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some overview tidy ups for T2 2023
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README.md

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#### GISC 422 T1 2021
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#### GISC 422 T2 2023
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# GISC 422 Spatial Analysis and Modelling
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This class introduces key concepts and methods of spatial analysis. Practical deployment in the *R* statistical analysis software package is emphasised, although other tools will be surveyed.
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## COVID Alert level changes
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<!--## COVID Alert level changes
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If COVID alert levels change, the class will continue as follows:
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+ **Level 1** Class as normal. Attendance in person preferred, streamed content will be available at the link posted on Blackboard. **Stay home if you are unwell**.
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+ **Level 2** Room entry must be recorded using COVID app and/or the sign-in sheet. Sanitise hands on entry and exit from the lab. Wipe down your workstation (keyboard, mouse) with wipes provided at start and end of session. And, since the sessions are 3 hours long, wear a mask. As at other levels class will be streamed and recorded for those unwilling or unable to attend. Above all **stay home if you are unwell**.
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+ **Level 3** or **Level 4** Class will be conducted solely over zoom with recordings available later for review.
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-->
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## Link to related video content
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A consolidated list of relevant video content for this class is available on [this page](video-links.md).
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Item | Dates
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-: | :-
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Trimester | 22 February to 19 June 2021
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Teaching period | 22 February to 28 May 2021
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Mid-trimester break | 5 April to 16 April 2021
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Last assessment item due (in this class) | 4 June 2021
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Trimester | 10 July to 9 November 2023
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Teaching period | 10 July to 13 October 2023
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Mid-trimester break | 21 August to 1 September 2023
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Last assessment item due (in this class) | TBA
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Study period | NA
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Examination period | NA
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Withdrawal dates | See [Course additions and withdrawals](www.victoria.ac.nz/home/admisenrol/payments/withdrawalsrefunds)
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If you cannot complete an assignment or sit a test or examination, refer to [Aegrotats](www.victoria.ac.nz/home/study/exams-and-assessments/aegrotat)
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## Lecture and lab schedule
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Lectures are in Cotton 110 at 9AM on Mondays and will be followed immediately by related lab sessions in the same location. The combined session will last up to three hours, finishing before noon.
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TBA
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<!--Lectures are in Cotton 110 at 9AM on Mondays and will be followed immediately by related lab sessions in the same location. The combined session will last up to three hours, finishing before noon.-->
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## Contact details
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### Lecturer/coordinator
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**Prof. [David O'Sullivan](mailto:david.osullivan@vuw.ac.nz)**
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**Office** CO227 **Extn.** 6492 **Office hours preferably by appointment** [click here](http://calendly.com/dosullivan) but direct message me on [the Slack](https://vuwgisc2021.slack.com) and we can arrange contact. The office phone system is not a good way to reach me.
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### GIS Technician
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**[Andrew Rae](mailto:andrew.rae@vuw.ac.nz)**
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NA
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<!--**[Andrew Rae](mailto:andrew.rae@vuw.ac.nz)**
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**Office** CO502 **Office hours** 1-3PM Mondays
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-->
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## Lab and lecture timetable
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Here's the trimester schedule we will aim to follow. **Bolded labs** have an associated assignment that must be submitted and contributes the indicated percentage of the course credit. General instructions for the labs are [here](labs/README.md). Relevant materials (lecture slides, lab scripts and datasets) are linked below, when available.
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Week# | Date | Lecture | Lab | Notes | [Videos](video-links.md)
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:-: | :-: | :-- | :-- | :-- | :--
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1 | 22 Feb | Course overview | [*R* and *RStudio* computing environment and Markdown documents](labs/intro-to-R-and-friends/README.md) | | [Practical](video-links.md#introducing-r-and-friends)
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2 | 1 Mar | [Why &lsquo;spatial is special&rsquo;](https://southosullivan.com/gisc422/spatial-is-special/) | [Making maps in *R*](labs/making-maps-in-r/README.md) | | [Lecture](video-links.md#lecture-on-spatial-is-special)<br />[Practical](video-links.md#practical-materials-on-making-maps-in-r)
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3 | 8 Mar | [Spatial processes](https://southosullivan.com/gisc422/spatial-processes/) | [Introducing `spatstat`](labs/introducing-spatstat/README.md) | | [Lecture](video-links.md#lecture-on-the-idea-of-a-spatial-process)<br />[Practical](video-links.md#practical-materials-on-spatial-processes)
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4 | 15 Mar | [Point pattern analysis](https://southosullivan.com/gisc422/point-pattern-analysis/) | [**Point pattern analysis**](labs/point-pattern-analysis/README.md) (15%) | Due 19 April | [Lecture](video-links.md#lecture-on-point-pattern-analysis)<br />[Practical](video-links.md#overview-of-lab-on-point-pattern-analysis)
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5 | 22 Mar | [Measuring spatial autocorrelation](https://southosullivan.com/gisc422/spatial-autocorrelation/) | [**Moran's *I***](labs/spatial-autocorrelation/README.md) (15%) | Due 3 May | [Lecture](video-links.md#lecture-on-spatial-autocorrelation)<br />[Practical](video-links.md#overview-of-lab-on-spatial-autocorrelation)
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6 | 29 Mar | [Spatial interpolation](https://southosullivan.com/gisc422/interpolation/) | ['Simple' interpolation in R](labs/interpolation/README.md) | | [Lecture](video-links.md#lecture-on-simple-interpolation-methods)
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1 | 10 Jul | Course overview | [*R* and *RStudio* computing environment and Markdown documents](labs/intro-to-R-and-friends/README.md) | | [Practical](video-links.md#introducing-r-and-friends)
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2 | 17 Jul | [Why &lsquo;spatial is special&rsquo;](https://southosullivan.com/gisc422/spatial-is-special/) | [Making maps in *R*](labs/making-maps-in-r/README.md) | | [Lecture](video-links.md#lecture-on-spatial-is-special)<br />[Practical](video-links.md#practical-materials-on-making-maps-in-r)
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3 | 24 Jul | [Spatial processes](https://southosullivan.com/gisc422/spatial-processes/) | [Introducing `spatstat`](labs/introducing-spatstat/README.md) | | [Lecture](video-links.md#lecture-on-the-idea-of-a-spatial-process)<br />[Practical](video-links.md#practical-materials-on-spatial-processes)
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4 | 31 Jul | [Point pattern analysis](https://southosullivan.com/gisc422/point-pattern-analysis/) | [**Point pattern analysis**](labs/point-pattern-analysis/README.md) (15%) | Due 4 Sep | [Lecture](video-links.md#lecture-on-point-pattern-analysis)<br />[Practical](video-links.md#overview-of-lab-on-point-pattern-analysis)
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5 | 7 Aug | [Measuring spatial autocorrelation](https://southosullivan.com/gisc422/spatial-autocorrelation/) | [**Moran's *I***](labs/spatial-autocorrelation/README.md) (15%) | Due 11 Sep | [Lecture](video-links.md#lecture-on-spatial-autocorrelation)<br />[Practical](video-links.md#overview-of-lab-on-spatial-autocorrelation)
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6 | 14 Aug | [Spatial interpolation](https://southosullivan.com/gisc422/interpolation/) | ['Simple' interpolation in R](labs/interpolation/README.md) | | [Lecture](video-links.md#lecture-on-simple-interpolation-methods)
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| | **SEMESTER BREAK** | **NO TEACHING**
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7 | 19 Apr | [Geostatistics](https://southosullivan.com/gisc422/geostatistics/) | [**Interpolation**](labs/interpolation/README.md) (15%) | Due 10 May | [Lecture](video-links.md#lecture-on-geostatistical-methods)
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8 | 26 Apr | **NO CLASS** | ANZAC Day |
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9 | 3 May | Multivariate methods | [**Geodemographics**](labs/multivariate-analysis/README.md) (15%)| Due 24 May | [Lecture](video-links.md#week-9-multivariate-analysis)
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10 | 10 May | Overlay, regression models and related methods | [Lab content](labs/statistical-models/README.md) |
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11 | 17 May | [Cluster detection](https://southosullivan.com/gisc422/cluster-detection/) | TBD |
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12 | 24 May | [Network analysis](https://southosullivan.com/gisc422/network-analysis/) | [Tools for network analysis](labs/network-analysis/README.md)
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7 | 4 Sep | [Geostatistics](https://southosullivan.com/gisc422/geostatistics/) | [**Interpolation**](labs/interpolation/README.md) (15%) | Due 25 Sep | [Lecture](video-links.md#lecture-on-geostatistical-methods)
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8 | 11 Sep | Multivariate methods | [**Geodemographics**](labs/multivariate-analysis/README.md) (15%)| Due 9 Oct | [Lecture](video-links.md#week-9-multivariate-analysis)
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9 | 18 Sep | Overlay, regression models and related methods | [Lab content](labs/statistical-models/README.md) |
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10 | 25 Sep | [Cluster detection](https://southosullivan.com/gisc422/cluster-detection/) | TBD |
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11 | 2 Oct | [Network analysis](https://southosullivan.com/gisc422/network-analysis/) | [Tools for network analysis](labs/network-analysis/README.md)
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12 | 9 Oct | TBD | TBD
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## Lectures
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Lectures will generally consist of around an hour of presented material, followed by time for Q&A and discussion based on the materials and any related reading students have completed ahead of class.
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NA
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### Readings
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Details of any required readings will be provided ahead of class and where possible either publicly available, or linked from [Blackboard](https://blackboard.vuw.ac.nz/). Most readings will be from one or the other of
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The most useful materials are
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+ Bivand R, Pebesma E and Gómez-Rubilio V. 2013. [*Applied Spatial Data Analysis with R*](https://link-springer-com.helicon.vuw.ac.nz/book/10.1007%2F978-1-4614-7618-4) 2nd edn. Springer, New York.
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+ O'Sullivan D and D Unwin. 2010. [*Geographic Information Analysis*](http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470288574.html) 2nd edn. Wiley, Hoboken, NJ.
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The first of these is freely available as a full PDF download from the library, so where possible I will emphasise materials in that book. I wrote the second book and will provide pre-publication manuscript chapters where needed.
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The first of these is freely available as a full PDF download from the library, so where possible I will emphasise materials in that book.
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I wrote the second book and will provide pre-publication manuscript chapters where needed.
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A third book:
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+ Brunsdon C and L Comber. 2018. [*An Introduction to R for Spatial Analysis and Mapping*](https://au.sagepub.com/en-gb/oce/an-introduction-to-r-for-spatial-analysis-and-mapping/book241031) 2nd edn. Sage, London.
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+ Brunsdon C and L Comber. 2019. [*An Introduction to R for Spatial Analysis and Mapping*](https://au.sagepub.com/en-gb/oce/an-introduction-to-r-for-spatial-analysis-and-mapping/book258267 "Brunsdon and Comber Introduction to R book") 2nd edn. Sage, London.
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is more recent and is reasonably affordable, so you might consider purchasing it as a general reference and reminder of topics covered in the class.
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There are also many useful online resources that cover topics that are the subject of this class. For example:
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+ [*Geocomputation with R*](https://geocompr.robinlovelace.net/) by Lovelace, Novosad and Muenchow, 2019
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+ [*Spatial Data Science*](https://keen-swartz-3146c4.netlify.com/intro.html) a book in preparation from Bivand and Pebesma
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+ [*Spatial Data Science*](https://r-spatial.org/book/) a book in preparation from Bivand and Pebesma
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+ [Course materials for Geographic Data Science](http://darribas.org/gds15/) by Daniel Arribas-Bel at University of Liverpool
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+ [*Geospatial Analysis*](https://www.spatialanalysisonline.com/HTML/index.html) by deSmith, Longley and Goodchild
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For the final assignment you will need to do your own research and assemble materials concerning how spatial analysis has been applied in specific areas of study.
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## Labs
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Lab sessions follow the lecture sessions and will cover related practical topics. Lab materials will generally be found [here](labs/). Only four sessions have an associated assessed assignment, but you should attend all labs and particpate fully to broaden your knowledge of GIScience methods and tools as any of the approaches covered may prove useful for you in other parts of the program. (Note also that a portion of the course credit is for participation in all aspects of the course.)
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NA
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<!--Lab sessions follow the lecture sessions and will cover related practical topics. Lab materials will generally be found [here](labs/). Only four sessions have an associated assessed assignment, but you should attend all labs and particpate fully to broaden your knowledge of GIScience methods and tools as any of the approaches covered may prove useful for you in other parts of the program. (Note also that a portion of the course credit is for participation in all aspects of the course.)-->
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### Software
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Most of the lab work will be completed in the [*R*](https://www.r-project.org/) programming language for statistical computing, using various packages tailored to spatial analysis work. *R*
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We will use *R* from the [*RStudio*](https://www.rstudio.com/) environment which makes managing work more straightforward.
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Both *R* and *RStudio* are available on the lab computers. Both are freely downloadable for use on your own computer (they work on all three major platforms). We can take a look if you are having issues with your installation, but are likely to suggest that you uninstall and reinstall. In some cases problems might arise from different versions of key packages, in which case you will have to work with the lab machine versions as we can't support multiple versions across different platforms.
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Both *R* and *RStudio* are freely downloadable for use on your own computer (they work on all three major platforms). I can take a look if you are having issues with your installation, but are likely to suggest that you uninstall and reinstall. <!--In some cases problems might arise from different versions of key packages, in which case you will have to work with the lab machine versions as we can't support multiple versions across different platforms.-->
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## Course learning objectives (CLOs)
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1. Articulate the theoretical and practical considerations in the application of spatial analysis methods and spatial modelling
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Assessment item | Credit | Due date | CLOs
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:- | :-: | :-: | :-:
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Point pattern analysis | 15% | 19 April | 2 3 4
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Spatial autocorrelation | 15% | 3 May | 2 3 4
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Spatial interpolation | 15% | 10 May | 2 3 4
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Geodemographic analysis | 15% | 24 May | 2 3 4
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Written report on application of spatial analysis in a particular topic area | 30% | 4 June | 1
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Point pattern analysis | 15% | 4 September | 2 3 4
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Spatial autocorrelation | 15% | 11 September | 2 3 4
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Spatial interpolation | 15% | 25 September | 2 3 4
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Geodemographic analysis | 15% | 9 October | 2 3 4
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Written report on application of spatial analysis in a particular topic area | 30% | 20 October | 1
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Participation (including non-assessed labs) | 10% | NA | 1 2 3 4
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Some guidance on the written report assignment expectations is provided [here](report/README.md).
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Assessments are submitted electronically via dropbox on [Blackboard](https://blackboard.vuw.ac.nz/). I will aim to return coursework within 3 weeks. Extensions should be requested from the SGEES administration office. If you anticipate problems come and talk to me.
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Assessments to be submitted by email. I will aim to return coursework within 3 weeks. <!--Extensions should be requested from the SGEES administration office. If you anticipate problems come and talk to me.-->
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### Late submission penalties
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<!--### Late submission penalties
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All assignments must be handed in by their due dates. Non-submission by the required date will result in a 5% penalty off your grade for that assignment for each day or part thereof that the coursework is late. No submissions will be accepted more than 5 days after the due date.
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Computer crash or similar excuses are not acceptable. Save your material and make sure you have something to submit by the due date.
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+ [Student Contract](https://www.wgtn.ac.nz/home/admisenrol/enrol/studentcontract)
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+ [Turnitin](http://www.cad.vuw.ac.nz/wiki/Turnitin.html)
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+ [VUWSA](https://www.vuwsa.org.nz)
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-->

video-links.md

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# Consolidated index of video content
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## Week 1 Introducing R and friends
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These were made for the class Geog 315, but are equally applicable to this course
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+ [Overview of the RStudio interface](http://southosullivan.com/geog315/video/week-02-lab/geog315-week02-01-r-intro-overview-of-interface.mp4)
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+ [Opening a dataset and *following the instructions*](http://southosullivan.com/geog315/video/week-02-lab/geog315-week02-02-r-intro-read-the-instructions.mp4)
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+ [Making a map](http://southosullivan.com/geog315/video/week-02-lab/geog315-week02-03-r-intro-make-a-map.mp4)
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+ [Installing packages](http://southosullivan.com/geog315/video/week-02-lab/geog315-week02-04-r-intro-installing-packages.mp4)
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### Introducing _R_ and _RStudio_
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+ [Overview of lecture](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-02.mp4) 1m21s
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+ [What _R_ and _RStudio_ are](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-03.mp4) 3m27s
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+ [Origins of _R_](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-04.mp4) 2m15s
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+ [Overview of _RStudio_ interface](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-05.mp4) 3m34s
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+ [Some basic concepts in _R_](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-06.mp4) 5m38s
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### Handling basic data in _R_
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+ [Values, vectors and dataframes](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-07.mp4) 4m37s
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+ [More about dataframes](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-08.mp4) 2m22s
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+ [Manipulating values as single objects](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-09.mp4) 3m18s
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+ [Plotting data](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-10.mp4) 4m56s
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### Packages including `sf` and `tmap`
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+ [Installing and loading packages](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-11.mp4) 6m27s
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+ [Reading and plotting spatial data with `sf`](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-12.mp4) 2m54s
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+ [Making maps with `tmap` and wrap up](https://southosullivan.com/geog315/video/week-02-lecture-01/geog315-03-2022-starting-r-13.mp4) 2m41s
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***
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## Week 2 Making maps in *R*

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