occupancy and detection analysis with appropriatecovariates), and on the legibility of the graphs. Are the graphs and captions adequate? Have only thosegraphs needed to address the aims been shown? Is the text a legible size? Is the graph understandable fromreading the caption alone?