Difference between revisions of "ISSS608 2017-18 T3 Assign Chen Pin-an"

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<font size = 5; color="#000000" style="Calibri">Mini-Challenge 2 Overview: Like a Duck to Water
 
<font size = 5; color="#000000" style="Calibri">Mini-Challenge 2 Overview: Like a Duck to Water
 
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==Background==
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==Introduction: VAST 2018 MC2  ==
Animal migration has long received much attention as a research topic in biology. Information about animal movement serves to allow us to understand animal behavior and their interactions with each other and the environment. In addition, it allows us to address environmental challenges such as climate and land use change.
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Last year, the Kasios Furniture Company was implicated in environmental damage to the Boonsong Lekagul Wildlife Preserve for both dumping toxic waste and polluting the air with chemicals from its manufacturing process. But Kasios is not taking these accusations lying down, and they deny any accusation of industrial waste dumping! Kasios’ spokespersons state that there isn’t any ground contamination near the remote ranger station that was suggested by last year’s mini-challenge 1 and 3 participants, and they have inspected that area and found it as pristine as the rest of the preserve.  
  
Understanding animal migration helps conservationists to conserve these animals through the protection of their habitats and their resources.
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Outraged ornithology professors from Mistford College journeyed out to look over the dumping site themselves and perform soil analyses. They returned to report that the site looked like there had been recent excavation and building activities going on. Boonsong Preserve rangers later confirmed that a new ranger station was being built at that site! Soil samples taken from the site were inconclusive in detecting Methylosmolene (the toxic manufacturing chemical in the suspected dumping) or any other contaminant, as new top soil had been trucked in.
  
An interactive visual analytics approach would provide valuable insights to the scientific community on the migration of these animals.
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==Challenge==
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With a primary piece of evidence against Kasios now gone, investigators will need to take another approach. Professors in the Mistford College Hydrology Department have come forward with several years of water sensor readings from rivers and streams in the preserve. These samples were taken from different locations scattered throughout the area and contain measurements of several chemicals of possible interest, but they have never been analyzed due to lack of funding. Could visual analytics help reveal something in this data that could make up for the soil evidence that was destroyed?
  
==Objective==
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Your task is to investigate the hydrology data from across the Preserve. You are given a map of the Preserve (with the same base as last year’s challenge), with named sampling sites indicated on the map (the names have local significance but are just mnemonics for your study) You are also provided with readings from each sampling station over time for several different chemicals and water properties.
We present an interactive visual approach to explore and analyze animal movement data. We applied this approach to a data set of Osprey bird migration flows for a ten-year period spanning 2007 to 2017.  
 
  
Through this project, we hope that ecologists and conservationists alike will be able to gain insights into the following:
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==Question==
  
*Bird migration (both as a group and individual) flight path over a period of time.
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1. Characterize the past and most recent situation with respect to chemical contamination in the Boonsong Lekagul waterways. Do you see any trends of possible interest in this investigation? Your submission for this question should contain no more than 10 images and 1000 words.
*How differences in individual characteristics (e.g. female vs male, juvenile vs adult) affect flight behavior.
 
*The home range and territory range of these birds.
 
*Uniqueness of stopover sites.
 
*Impact of environment data on bird migration.
 
  
==Methodology==
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2. What anomalies do you find in the waterway samples dataset? How do these affect your analysis of potential problems to the environment? Is the Hydrology Department collecting sufficient data to understand the comprehensive situation across the Preserve? What changes would you propose to make in the sampling approach to best understand the situation? Your submission for this question should contain no more than 6 images and 500 words.
===Time Series Analysis===
 
======Calendar Chart======
 
The Calendar Chart will be used to explore the cycle, variability and trend of the migration data. From the calendar chart, a user can see the entire duration of either a group or the individual bird’s journey over the required time period as desired.
 
  
====Line Chart====
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3. After reviewing the data, do any of your findings cause particular concern for the Pipit or other wildlife? Would you suggest any changes in the sampling strategy to better understand the waterways situation in the Preserve? Your submission for this question should contain no more than 6 images and 500 words.
We will use the line chart based on the time, such as year, month, day and hour, to further explore the flight pattern of group and individuals, as well as how differences in individual characteristics such as sex and adulthood affect flight pattern.
 
====Scatter Plot====
 
Scatter plots show how much one variable is affected by another. It allows us to find out the correlation between them. In addition, it helps to identify outliers in the data set.
 
===Geographic Analysis===
 
====Map====
 
Various different map views will provide the visualization of the locations which the birds visit during the duration of their flight path.
 
====Bin Chart====
 
The bin chart will show the amount of time birds spend at each place. Coloring will be used to differentiate the time period, so that the user is able to tell the location at which the bird spends the longest time at.
 
====Circular Migration Flow Plots====
 
A circular migration plot displays a large amount of information on the flow of Osprey in a global/regional system as representations of position, size, and color.
 
 
 
 
 
==Data Sets==
 
<p>
 
1. Bird migration data “Osprey North and South America” available at:<br>
 
https://www.movebank.org/panel_embedded_movebank_webapp<br><br>
 
 
 
2. Environment data “Osprey North and South America” available at:<br>
 
https://www.movebank.org/panel_embedded_movebank_webapp<br><br>
 
</p>
 
 
 
==Tools selection/package==
 
===ggplot2===
 
ggplot2 is a system for creating graphics, based on The Grammar of Graphics. Here we are going to use the ggplot2 to make the calendar chart, line chart and scatter plot.
 
 
 
===gganimate===
 
gganimate is a package based on the ggplot2. It can show an animation of a ggplot2 object that contains a frame aesthetic. The frame aesthetic will determine which frame the animation is shown in.
 
 
 
===ggmap===
 
ggmap is a package to show the spatial data visualization. It can retrieve various online sources (e.g. Google Maps) for user to download and use as layers within the ggplot2 plotting system.
 
 
 
===circlize===
 
circlize is a package to show multi-layered annotations of one or more scales and relationships. It can create figures from data from genomics to visualizing migration.
 
 
 
===move===
 
move is a R package for accessing movebank data and visualize and statistically analyze animal movement data. It is useful to build the animal tracking model and help answer ecology questions.
 
 
 
===tibbletime===
 
tibble package is an extension to partition an index column by time and change the periodicity of a time-based tibble. This allows easily changing from a daily dataset to a monthly or yearly dataset.
 
 
 
===lubridate===
 
lubridate is an R package that makes it easier to work with dates and times. It can easily handle the timestamps including both the date and time to help address time series problems.
 
 
 
==References==
 
1. Graph Analytics: Visualizing and Analyzing Network Data:<br>
 
https://slides.com/tskam/isss608-lesson10_ay2017-18t3/fullscreen#/<br><br>
 
2. Visualizing and Analyzing Time-Oriented Data:<br>
 
https://slides.com/tskam/isss608-lesson08_ay2017-18t3/fullscreen#/<br><br>
 
3. Andrienko, N., & Andrienko, G. 2013a. V''isual analytics of movement: An overview of methods, tools and procedures''. Information Visualization, 12(1), 3–24<br><br>
 
4. N Sander, GJ Abel, R Bauer, J Schmidt. 2014. ''Visualising migration flow data with circular plots''.  Vienna Institute of Demography, Working Papers<br><br>
 
5. D. Spretke, H. Janetzko, F. Mansmann, P. Bak, B. Kranstauber, S. Davidson and M. Mueller. 2011. ''Exploration through Enrichment: A Visual Analytics Approach for Animal Movement.'' Proceedings of the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 421–424 <br><br>
 

Latest revision as of 21:59, 11 July 2018

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Mini-Challenge 2 Overview: Like a Duck to Water

Background Data Preparation Visualization Observations & Insights Assignments


Introduction: VAST 2018 MC2

Last year, the Kasios Furniture Company was implicated in environmental damage to the Boonsong Lekagul Wildlife Preserve for both dumping toxic waste and polluting the air with chemicals from its manufacturing process. But Kasios is not taking these accusations lying down, and they deny any accusation of industrial waste dumping! Kasios’ spokespersons state that there isn’t any ground contamination near the remote ranger station that was suggested by last year’s mini-challenge 1 and 3 participants, and they have inspected that area and found it as pristine as the rest of the preserve.

Outraged ornithology professors from Mistford College journeyed out to look over the dumping site themselves and perform soil analyses. They returned to report that the site looked like there had been recent excavation and building activities going on. Boonsong Preserve rangers later confirmed that a new ranger station was being built at that site! Soil samples taken from the site were inconclusive in detecting Methylosmolene (the toxic manufacturing chemical in the suspected dumping) or any other contaminant, as new top soil had been trucked in.

Challenge

With a primary piece of evidence against Kasios now gone, investigators will need to take another approach. Professors in the Mistford College Hydrology Department have come forward with several years of water sensor readings from rivers and streams in the preserve. These samples were taken from different locations scattered throughout the area and contain measurements of several chemicals of possible interest, but they have never been analyzed due to lack of funding. Could visual analytics help reveal something in this data that could make up for the soil evidence that was destroyed?

Your task is to investigate the hydrology data from across the Preserve. You are given a map of the Preserve (with the same base as last year’s challenge), with named sampling sites indicated on the map (the names have local significance but are just mnemonics for your study) You are also provided with readings from each sampling station over time for several different chemicals and water properties.

Question

1. Characterize the past and most recent situation with respect to chemical contamination in the Boonsong Lekagul waterways. Do you see any trends of possible interest in this investigation? Your submission for this question should contain no more than 10 images and 1000 words.

2. What anomalies do you find in the waterway samples dataset? How do these affect your analysis of potential problems to the environment? Is the Hydrology Department collecting sufficient data to understand the comprehensive situation across the Preserve? What changes would you propose to make in the sampling approach to best understand the situation? Your submission for this question should contain no more than 6 images and 500 words.

3. After reviewing the data, do any of your findings cause particular concern for the Pipit or other wildlife? Would you suggest any changes in the sampling strategy to better understand the waterways situation in the Preserve? Your submission for this question should contain no more than 6 images and 500 words.