2 Dec 2013

Cartography and Visualisation III: Map Elements

This is gonna be a short post. It'll cover the essential elements of a map - what most maps should have within the "area". However, it is subject to the requirements of the publication/ report.

This is Part III of the four-part instalment on: 

1) projections,
2) geographical phenomenon and data representation,
3) map elements,
4) map design (colour, typography, planar organisation and hierarchical organisation)




Just a teaser to begin with: WHY MAPS ARE COOL


Ok back to business:

Map was made by myself for an assignment.

Title/Subtitle: for a concise description of the map’s theme (not wordy, no abbreviations). This can be replaced with a caption, if in the case of a report.

Legend: defines all of the thematic symbols of a map; symbols that are self-explanatory or not directly related to map’s theme are normally omitted

Frame line: encloses the entire map and neat line: encloses the mapped area

Data source, credits: where the data for the thematic map is obtained, base information normally omitted

Scale: representative fraction of the map to reality and could be a verbal or bar scale. However, whether to use a scale might depend on whether the map is equal-area or not. If it is not equal area, then putting the scale bar is meaningless.

Orientation represented by north arrow, graticule. However, whether to use a north arrow might depend on whether the angles varies throughout the map. If it does significantly, then adding the north arrow is pointless.

Inset: a smaller map included within the context of a larger map

Place names/ labelling

Cartography and Visualisation II: Geographic Phenomenon & Data Representation

In this second instalment, I will cover Geographic Phenomenon & Data Representation.

This is Part II of the four-part instalment on:
1) projections,
2) geographical phenomenon and data representation,
3) map elements,
4) map design (colour, typography, planar organisation and hierarchical organisation)

What is geographic phenomenon?

It is a data that is spatially distributed. It can hence be abrupt or smooth in nature (with reference to whether there is a break in the data, usually between enumeration units), and can also be continuous or discrete (with reference to the number of decimal places on the number).

Data can be qualitative (=deals with apparent qualities [subjective properties]), or quantitative (=type of information based on quantities [objective, measureable]).

Qualitative data -> nominal
Quantitative data -> ordinal (ranking), interval (arbitrary 0), ratio (non-arbitrary 0)

There are a total of FIVE common mapping methods.

How can geographic phenomenon be represented?

It is usually represented in a thematic map, which is made up of a basemap and a thematic layer. A thematic map usually shows a specific theme connected with a geographic area. This is as opposed to a general purpose map (=General purpose map: many types of information on one map; most atlas maps, wall maps, road maps fall into this category; the map aims to give a broad understanding of location and features of an area (e.g., location of urban places, type of landscape, major transportation routes).

Different types of data can be represented in different types of 'conventional methods'.

Choropleth: having enumeration units (e.g. area) bounded by isolines to represent a distinctive colour/shading to represent a particular geographical phenomenon; values represented can be derived or totals; areas represented are usually administrative areas or statistical areas

Choropleth map with different classification methods

Dasymetric: using ancillary information to map enumeration units at a finer scale; corrects for ‘ecological fallacy’ that occurs with choropleth mapping; uses standardized data but places areal symbols that take into consideration actual changing densities within the boundaries of the map

-> Enumeration units: (in the case of a choropleth map) a uniform unit representing a single data point and is bounded by lines

-> Classification methods: grouping data into various classes by a certain method (e.g., 1) equal interval; 2) standard deviation; 3) Quantiles; 4) Natural breaks (Jenks); 5) Arbitrary)
  • Equal interval: each class occupies an equal interval along the number line
  • Standard deviation: class boundaries are defined by standard deviation
  • Quantiles: assures an equal number of values in each class
  • Natural areas: idiographic data classification that classify data into distinct groups based on a histogram distribution; via visual inspection or Jenks optimization
  • Arbitrary schemes: using arbitrarily-set classes; using regular rounded numbers having no relevance as distributional classes

Dot mapping: using dots to represent absolute numbers within an enumeration unit; the placement of dots can be uniform, geographically weighted (i.e., spatial autocorrelation) and geographically based (on ancillary information)

-> Ancillary information: complementary information that includes existing topographic maps, remote sensing data, meterological data, policies etc.

Isoarithmic: (e.g., isometric -> true point data to isoplethic -> conceptual point data) planimetric graphic representation of a three-dimensional volume via a system of line symbols to represent a 3D volume or mental construct; requires interpolation between control points

-> Interpolation: joining of points (i.e. control points) via a manual or automated process to form a continuous line representing a particular value
-> Manual interpolation: via methods of joining neighbouring control points with straight lines, to create lines of contours (isolines), in assuming that distribution of mapped changes in a linear fashion
-> Automated interpolation: via automated methods such as Delaunay triangles (via triangulation, triangle-based) Theissen polygons (via triangulation, polygon-based), Inverse-distance (gridding: making use of a grid and interpolating distances between nodes to get an estimation), Kriging 


Proportional symbol: a type of thematic map where data represented by a point symbol whose size varies with the data attribute values (goal of the map to show relative magnitudes [e.g., true point data or conceptual point data] of phenomena at specific locations); can be used for ordinal, interval and ratio data (quantitative data)

Proportional symbols, with range-grading (Dent).


Three Methods:
-> Absolute scaling: direct proportional scaling with the values it represents
-> Apparent-magnitude scaling: based on perception, with Flannery’s adjustment factor
-> Range-grading: (based on Dent 1999 or Meihoefer 1969) dividing data into groups, each group represented by a distinguishable proportional symbol; recommended to use five adjacent circles on a small scale map

Extra terminology:

Small scale map: large area
Large scale map: small area

Cartography and Visualisation I: Projections

I am writing a post about the terminologies in relation to Cartography and Visualisation, and in specific, how cartographic projections (i.e., the maps we hold in our hands) come about.

This is Part I of the four-part instalment on:
1) projections,
2) geographical phenomenon and data representation,
3) map elements,
4) map design (colour, typography, planar organisation and hierarchical organisation) 
The aim of this post is to be as concise as possible, adding definitions and diagrams to aid in your understanding of how projections came about, and also partly to help in my revision for the examinations (heh heh). The definitions are adapted in my own words from the online resources that I have read and my Cartography and Visualisation lecture notes.


Just a teaser to start:


Adapted from GE2227 notes. Redrawn by Eunice Soh.

Geoid: a hypothetical surface representing the form the earth’s oceans would take if there was no land and the water were free to respond to the earth’s gravitational and centrifugal forces; can vary up to 75 metres above/ 100 metres below the ellipsoid (i.e., orthometric height)

Here's a geoid viewer: http://geomatica.como.polimi.it/elab/geoid/geoidViewer.html

A video on geodesy

How all the cartography terminology are linked. First, one starts off with an ellipsoid which is a mathematical representation of the geoid. The ellipsoid is defined by its geodetic datum, with the following parameters: origin, semi-major axis and semi-minor axis. 

Reference spheroid/sphere/ellipsoid: a mathematically-defined surface that approximates the geoid, the truer figure of the earth, or other planetary body (e.g., WGS1984)

Datum:  a set of values that act as a base to which a geoid is referenced at a single point; (as geodetic datum): a model that describes the location, direction and scale relationships with respect to an origin on the Earth’s surface (i.e., semi-major axis [a], semi-minor axis [b], flattening ratio [b/a], origin); Singapore’s datum is SVY21 which is based on the WGS84 datum except for the difference in origin

A geographic coordinate system is a coordinate system that enables every location on the Earth to be specified by a set of numbers or letters.

Prime meridian: a longtitude which is defined as 0o; it is arbitrary, unlike the equator (vertical)
Equator: a latitude which is defined as 0oat the axis of rotation of the earth (horizontal)

What is a rhumbline (loxodrome)

Projected Coordinate Systems and their various properties. The black box are the actual names of the projection.

A projected coordinate system is a coordinate system projected from a geographic coordinate system, where a map projection is the systematic transformation of the curved, three dimensional surface of the planet into flat, two dimensional plane, resulting in distortion.

For a great video on projections, look here: http://education.nationalgeographic.com/education/media/selecting-map-projection/ and a cute cartoon about map projections: http://xkcd.com/977/

Another video on projections


How did the Mercator projection (azimuthal) come about 

Distortion: any projection that distorts the earth in some way (e.g., conformal -> angles preserved, areas distorted; equal area -> area preserved, angles distorted)

Certain projections can be a "compromise" (figure above).

A good read would be http://en.wikipedia.org/wiki/Map_projection


Decisions of a projection would depend on

  • Properties of the projection
  • Characters (scale, interrupted, aspect)
  • Deformation across mapped area
  • Projection centre
  • Familiarity

Properties of a projection

Major factors

  • Equivalence: Equal area 
  • Conformality: Equal angles 
Minor factors

  • Distance: Equidistance 
  • Direction: e.g., Azimuthal

1 Dec 2013

Ants of Kent Ridge: Part I (the ants)

An Informal List of the Ants of Kent Ridge (and adjacent green areas)

Kent Ridge has a myriad of ant species that forage about on the ground. These are ant species obtained by baiting with honey, tuna and peanut butter. The ants are also given a size "score" based on total length: tiny (<=3mm), medium (>3mm), large (>9mm). 

Subfamilies represented: Myrmicinae, Ponerinae, Dolichoderinae, Formicinae

Photographs by Eunice S.

If there are any misidentifications you feel strongly about, please feel free to comment on this blog and I will review it. As much as possible, I've tried to use the available taxonomic keys to identify them. 

Anoplolepis gracilipes (Smith 1857) Yellow Crazy Ant
Size: Medium
Nesting habit: in cracks, in the ground (opportunistic)

Camponotus cf. auriventris Emery 1889
Size: Medium
Nesting habit: excavates and nest in soil

Camponotus sp. 2 [cf. maculatus-group]
Size: Large
Nesting habit: Unsure

Camponotus sp. 3 [cf. albosparsus]
Size: Medium
Nesting habit: Nests in the ground.

[Camponotus sp. 4 is part of another inventory]

Camponotus sp. 5
Size: Large
Nesting habit: Likely arboreal.


Plagiolepis cf. exigua Forel 1894
Size: small
Nesting habit: In the ground.


Crematogaster (Orthocrema) biroi bandarensis Mayr, 1897 [ID by Shingo Hosoishi, Crematogaster expert]
Size: Medium
Nesting habit: Very likely to be in the ground (known from the subgenus) 

Crematogaster (Physocrema) sewardi Forel 1901 [ID by Shingo Hosoishi, Crematogaster expert]
http://www.antwiki.org/wiki/Crematogaster_sewardi 
Size: Medium
Nesting habit: Likely arboreal but not fully ascertained.


Philidris sp. 1 
Size: Medium
Nesting habit: Arboreal

Dolichoderus thoracicus (Smith 1860)
Size: Medium
Nesting habit: Arboreal, lives in hollow branches

Meranoplus bicolor (Guerin-Meneville 1844)
Size: Medium
Nesting habit: In the ground. Excavates its own nest.

Monomorium monomorium Bolton 1987
Size: Small
Nesting habit: Uncertain. Likely in the ground.

Oecophylla smaragdina smaragdina (Fabricius 1775)
Size: Large
Nesting habit: Uses leaves to make nest arboreally.

Nylandaria sp.
[corrected by James Trager, Myrmecologists Facebook forum]
Size: Medium
Nesting habit: unknown

Pheidole cf. parva Mayr 1865
Size: Small - Medium
Nesting habit: in the ground

[No photographs for Pheidole sp. 2 and Pheidole sp. 3]

Pheidole sp. 4
Size: Small - Medium
Nesting habit: in the ground

Pheidole sp. 5
Size: Medium
Nesting habit: unknown, probably in the ground

Pheidologeton (or Carebara sensu Fisher 2014) diversus (Jerdon 1851)
Size: Medium - Large
Nesting habit: in the ground and on the surface (but covered with sand)

Polyrhachis cf. proxima Bingham 1903
[not really sure if illaudata or proxima, but compared images on AntWeb and seem closer to proxima]
http://www.antweb.org/description.do?rank=species&name=proxima&genus=polyrhachis
Size: Large
Nesting habit: in the ground

Polyrhachis cf. abdominalis Emery 1896 [as suggested by Gordon Yong]
http://www.antweb.org/description.do?rank=species&name=abdominalis&genus=polyrhachis
Size: Large
Nesting habit: in bamboo

Tapinoma cf. melanocephalum Forel 1895 
[corrected by Jim Wetterer, Myrmecologists Facebook forum]
Size: Medium
Nesting habit: in cracks of the ground (opportunistic)

Tetramorium (tortosum species-group) sp. 1
Size: Medium
Nesting habit: in the ground 

Diacamma cf. rugosum (Le Guillou, 1842)
Size: Large
Nesting habit: in the ground, excavates its own nest

Odontomachus rixosus Smith 1857
Size: Large
Nesting habit: in the ground
Note: not present in Kent Ridge, for comparison purposes

Odontomachus simillimus Smith 1858
Size: Large
Nesting habit: in the ground, usually at the base of trees

Odontoponera denticulata (Smith 1857) 
[ID suggested by Wendy Wang, pers. comm. but haven't had the chance to examine the specimen properly; the antennal scape is quite short, dark integument seems to suggest it is denticulata but its rugae is fine, suggesting its transversa, have to check eye size, incision at petiole and propodeal denticles; also I do think both species (transversa and denticulata) exist in Singapore as I've gotten reddish forms found in forests and this darker form, found in urban areas]
Size: Large
Nesting habit: in the ground, excavates its own tunnel in the soil

13 Oct 2013

Things we do for class - Bivalve dissection


Chama pacifica Chamidae

Just last week we did another dissection practical. This time, for bivalves! We got to dissect a Meretrix sp. ("La La", a heterodont), Nuculana sp. (which was really tiny, a protobranch), Anodonata sp. ("Mussel", family Mytillidae, a pteriomorph), Anadara sp. ("Blood Cockle", a heterodont).

Bivalves are molluscs that are laterally compressed and have a hinge, enclosing two hinged parts. The shell is made up of calcium carbonate secreted by the mantle lobes and mantle. The calcium carbonate can be either aragonitic (nacreous inner layer - sheet or lenticular, prismatic, cross lamellar structure - simple or complex) or calcitic (outer foliose, prismatic). The calcium carbonate of a shell is never entirely calcitic though, mostly it is a mix of aragonite and calcite. Certain bivalves though, like oysters have almost all calcitic. On the contrary, some families are entirely aragonitic.

Lima vulgaris Limidae with wholly aragonitic shells
They have a D-larva split into two stages, Prodissoconch I and Prodissoconch II which have the velum to help it with motility with the exception of the Paleoheterodonts which have glochidium/ lasidium larvae.

They are generally split into different clades based on gill type, presence of palps, type of stomach, fusion of mantle & siphon position (higher taxa); hinge teeth type (higher or lower taxa); foot size, position of adductor muscles (lower taxa):

(photographs were identified by Tan Siong Kiat in 2011 as part of Project Semakau: bivalve page)

- Protobranch (small group, 3 orders, considered 'ancient', small in size, bipectinate lamellae (simple) gills with palp probocoides (for Nuculidae and Nuculanidae), foot frilled with papillae, do not filter feed but scrape detritus or symbiotic with sulphur oxidising bacteria in gills (only Solemyida))
e.g. Nuculana

- Paleoheterodont (mostly in the family Unionidae but there are 6 other families; mostly are freshwater except one of which is salt-water - Trigoniidae)

- Heterodont (unequal hinge teeth, eulamellibranch gills, mantle edges are fused at the posterior end as an inhalant tube) and Anomalodesmatans (typically lack hinge teeth, aragonitic shells, long siphons, fourth pallial aperture, vestigial gill filaments; Septibranchia is carnivorous with a type II stomach)
e.g. Heart Cockle (Cartiidae), La La Siput (Veneridae), Meretrix (Veneridae)


Cordissum cardissa Cartiidae
Dosinia amphismoides Veneridae

Teredo sp. Terenidae
Tellina virgata Tellinidae


- Pteriomorphs  (reduced foot, filibranch gills (Oysters (orders Ostreida, Pectinida) are exceptions - they have eumellibranch gills with the exception of Plicatuloidea (superfamily)), mantle edges generally not fused, taxodont or dysodont hinge teeth)
 e.g. Green Mussel Perna sp. (Mytilidae), Hammer Oyster (Isognomonidae), See Hum Anadara sp. (Arcidae), File Shell (Limopsidae), Scallops (Pectinidae), Spiny Oysters (Spondylidae)

Lithophaga teres Mytilidae
Isognomon isognomon Isognomidae

Pinna bicolor Pinnidae

Spondylus niobarensis Spondylidae
A related species to Spondylus, the Comptopallium radula
Notes:
- filibranch is ancestral to eulamellibranch gills
- heterodont/schizodont/isodont/dysodont teeth is more derived than taxodont teeth


Important parts of the bivalves are:

Of the valves
- Hinge teeth: either cardinal or lateral; isodont/schizodont/heterodont/dysodont/taxodont

Taxodont hinge of Anadara antiquata Arcidae
- Umbo: a knobbly protuberance (determines dorsal)
- Lunule (typically anterior but the mouth position determines anterior/posterior)
- Estucheon (typically posterior)
- Periostracum - either secreted by the mantle edge or foot

- Pallial line, where the mantle edge is
- Pallial sinus, a groove where the siphons are retracted into

Anatomy
- Ligament: inner (lamellar), outer (fibrous); can be alivincular, duplivincular, parivincular, multivicular, either amphidetic (either side of the umbo; usually only for alivincular or dulivincular only) or opisthodetic (anterior of umbo; usually for parivincular or multivincular only); e.g. opisthodetic parivincular are typically of the heterodonts, multivincular opisthodetic are typically of the Isognomidae ("Hammer Oysters"), duplivincular amphidetic (Arcidae), alivincular amphidetic (Limopsidae),

- Gills: made up of lamellae with cillia (Protobranchs); when fused, form demibranches connected by tissue between lamella but not always so; might have cillary junctions (filibranch; Pteriomorphs); when filaments are fused with adjacent filaments, form interfilament junctions, exclusively NO cillary junctions (eulamellibranch; Heterodonts); typically one pair of ctenidia on each side of the visceral mass; each ctenidia with a descending and descending lamella for the eulamellibrach condition; Septibranch condition is a poorly-developed septum with vestigial gills but has tentacles on inhalant siphons to suck small prey up

- Adductor muscle - present most of the times in the anterior and posterior position (isomyarian/heteromyarian/monomyarian); typically one pair of adductor muscle(s) on each valve; for example, Green Mussels (Perna viridris) only has posterior adductor mussel, scallops have one large adductor (central) muscle (monomyarian)

Saccostrea cucullata Ostreidae with an adductor muscle scar

- Other retractor muscles 

- Mantle (inner, mid, outer folds; outer - secretory, may be sensory; mid - sensory, have tentacles, sometimes eyes; inner - muscular and attached to shells) with type A/B/C fusion

- Visceral mass which contains heart (2 auricles, 1 ventricle; open circulatory but certain families have haemoglobin and is 'bloody'), digestive organs (esophagus/ stomach - crystalline style, typhosole, sorting area/ intestines/ anus), reno-pericardial complex, gonads

- Periocardial complex
- Two ganglia (cerebro-pleural ganglia innervates palps, anterior adductor muscle, otocysts, part of mantle and visceral ganglia innervates gills, heart, pericardium, posterior adductor muscle, most mantle regions, siphons and pallial sense organs) 

- Byssus - secreted by foot typically
- Eyes - pallial (marginal or siphonal, innervated by mantle) or cephalic (inner demibranchs of ctenidia, innervated by cerebral ganglia)

- Siphon - for respiratory purposes/ suspension feeding

- Labial palps (2 pairs)/ palp probosoides (not always present)/ mouth; sometimes labial palps can be hypertrophied (such as in Scallops) to helps food items not 'fall out' while swimming


That was a spam of essential terms. Anyway, here're some photographs by Xin Rui during the practical.


Meretrix sp. ("La La") which is a heterodont. Photo source: Ong Xin Rui

The internal anatomy of the Meretrix sp. ("La La"), the same as above. For our practical session, we were required to draw the anatomy. Please note that the posterior and anterior ends should be exchanged. Photo source: Ong Xin Rui

Further reading
[1] About Glochidium/Lasidium larvae: http://mussel-project.uwsp.edu/evol/syst/larvae.html
[2] About hinge types: http://paleo.cortland.edu/tutorial/Bivalves/bivalvemorph.htm
[3] Pictures of bivalves: http://www.nmr-pics.nl/index.htm

I shall update this page again, after I have dug up my bivalve photographs. Everything makes more sense now after this class...

Please correct if you spot any errors. Information taken and summarized from Bivalve lecture notes.