FISH 6002: Week 11 - Maps

Updated Nov 16

Transcript

1. Week 11: Maps FISH 6000: Science Communication for Fisheries Brett Favaro 2017 This work is licensed under a Creative Commons Attribution 4.0 International License
2. You always need a map • Plot your study sites • Orient people as to the location of your work • Demonstrate spatial scale of research
3. Why not just use google maps? • Rules for data visualizations involving maps have the same basic rules as other plots: Minimize chartjunk, eliminate irrelevant content • Need to add a scale bar and graphics demonstrating location relative to rest of world • Google Maps has built-in topography, but not bathymetry
4. • If you work near the poles, Google maps start to badly distort geography (more on that soon)
5. Positions on Earth are represented as… latitude (lat) longitude (long) Intro to maps
6. Lat/long units are expressed as: Degree, Minute, Second 1 degree = 60 minutes 1 minute = 60 seconds Therefore 1 degree = 3600 seconds This is a base-sixty, or sexagesimal notation Latitude: 1 degree = 111 km (110.5 km at equator, 111.7 at poles) 1 minute ~ 1 nautical mile Longitude: Not fixed. 1 degree is narrow at the poles, wide at equator 1 degree long = cosine (latitude in radians) * 69.172 length of degree in miles at equator
7. Longitude extends from zero (prime meridian) to 180° E and 180° W Also expressed as: +180° to -180° Latitude goes from zero (equator) to 90° N and 90° S. Also expressed as: +90° to -90°
8. Different ways to express lat/long: N, S, E, W Positive, Negative Degree, Min, Sec 47° 33’ 37.94” N, 52° 42’ 46.18” W 47° 33’ 37.94”, -52° 42’ 46.18” Degree, Min 47° 33.632’ N, 52° 42.771’ W 47° 33.632’, -52° 42.771’ Decimal degree 47.5605° N, 52.7128° W 47.5605°, -52.7128° Decimal Degrees = degrees + (minutes/60) + (seconds/3600) Location of St. John’s NL On fishing boats, GPS almost always expresses as degree min In R, generally plot Decimal degree
9. http://bestanimations.com/Earth&Space/Earth/earth-spinning-rotating-animation-24.gif The Earth is round (mostly) Paper is flat Maps tend to be on paper (or screens) How do we do it?
10. https://www.youtube.com/watch?v=vVX-PrBRtTY
11. PROJECTED
13. http://blog.revolutionanalytics.com/2017/08/maps-in-r.html There are a huge variety of mapping packages in R https://www.computerworld.com/article/2921176/business-intelligence/great-r-packages-for-data-import-wrangling-visualization.html Let’s start with a basic problem: Plot a few dots representing field sites onto a basic map You can do advanced GIS work in R (beyond the scope of this course)
14. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073051 Also important: PBSMapping https://github.com/pbs-software/pbs-mapping
17. Note: The R studio preview is always distorted in this package Here is the actual image that would be produced
18. Label isobaths Deeper isobaths are lighter grey Deeper isobaths are lighter grey
20. This would be a minimally acceptable map
21. Alternatively, you may want to show a fishing area rather than points
23. You can zoom in on smaller scales too – but use a higher resolution
24. from: https://cran.r-project.org/web/packages/marmap/vignettes/marmap-DataAnalysis.pdf
28. Shortest Great Circle distance
30. Now (IF WE HAVE TIME): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073051 • Make a map of the region in which you will conduct the bulk of your fieldwork • Make two plots: one minimalist, one with bathymetry • Experiment with the fancier features. Try plotting a course between two points • Notice the sample code at the end of the paper
31. • Projections • High resolution maps • Insets • NAFO zones • PBSmapper
32. Database of global administrative areas: http://gadm.org/
34. http://www.gadm.org/maps/
35. Level 0 = Country
36. Level 1 = “First level subdivisions” Provinces and territories* *Nunavut has three subdivisions
37. Level 2 = “Second level subdivisions” Some places have level 3 and 4 subdivisions Level 2 contains all info from level 1 Level 1 contains all info from level 0
38. More info about plotting maps in ggplot2: http://rmhogervorst.nl/cleancode/bl og/2017/01/06/plotting-a-map- with-ggplot2.html
41. Database of map projections http://www.csiss.org/m ap-projections/
46. https://www.cryopolitics.com/2014/07/2 8/mapping-and-distorting-the-arctic/ Plotting in the Arctic Option 1: Stereographic projection
47. Option 2: Albers projection
48. Let’s plot NL
49. Stereographic Mercator
50. http://www.flr.gov.nl.ca/lands/maps/standards.html Many places have official projection standards Projection information: https://proj4.org/operations/projections/etmerc.html This projection is not built-in to ggplot2 at this time See: https://www.r-bloggers.com/a-path-towards-easier- map-projection-machinations-with-ggplot2/
51. Let’s make a map for real Imagine a study based on Fogo Island We want to plot our study sites Bathymetry not important https://peerj.com/articles/2953/
52. Load regional data
53. Let’s zoom in These will be our X and Y ranges Good to write out in this way, as it makes code more readable and easier to tweak
54. Okay, but kind of ugly
55. Next: Fix axis labels This isn’t wrong, but it’s not intuitive
56. Set breaks in a sequence from the minimum latitude (latmin) to the maximum latitude (latmax) in increments of 0.1 (i.e. 49.5, 49.6, 49.7…)
57. Paste together a sequence of labels made up of three parts: 1. The numerical value ranging from latmin to latmax, incrementing by 0.1 (i.e. 49.5, 49.6, 49.7…) 2. A string of characters consisting of the degree sign and N 3. Insert no value between these two strings
58. What’s wrong with the longitude values?
59. Make the axis label use the ABSOLUTE VALUE Getting better… need a scale bar and north arrow See: http://editerna.free.fr/wp/?p=76
62. Add a town for reference
63. Show where the study site is located with an inset First, create a map that will serve as the inset map Strip away unnecessary elements
66. From: https://www.r-bloggers.com/creating-inset-map-with-ggplot2/
67. Let’s add some data to the map
68. Convert to decimal degrees
71. NAFO zones https://archive.nafo.int/open/sc/2013/scs13-22.pdf
72. Go to: https://www.nafo.int/Data/GIS
73. Shape files have polygons and attributes See attributes with: NAFO@data
76. The annotation is text (see: http://ggplot2.tidyverse.org/reference/an notate.html) coordinates() returns the centre point of a polygon Return all the X values (column 1) of centre points of polygons Return all the Y values (column 2) of centre points of polygons The label is the “ZONE” attribute within NAFO
77. When plotting two shapefiles at the same time, make sure they use equivalent coordinate systems: Zoomed out, this won’t have a huge effect Zoomed in, and it could be an issue
78. PBSmapping https://github.com/pbs-software/pbs-mapping • PBSmapping was developed by scientists at the Pacific Biological Station • I didn’t have time to prepare a full tutorial on this, but see link above for documentation
79. 900 910 920 930 940 5380 5390 5400 5410 5420 5430 5440 U TM East in g (km) UTM Northing (km) Saltspring 193 San Juan 149 Galiano 63 N Pender 30 Mayne 26 Saturna 35 V ancouver I sland Strait of Georgia
80. All new! https://edzer.github.io/sp/  sp package
81. More • Sf package: https://www.r-spatial.org/r/2018/10/25/ggplot2-sf.html • Rayshader: https://github.com/PennMUSA/MasterClass2019_3DMappingAndViz