PBS Mapping: Draw Maps and Implement Other GIS Procedures

Description

This software has evolved from fisheries research conducted at the Pacific Biological Station (PBS) in Nanaimo, British Columbia, Canada. It extends the R language to include two-dimensional plotting features similar to those commonly available in a Geographic Information System (GIS). Embedded C code speeds algorithms from computational geometry, such as finding polygons that contain specified point events or converting between longitude-latitude and Universal Transverse Mercator (UTM) coordinates. It includes data for a global shoreline and other data sets in the public domain.

For a complete user's guide, see the file PBSmapping-UG.pdf in the R directory .../library/PBSmapping/doc.

PBSmapping includes 10 demos that appear as figures in the User's Guide. To see them, run the function .PBSfigs().

More generally, a user can view all demos available from locally installed packages with the function runDemos() in our related (and recommended) package PBSmodelling.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2008-09-03

EventData Objects

Description

An EventData object comprises a data frame with at least three fields named EID, X, and Y; each row specifies an event that occurs at a specific point.

PBSmapping functions that expect EventData will accept properly formatted data frames in their place (see 'Details').

as.EventData attempts to coerce a data frame to an object with class EventData.

is.EventData returns TRUE if its argument is of class EventData.

Usage

as.EventData(x, projection = NULL, zone = NULL)
is.EventData(x, fullValidation = TRUE)

Arguments

Details

Conceptually, an EventData object describes events (EID) that take place at specific points (X,Y) in two-dimensional space. Additional fields can specify measurements associated with these events. In a fishery context, EventData could describe fishing events associated with trawl tows, based on the fields:

• EID - fishing event (tow) identification number;

• X, Y - fishing location;

• Duration - length of time for the tow;

• Depth - average depth of the tow;

• Catch - biomass captured.

Like PolyData, EventData can have attributes projection and zone, which may be absent. Inserting the string "EventData" as the class attribute's first element alters the behaviour of some functions, including print (if PBSprint is TRUE) and summary.

Value

The as.EventData method returns an object with classes "EventData" and "data.frame", in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2015-04-23

See Also

PolySet, PolyData, LocationSet

LocationSet Objects

Description

A LocationSet comprises a data frame that summarises which EventData points (EID) lie in which PolySet polygons (PID) or (PID, SID). Events not located in target polygons are not reported. If an event lies on a polygon boundary, an additional LocationSet field called Bdry is set to TRUE. One event can also occur in multiple polygons.

PBSmapping functions that expect LocationSet's will accept properly formatted data frames in their place (see 'Details').

as.LocationSet attempts to coerce a data frame to an object with class LocationSet.

is.LocationSet returns TRUE if its argument is of class LocationSet.

Usage

as.LocationSet(x)
is.LocationSet(x, fullValidation = TRUE)

Arguments

Details

A PolySet can define regional boundaries for drawing a map, and EventData can give event points on the map. Which events occur in which regions? Our function findPolys resolves this problem. The output lies in a LocationSet, a data frame with three or four columns (EID, PID, SID, Bdry), where SID may be missing. One row in a LocationSet means that the event EID occurs in the polygon (PID, SID). The boundary (Bdry) field specifies whether (Bdry=T) or not (Bdry=F) the event lies on the polygon boundary. If SID refers to an inner polygon boundary, then EID occurs in (PID, SID) only if Bdry=T. An event may occur in multiple polygons. Thus, the same EID can occur in multiple records. If an EID does not fall in any (PID, SID), or if it falls within a hole, it does not occur in the output LocationSet. Inserting the string "LocationSet" as the first element of a LocationSet's class attribute alters the behaviour of some functions, including print (if PBSprint is TRUE) and summary.

Value

The as.LocationSet method returns an object with classes "LocationSet" and "data.frame", in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2015-04-23

See Also

PolySet, PolyData, EventData

Specify Whether to Print Summaries

Description

Specify whether PBS Mapping should print object summaries or not. If not, data objects are displayed as normal.

Usage

PBSprint

Details

If PBSprint = TRUE, the mapping software will print summaries rather than the data frames for EventData, LocationSet, PolyData, and PolySet objects. If PBSprint = FALSE, it will print the data frames.

This variable's default value is FALSE.

Value

TRUE or FALSE, depending on the user's preference.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2007-06-06

See Also

summary.

PolyData Objects

Description

A PolyData object comprises a data frame that summarises information for each polyline/polygon in a PolySet; each PolyData record is defined by a unique PID or (PID, SID combination).

PBSmapping functions that expect PolyData will accept properly formatted data frames in their place (see 'Details').

as.PolyData attempts to coerce a data frame to an object with class PolyData.

is.PolyData returns TRUE if its argument is of class PolyData.

Usage

as.PolyData(x, projection = NULL, zone = NULL)
is.PolyData(x, fullValidation = TRUE)

Arguments

Details

We define PolyData as a data frame with a first column named PID and (optionally) a second column named SID. Unlike a PolySet, where each contour has many records corresponding to the vertices, a PolyData object must have only one record for each PID or each (PID, SID) combination. Conceptually, this object associates data with contours, where the data correspond to additional fields in the data frame. The R language conveniently allows data frames to contain fields of various atomic modes ("logical", "numeric", "complex", "character", and "null"). For example, PolyData with the fields (PID, PName) might assign character names to a set of primary polygons. Additionally, if fields X and Y exist (perhaps representing locations for placing labels), consider adding attributes zone and projection. Inserting the string "PolyData" as the class attribute's first element alters the behaviour of some functions, including print (if PBSprint is TRUE) and summary.

Our software particularly uses PolyData to set various plotting characteristics. Consistent with graphical parameters used by the R/S functions lines and polygon, column names can specify graphical properties:

• lty - line type in drawing the border and/or shading lines;

• col - line or fill colour;

• border - border colour;

• density - density of shading lines;

• angle - angle of shading lines.

When drawing polylines (as opposed to closed polygons), only lty and col have meaning.

Value

The as.PolyData method returns an object with classes "PolyData" and "data.frame", in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2015-04-23

See Also

PolySet, EventData, LocationSet

PolySet Objects

Description

A PolySet object comprises a data frame that defines a collection of polygonal contours (i.e., line segments joined at vertices). These contours can be open-ended (polylines) or closed (polygons).

PBSmapping functions that expect PolySet's will accept properly formatted data frames in their place (see 'Details').

as.PolySet attempts to coerce a data frame to an object with class PolySet.

is.PolySet returns TRUE if its argument is of class PolySet.

Usage

as.PolySet(x, projection = NULL, zone = NULL)
is.PolySet(x, fullValidation = TRUE)

Arguments

Details

In our software, a PolySet data frame defines a collection of polygonal contours (i.e., line segments joined at vertices), based on four or five numerical fields:

• PID - the primary identification number for a contour;

• SID - optional, the secondary identification number for a contour;

• POS - the position number associated with a vertex;

• X - the horizontal coordinate at a vertex;

• Y - the vertical coordinate at a vertex.

The simplest PolySet lacks an SID column, and each PID corresponds to a different contour. By analogy with a child's “follow the dots” game, the POS field enumerates the vertices to be connected by straight lines. Coordinates (X, Y) specify the location of each vertex. Thus, in familiar mathematical notation, a contour consists of n points (x_{i}, y_{i}) with i = 1, ..., n, where i corresponds to the POS index. A PolySet has two potential interpretations. The first associates a line segment with each successive pair of points from 1 to n, giving a polyline (in GIS terminology) composed of the sequential segments. The second includes a final line segment joining points n and 1, thus giving a polygon.

The secondary ID field allows us to define regions as composites of polygons. From this point of view, each primary ID identifies a collection of polygons distinguished by secondary IDs. For example, a single management area (PID) might consist of two fishing areas, each defined by a unique SID. A secondary polygon can also correspond to an inner boundary, like the hole in a doughnut. We adopt the convention that POS goes from 1 to n along an outer boundary, but from n to 1 along an inner boundary, regardless of rotational direction. This contrasts with other GIS software, such as ArcView (ESRI 1996), in which outer and inner boundaries correspond to clockwise and counter-clockwise directions, respectively.

The SID field in a PolySet with secondary IDs must have integer values that appear in ascending order for a given PID. Furthermore, inner boundaries must follow the outer boundary that encloses them. The POS field for each contour (PID, SID) must similarly appear as integers in strictly increasing or decreasing order, for outer and inner boundaries respectively. If the POS field erroneously contains floating-point numbers, fixPOS can renumber them as sequential integers, thus simplifying the insertion of a new point, such as point 3.5 between points 3 and 4.

A PolySet can have a projection attribute, which may be missing, that specifies a map projection. In the current version of PBS Mapping, projection can have character values "LL" or "UTM", referring to “Longitude-Latitude” and “Universal Transverse Mercator”. We explain these projections more completely below. If projection is numeric, it specifies the aspect ratio r, the number of x units per y unit. Thus, r units of x on the graph occupy the same distance as one unit of y. Another optional attribute zone specifies the UTM zone (if projection="UTM") or the preferred zone for conversion from Longitude-Latitude (if projection="LL").

A data frame's class attribute by default contains the string "data.frame". Inserting the string "PolySet" as the class vector's first element alters the behaviour of some functions. For example, the summary function will print details specific to a PolySet. Also, when PBSprint is TRUE, the print function will display a PolySet's summary rather than the contents of the data frame.

Value

The as.PolySet method returns an object with classes "PolySet" and "data.frame", in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2022-09-06

References

Environmental Systems Research Institute (ESRI). (1996) ArcView GIS: The Geographic Information System for Everyone. ESRI Press, Redlands, California. 340 pp.

See Also

PolyData, EventData, LocationSet

Convert RGB to RYB and RYB to RGB

Description

Convert RGB (red-green-blue) colours to RYB (red-yellow-blue) colours, and vice versa. Algorithm based on Sugita and Takahashi (2015, 2017)

Usage

RGB2RYB(RGBmat)
RYB2RGB(RYBmat)

Arguments

Details

The RYB colour wheel is more commonly used by artists, and provides a more intuitive system when blending colours – red and yellow makes orange, yellow and blue makes green, blue and red makes purple. On the RYB colour wheel, red lies opposite green, but on the RGB colour wheel, red lies opposite cyan.

Value

Matrix of RGB or RYB primary colour intensities, where rows are records and columns are primary colours.

Note

Opposite colours calculated in RYB space (1-RYB) are not always what one expects. For example the colour "purple", RGB {160, 32, 240}, might better be specified as RGB {126, 0, 255} before converting to RYB and inverting.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Regional Headquarters, Vancouver BC
Last modified Rd: 2022-07-06

References

Sugita, J. and Takahashi, T. (2017) Computational RYB Color Model and its Applications. IIEEJ Transactions on Image Electronics and Visual Computing 5(2): 110-122.

Sugita, J. and Takahashi, T. (2015) RYB Color Compositing. International Workshop on Applications in Information Technology, October 8-10, 2015.

See Also

In package PBSmapping:
addBubbles

In package grDevices:
col2rgb, rgb, rgb2hsv

Add Bubbles to Maps

Description

Add bubbles proportional to some EventData's Z column (e.g., catch or effort) to an existing plot, where each unique EID describes a bubble.

Usage

addBubbles(events, type=c("perceptual","surface","volume"),
   z.max=NULL, min.size=0, max.size=0.8, symbol.zero="+",
   symbol.fg=rgb(0,0,0,0.60), symbol.bg=rgb(0,0,0,0.30),
   legend.pos="bottomleft", legend.breaks=NULL,
   show.actual=FALSE, legend.type=c("nested","horiz","vert"),
   legend.title="Abundance", legend.cex=.8, neg.col="RYB", ...)

Arguments

Details

Modified from (and for the legend, strongly inspired by) Tanimura et al. (2006) by Denis Chabot to work with PBSmapping.

Furthermore, Chabot's modifications make it possible to draw several maps with bubbles that all have the same scale (instead of each bubble plot having a scale that depends on the maximum z-value for that plot). This is done by making z.max equal to the largest z-value from all maps that will be plotted.

The user can also add a legend in one of four corners (see legend) or at a specific c(X,Y) position. If legend.pos is NULL, no legend is drawn.

Author(s)

Denis Chabot, Research Scientist
Maurice-Lamontagne Institute, Fisheries & Oceans Canada (DFO), Mont-Joli QC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Offsite, Vancouver BC
Last modified Rd: 2024-09-25

References

Tanimura, S., Kuroiwa, C., and Mizota, T. (2006) Proportional symbol mapping in R. Journal of Statistical Software 15(5).

See Also

In package PBSmapping:
addPolys, EventData, RGB2RYB, surveyData

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- common code for both examples below
  data(nepacLL,surveyData,envir=.PBSmapEnv)
  surveyData$Z <- surveyData$catch

  #--- plot a version that only varies the size
  plotMap(nepacLL, xlim=c(-131.8,-127.2), ylim=c(50.5,52.7),
    col="gainsboro",plt=c(.08,.99,.08,.99), cex.axis=1.2, cex.lab=1.5)
  addBubbles(surveyData, symbol.bg=rgb(.9,.5,0,.6),
    legend.type="nested", symbol.zero="+", col="grey")

  #--- plot a version that uses different symbol colours
  plotMap(nepacLL, xlim=c(-131.8,-127.2), ylim=c(50.5,52.7),
  col="gainsboro",plt=c(.08,.99,.08,.99), cex.axis=1.2, cex.lab=1.5)
  subset <- surveyData[surveyData$Z <= 1000, ]
  addBubbles(subset, symbol.bg=c("red", "yellow", "green"),
    legend.type="horiz", legend.breaks=pretty(range(subset$Z), n=11),
    symbol.zero=FALSE, col="grey", min.size=0.1, max.size=0.4)
  par(oldpar)
})

Add Compass Rose to Map

Description

Add a compass rose to an existing map, similar to those found on nautical charts showing both true north and magnetic north.

Usage

addCompass(X, Y, rot="magN", useWest=TRUE, year,
   cex=1, col.compass=c("gainsboro","blue","yellow","black"), ...)

Arguments

Details

The basic idea comes from Jim Lemon (see References), but is modified here to reflect a compass rose used on BC nautical charts.

The default rotation ("magN") is a calculation of the initial bearing of a great-circle arc from the compass position to the north geomagnetic rot using the function calcGCdist. The default year is the current year, but the user can choose years from 1900 to 2025 for approximate rot locations using model output from NOAA's IGRF-13 (International Geomagnetic Reference Field).

The user can also specify a fixed rotation (e.g. rot=-30) or no rotation (either rot=0 or rot="trueN").

Value

No value returned.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Regional Headquarters, Vancouver BC
Last modified Rd: 2022-07-05

References

[R-sig-Geo] How to display a compass rose on a map

Magnetic North, Geomagnetic and Magnetic Poles

See Also

addBubbles, addLabels, addPoints, addStipples, calcGCdist

Examples

local(envir=.PBSmapEnv,expr={
  data(nepacLL,envir=.PBSmapEnv)
  par(mfrow=c(1,1),mar=c(3,4,0.5,0.5))
  plotMap(nepacLL, xlim=c(-134.5,-124.5), ylim=c(48,55), plt=NULL,
    col="lightyellow", cex.axis=1.2, cex.lab=1.5)
  addCompass(-132, 49.5, rot=-12, cex=1.5)
})

Add Labels to an Existing Plot

Description

Add the label column of data to the existing plot.

Usage

addLabels (data, xlim = NULL, ylim = NULL, polyProps = NULL,
           placement = "DATA", polys = NULL, rollup = 3,
           cex = NULL, col = NULL, font = NULL, ...)

Arguments

Details

If data is EventData, it must minimally contain the columns EID, X, Y, and label. Since the EID column does not match a column in polys, set placement = "DATA". The function plots each label at its corresponding X/Y coordinate.

If data is PolyData, it must minimally contain the columns PID and label. If it also contains X and Y columns, set placement = "DATA" to plot labels at those coordinates. Otherwise, set placement to one of "CENTROID", "MEAN_RANGE", or "MEAN_XY". When placement != "DATA", supply a PolySet polys. Using this PolySet, the function calculates a centroid, mean range, or mean X/Y coordinate for each polygon, and then links those PolyData with data by PID/SID to determine label coordinates.

If data contains both PID and EID columns, the function assumes it is PolyData and ignores the EID column.

For additional help on the arguments cex, col, and font, please see par.

Value

EventData or PolyData with X and Y columns that can subsequently reproduce the labels on the plot. Modify this data frame to tweak label positions.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addPoints, calcCentroid, calcMidRange, calcSummary, EventData, plotPoints, PolyData.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create sample PolyData to label Vancouver Island
  labelData <- data.frame(PID=33, label="Vancouver Island");
  #--- load data
  if (!is.null(version$language) && (version$language == "R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- plot the map
  plotMap(nepacLL,xlim=c(-129,-122.6),ylim=c(48,51.1),col="lemonchiffon")
  #--- add the labels
  addLabels(labelData,placement="CENTROID",polys=nepacLL,cex=1.2,col=2,font=2)
  par(oldpar)
})

Add a PolySet to an Existing Plot as Polylines

Description

Add a PolySet to an existing plot, where each unique (PID, SID) describes a polyline.

Usage

addLines (polys, xlim = NULL, ylim = NULL,
    polyProps = NULL, lty = NULL, col = NULL, arrows = FALSE, ...)

Arguments

Details

The plotting routine does not connect the last vertex of each discrete polyline to the first vertex of that polyline. It clips polys to xlim and ylim before plotting.

For additional help on the arguments lty and col, please see par.

Value

PolyData consisting of the PolyProps used to create the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

calcLength, clipLines, closePolys, convLP, fixBound, fixPOS, locatePolys, plotLines, thinPolys, thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a PolySet to plot
  polys <- data.frame(PID=rep(1,4),POS=1:4,X=c(0,1,1,0),Y=c(0,0,1,1))
  polys <- as.PolySet(polys, projection=1)
  #--- plot the PolySet
  plotLines(polys, xlim=c(-.5,1.5), ylim=c(-.5,1.5), projection=1)
  #--- add the PolySet to the plot (in a different style)
  addLines(polys, lwd=5, col=3)
  par(oldpar)
})

Add EventData/PolyData to an Existing Plot as Points

Description

Add EventData/PolyData to an existing plot, where each unique EID describes a point.

Usage

addPoints (data, xlim = NULL, ylim = NULL, polyProps = NULL,
           cex = NULL, col = NULL, pch = NULL, ...)

Arguments

Details

This function clips data to xlim and ylim before plotting. It only adds PolyData containing X and Y columns.

For additional help on the arguments cex, col, and pch, please see par.

Value

PolyData consisting of the PolyProps used to create the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

combineEvents, convDP, findPolys, locateEvents, plotPoints.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,surveyData,envir=.PBSmapEnv)
  #--- plot a map
  plotMap(nepacLL, xlim=c(-136, -125), ylim=c(48, 57))
  #--- add events
  addPoints(surveyData, col=1:7)
  par(oldpar)
})

Add Polygon PolySet to Existing Plot

Description

Add a PolySet to an existing plot, where each unique (PID, SID) describes a polygon.

Usage

addPolys(polys, xlim = NULL, ylim = NULL, polyProps = NULL,
         border = NULL, lty = NULL, col = NULL, colHoles = NULL,
         density = NA, angle = NULL, ...)

.insertNAs(polys, idx)

.preparePolyProps(polysPID, polysSID, polyProps)

.rollupPolys(polys, rollupMode, exteriorCCW, closedPolys, addRetrace)

Arguments

Details

The plotting routine connects the last vertex of each discrete polygon to the first vertex of that polygon. It supports both borders (border, lty) and fills (col, density, angle). It clips polys to xlim and ylim before plotting.

For additional help on the arguments border, lty, col, density, and angle, please see polygon and par.

Value

PolyData consisting of the PolyProps used to create the plot.

Note

Auxiliary dot function '.insertNAs' facilitates (hastens) the plotting of polygons and polylines. It also reduces the incidence of retrace lines.

Auxiliary dot function '.preparePolyProps' performs at least one of the following tasks:
1) creates 'polyProps' if it equals NULL;
2) adds 'SID' column to 'polyProps' if one exists in 'polys';
3) removes from 'polyProps' any PIDs that do not exist in 'polys'.
Returns a polyProps object.

Auxiliary dot function '.rollupPolys' does not validate a PolySet; returns a rolled-up PolySet or NULL.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addLabels, addLines (also uses '.preparePolyProps' and '.insertNAs'), addPoints, addStipples
'.rollupPolys' is also called by:
calcArea, calcCentroid, calcLength, calcSummary, fixPOS

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a PolySet to plot
  polys <- data.frame(PID=rep(1,4),POS=1:4,X=c(0,1,1,0),Y=c(0,0,1,1))
  polys <- as.PolySet(polys, projection=1)
  #--- plot the PolySet
  plotPolys(polys,xlim=c(-.5,1.5),ylim=c(-.5,1.5),density=0,projection=1)
  #--- add the PolySet to the plot (in a different style)
  addPolys(polys,col="green",border="blue",lwd=3)
  par(oldpar)
})

Add Stipples to an Existing Plot

Description

Add stipples to an existing plot.

Usage

addStipples (polys, xlim=NULL, ylim=NULL, polyProps=NULL,
   side=1, density=1, distance=4, ...)

Arguments

Details

This function locates stipples based on the PolySet polys and does not stipple degenerate lines.

Value

PolyData consisting of the PolyProps used to create the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addPoints, addPolys, plotMap, plotPoints, plotPolys, points, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- plot a map
  plotMap(nepacLL,xlim=c(-128.66,-122.83),ylim=c(48.00,51.16))
  #--- add stippling
  addStipples(nepacLL,col="purple",pch=20,cex=0.25,distance=2)
  par(oldpar)
})

Append a Two-Column Matrix to a PolySet

Description

Append a two-column matrix to a PolySet, assigning PID and possibly SID values automatically or as specified in its arguments.

Usage

appendPolys (polys, mat, PID = NULL, SID = NULL, isHole = FALSE)

Arguments

Details

If the PID argument is NULL, the appended polygon's PID will be one greater than the maximum within polys (if defined); otherwise, it will be 1.

If polys contains an SID column and the SID argument equals NULL, this function uses the next available SID for the corresponding PID.

If polys does not contain an SID column and the caller passes an SID argument, all existing polygons will receive an SID of 1. The new polygon's SID will match the SID argument.

If isHole = TRUE, the polygon's POS values will appropriately represent a hole (reverse order of POS).

If (PID, SID) already exists in the PolySet, the function will issue a warning and duplicate those identifiers.

Value

PolySet containing mat appended to polys. The function retains attributes from polys.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addPolys, clipPolys, closePolys, convLP, fixBound, fixPOS, joinPolys, plotMap, plotPolys.

Examples

local(envir=.PBSmapEnv,expr={
  #--- create two simple matrices
  a <- matrix(data=c(0,0,1,0,1,1,0,1),ncol=2,byrow=TRUE);
  b <- matrix(data=c(2,2,3,2,3,3,2,3), ncol=2,byrow=TRUE);
  #--- build a PolySet from them
  polys <- appendPolys(NULL, a);
  polys <- appendPolys(polys, b);
  #--- print the result
  print (polys);
})

Data: Bathymetry Spanning BC Coast

Description

Bathymetry data spanning British Columbia's coast.

Usage

data(bcBathymetry)

Format

Three-element list: x = vector of horizontal grid line locations, y = vector of vertical grid line locations, z = (x by y) matrix containing water depths measured in meters. Positive values indicate distance below sea level and negative values above it.

The functions 'graphics::contour' and 'grDevices::contourLines' expect data in this format. Function convCP converts the output from 'grDevices::contourLines' into a PolySet.

Note

In R, the data must be loaded using the 'utils::data' function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Regional Headquarters, Vancouver BC
Last modified Rd: 2022-07-07

Source

Bathymetry data acquired from the Scripps Institution of Oceanography at the University of San Diego.

Using their online form, we requested bathymetry data for the complete nepacLL region. At forty megabytes, the data were not suitable for distribution in our mapping package. Therefore, we reduced the data to the range -140^\circ \le x \le -122^\circ and 47^\circ \le y \le 61^\circ.

References

Smith, W.H.F. and Sandwell, D.T. (1997) Global seafloor topography from satellite altimetry and ship depth soundings. Science 277, 1957-1962.
Website: https://topex.ucsd.edu/WWW_html/mar_topo.html

See Also

In package graphics:
contour
In package grDevices:
contourLines
In package PBSmapping:
convCP, nepacLL, nepacLLhigh

Calculate the Areas of Polygons

Description

Calculate the areas of polygons found in a PolySet.

Usage

calcArea (polys, rollup = 3)

Arguments

Details

If rollup equals 1, the results contain an area for each unique PID only. When it equals 2, they contain entries for outer contours only. Finally, setting it to 3 prevents roll-up, and they contain areas for each unique (PID, SID).

Outer polygons have positive areas and inner polygons negative areas. When polygons are rolled up, the routine sums the positive and negative areas and consequently accounts for holes.

If the PolySet's projection attribute equals "LL", the function projects the PolySet in UTM first. If the PolySet's zone attribute exists, it uses it for the conversion. Otherwise, it computes the mean longitude and uses that value to determine the zone. The longitude range of zone i is -186 + 6 i^\circ < x \le -180 + 6 i^\circ.

Value

PolyData with columns PID, SID (may be missing), and area. If the projection equals "LL" or "UTM", the units of area are square kilometres.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2022-09-06

See Also

calcCentroid, calcLength, calcMidRange, calcSummary, locatePolys.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language == "R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- convert LL to UTM so calculation makes sense
  attr(nepacLL, "zone") <- 9
  nepacUTM <- convUL(nepacLL)
  #--- calculate and print the areas
  print(calcArea(nepacUTM))
})

Calculate the Centroids of Polygons

Description

Calculate the centroids of polygons found in a PolySet.

Usage

calcCentroid (polys, rollup = 3)

Arguments

Details

If rollup equals 1, the results contain a centroid for each unique PID only. When it equals 2, they contain entries for outer contours only. Finally, setting it to 3 prevents roll-up, and they contain a centroid for each unique (PID, SID).

Value

PolyData with columns PID, SID (may be missing), X, and Y.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

calcArea, calcLength, calcMidRange, calcSummary, locateEvents, locatePolys.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- calculate and print the centroids for several polygons
  print(calcCentroid(nepacLL[is.element(nepacLL$PID,c(33,39,47)),]))
})

Calculate Convex Hull for a Set of Points

Description

Calculate the convex hull for a set of points.

Usage

calcConvexHull(xydata, keepExtra=FALSE)
.closestPoint(pts, pt)

Arguments

Details

Uses the function chull() in the package grDevices. By default, it ignores all columns other than X and Y; however, the user can choose to retain additional columns in xydata by specifying keepExtra=TRUE.

Value

PolySet with columns PID, POS, X, Y, and additional columns in xydata if keepExtra=TRUE.

Auxiliary dot function '.closestPoint' returns a vector of length 'pts' where TRUE indicates that the point is closest to 'pt'. Returns several TRUE values when several points are equidistant.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addPoints, addPolys, calcArea, calcCentroid, calcMidRange, calcSummary, locateEvents, plotMap, plotPoints, plotPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  data(surveyData,envir=.PBSmapEnv)
  #--- plot the convex hull, and then plot the points
  plotMap(calcConvexHull(surveyData),col="moccasin")
  addPoints(surveyData,col="blue",pch=17,cex=.6)
  par(oldpar)
})

Calculate Great-Circle Distance

Description

Calculate the great-circle distance between geographic (LL) coordinates. Also calculate the initial bearing of the great-circle arc (at its starting point).

Usage

calcGCdist(lon1, lat1, lon2, lat2, R=6371.2)

Arguments

Details

The great-circle distance is calculated between two points along a spherical surface using the shortest distance and disregarding topography.

Method 1: Haversine Formula

a = \sin^2((\phi_2 - \phi_1)/2) + \cos(\phi_1) \cos(\phi_2) \sin^2((\lambda_2 - \lambda_1)/2)

c = 2~\mathrm{atan2}(\sqrt{a}, \sqrt{1-a})

d = R c

where
\phi = latitude (in radians),
\lambda = longitude (in radians),
R = radius (km) of the Earth,
a = square of half the chord length between the points,
c = angular distance in radians,
d = great-circle distance (km) between two points.

Method 2: Spherical Law of Cosines

d = \mathrm{acos}(\sin(\phi_1)\sin(\phi_2) + \cos(\phi_1)\cos(\phi_2)\cos(\lambda_2 - \lambda_1)) R

The initial bearing (aka forward azimuth) for the start point can be calculated using:

\theta = \mathrm{atan2}(\sin(\lambda_2-\lambda_1)\cos(\phi_2), \cos(\phi_1)\sin(\phi_2) - \sin(\phi_1)\cos(\phi_2)\cos(\lambda_2-\lambda_1))

Value

A list obect containing:
a – Haversine a = square of half the chord length between the points,
c – Haversine c = angular distance in radians,
d – Haversine d = great-circle distance (km) between two points,
d2 – Law of Cosines d = great-circle distance (km) between two points,
theta – Initial bearing \theta (degrees) for the start point.

Note

If one uses the north geomagnetic pole as an end point, \theta crudely approximates the magnetic declination.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-03-11

References

Movable Type Scripts – Calculate distance, bearing and more between Latitude/Longitude points

See Also

In package PBSmapping:
addCompass, calcArea, calcCentroid, calcLength

Examples

local(envir=.PBSmapEnv,expr={
  #-- Distance between southern BC waters and north geomagnetic pole
  print(calcGCdist(-126.5,48.6,-72.7,80.4))
})

Calculate the Length of Polylines

Description

Calculate the length of polylines found in a PolySet.

Usage

calcLength (polys, rollup = 3, close = FALSE)

Arguments

Details

If rollup equals 1, the results contain an entry for each unique PID only. Setting it to 3 prevents roll-up, and they contain an entry for each unique (PID, SID).

If the projection attribute equals "LL", this routine uses Great Circle distances to compute the surface length of each polyline. In doing so, the algorithm simplifies Earth to a sphere.

If the projection attribute equals "UTM" or 1, this routine uses Pythagoras' Theorem to calculate lengths.

Value

PolyData with columns PID, SID (may be missing), and length. If projection equals "UTM" or "LL", lengths are in kilometres. Otherwise, lengths are in the same unit as the input PolySet.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

calcArea, calcCentroid, calcMidRange, calcSummary, locatePolys.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- calculate the perimeter of Vancouver Island
  print(calcLength(nepacLL[nepacLL$PID==33, ]))
})

Calculate the Midpoint of the X/Y Ranges of Polygons

Description

Calculate the midpoint of the X/Y ranges of polygons found in a PolySet.

Usage

calcMidRange (polys, rollup = 3)

Arguments

Details

If rollup equals 1, the results contain a mean range for each unique PID only. When it equals 2, they contain entries for outer contours only. Finally, setting it to 3 prevents roll-up, and they contain a mean range for each unique (PID, SID).

Value

PolyData with columns PID, SID (may be missing), X, and Y.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

calcArea, calcCentroid, calcLength, calcSummary.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- calculate and print the centroids for several polygons
  print(calcMidRange(nepacLL[is.element(nepacLL$PID,c(33,39,47)),]))
})

Apply Functions to Polygons in a PolySet

Description

Apply functions to polygons in a PolySet.

Usage

calcSummary (polys, rollup = 3, FUN, ...)

Arguments

Details

If rollup equals 1, the results contain an entry for each unique PID only. When it equals 2, they contain entries for outer contours only. Finally, setting it to 3 prevents roll-up, and they contain an entry for each unique (PID, SID).

Value

PolyData with columns PID, SID (may be missing), X, and Y. If FUN returns a vector of length greater than 1 (say n), names the columns X1, X2, ..., Xn and Y1, Y2, ..., Yn.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

calcArea, calcCentroid, calcConvexHull, calcLength, calcMidRange, combineEvents, findPolys, locateEvents, locatePolys, makeGrid, makeProps.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- calculate and print the centroids for several polygons
  print(calcSummary(nepacLL[is.element(nepacLL$PID,c(33,39,47)),],
    rollup=3, FUN=mean))
})

Calculate Voronoi Tesselation

Description

Calculate the Voronoi (Dirichlet) tesselation for a set of points.

Usage

calcVoronoi(xydata, xlim=NULL, ylim=NULL, eps=1e-09, frac=0.0001)

.expandEdges(polys, pts, xlim, ylim)

Arguments

Details

This routine ignores all columns other than 'X' and 'Y'.

If the user leaves 'xlim' and 'ylim' unspecified, the function defaults to the range of the data with each extent expanded by ten percent of the range.

This function sets the attribute 'projection' to 1 and the attribute 'zone' to NULL as it assumes this projection in its calculations.

Value

'PolySet' with columns 'PID', 'POS', 'X', and 'Y'.

Auxiliary dot function '.expandEdges' returns an expanded 'PolySet'.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addPoints, addPolys, calcArea, calcCentroid, calcConvexHull, calcMidRange, calcSummary, locateEvents, plotMap, plotPoints, plotPolys, PolySet

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create some EventData
  events <- as.EventData(data.frame(
    EID=1:200, X=rnorm(200), Y=rnorm(200)), projection=1)
  #--- calculate the Voronoi tesselation
  polys <- calcVoronoi(events)
  #--- create PolyData to color it based on area
  polyData <- calcArea(polys)
  names(polyData)[is.element(names(polyData), "area")] <- "Z"
  colSeq <- seq(0.4, 0.95, length=4)
  polyData <- makeProps(polyData,
    breaks=quantile(polyData$Z,c(0,.25,.5,.75,1)),
    propName="col", propVals=rgb(colSeq,colSeq,colSeq))
  #--- plot the tesselation
  plotMap(polys, polyProps=polyData)
  #--- plot the points
  addPoints(events, pch=19)
  par(oldpar)
})

Clip a PolySet as Polygons or Polylines

Description

Clip a 'PolySet', where each unique ('PID', 'SID') describes a polygon or polyline.

Usage

clipPolys (polys, xlim, ylim, keepExtra = FALSE)

clipLines (polys, xlim, ylim, keepExtra = FALSE)

.clip(polys, xlim, ylim, isPolygons, keepExtra)

Arguments

Details

For each discrete polygon, the function connects vertices 1 and N (does not connect vertices 1 and N for discrete polylines). It recalculates the 'POS' values for each vertex, saving the old values in a column named 'oldPOS'. For new vertices, it sets 'oldPOS' to NA.

Value

'PolySet' containing the input data, with some points added or removed. A new column 'oldPOS' records the original 'POS' value for each vertex.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addLines, addPolys, addStipples, PolySet

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a triangle that will be clipped
  polys <- data.frame(PID=rep(1, 3), POS=1:3, X=c(0,1,.5), Y=c(0,0,1))
  #--- clip the triangle in the X direction, and plot the results
  plotPolys(clipPolys(polys,xlim=c(0,.75),ylim=range(polys[,"Y"])),col=2)
  par(oldpar)
})

Close a PolySet

Description

Close a PolySet of polylines to form polygons.

Usage

closePolys (polys)

Arguments

Details

Generally, run fixBound before this function. The ranges of a PolySet's X and Y columns define the boundary. For each discrete polygon, this function determines if the first and last points lie on a boundary. If both points lie on the same boundary, it adds no points. However, if they lie on different boundaries, it may add one or two corners to the polygon.

When the boundaries are adjacent, one corner will be added as follows:

• top boundary + left boundary implies add top-left corner;

• top boundary + right boundary implies add top-right corner;

• bottom boundary + left boundary implies add bottom-left corner;

• bottom boundary + right boundary implies add bottom-right corner.

When the boundaries are opposite, it first adds the corner closest to a starting or ending polygon vertex. This determines a side (left-right or bottom-top) that connects the opposite boundaries. Then, it adds the other corner of that side to close the polygon.

Value

PolySet identical to polys, except for possible additional corner points.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

fixBound, fixPOS.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- 4 corners
  polys <- data.frame(
    PID = c(1, 1, 2, 2, 3, 3, 4, 4),
    POS = c(1, 2, 1, 2, 1, 2, 1, 2),
    X   = c(0, 1, 2, 3, 0, 1, 2, 3),
    Y   = c(1, 0, 0, 1, 2, 3, 3, 2))
  plotPolys(closePolys(polys), col=2)

  #--- 2 corners and 1 opposite
  polys <- data.frame(
    PID = c(1, 1, 2, 2, 3, 3, 3),
    POS = c(1, 2, 1, 2, 1, 2, 3),
    X   = c(0, 1, 0, 1, 5, 6, 1.5),
    Y   = c(1, 0, 2, 3, 0, 1.5, 3))
  plotPolys(closePolys(polys), col=2)
  par(oldpar)
})

Combine Measurements of Events

Description

Combine measurements associated with events that occur in the same polygon.

Usage

combineEvents (events, locs, FUN, ..., bdryOK = TRUE)

Arguments

Details

This function combines measurements associated with events that occur in the same polygon. Each event (EID) has a corresponding measurement Z. The locs data frame (usually output from findPolys) places events within polygons. Thus, each polygon (PID, SID) determines a set of events within it, and a corresponding vector of measurements Zv. The function returns FUN(Zv), a summary of measurements within each polygon.

Value

PolyData with columns PID, SID (if in locs), and Z.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

findCells, findPolys, locateEvents, locatePolys, makeGrid, makeProps.

Examples

local(envir=.PBSmapEnv,expr={
  #--- create an EventData data frame: let each event have Z = 1
  events <- data.frame(EID=1:10, X=1:10, Y=1:10, Z=rep(1, 10))
  #--- example output from findPolys where 1 event occurred in the first
  #--- polygon, 3 in the second, and 6 in the third
  locs <- data.frame(EID=1:10,PID=c(rep(1,1),rep(2,3),rep(3,6)),Bdry=rep(0,10))
  #--- sum the Z column of the events in each polygon, and print the result
  print(combineEvents(events=events, locs=locs, FUN=sum))
})

Combine Several Polygons into a Single Polygon

Description

Combine several polygons into a single polygon by modifying the PID and SID indices.

Usage

combinePolys (polys)

Arguments

Details

This function accepts a PolySet containing one or more polygons (PIDs), each with one or more components or holes (SIDs). The SID column need not exist in the input. The function combines these polygons into a single polygon by simply renumbering the PID and SID indices. The resulting PolySet contains a single PID (with the value 1) and uses the SID value to differentiate between polygons, their components, and holes.

Value

PolySet, possibly with the addition of an SID column if it did not already exist. The function may also reorder columns such that PID, SID, POS, X and Y appear first, in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2007-06-06

See Also

dividePolys

Convert Contour Lines into a PolySet

Description

Convert output from contourLines into a PolySet.

Usage

convCP (data, projection = NULL, zone = NULL)

Arguments

Details

data contains a list as described below. The contourLines function create a list suitable for the data argument.

A three-element list describes each contour. The named elements in this list include the scalar level, the vector x, and the vector y. Vectors x and y must have equal lengths. A higher-level list (data) contains one or more of these contours lists.

Value

A list with two named elements PolySet and PolyData. The PolySet element contains a PolySet representation of the contour lines. The PolyData element links each contour line (PID, SID) with a level.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

contour, contourLines, convLP, makeTopography.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create sample data for the contourLines() function
  x <- seq(-0.5, 0.8, length=50);  y <- x
  z <- outer(x, y, FUN = function(x,y) { sin(2*pi*(x^2+y^2))^2; } )
  data <- contourLines(x, y, z, levels=c(0.2, 0.8))
  #--- pass that sample data into convCP()
  result <- convCP(data)
  #--- plot the result
  plotLines(result$PolySet, projection=1)
  print(result$PolyData)
  par(oldpar)
})

Convert EventData/PolyData into a PolySet

Description

Convert EventData/PolyData into a PolySet.

Usage

convDP (data, xColumns, yColumns)

Arguments

Details

This function expects data to contain several X- and Y-columns. For example, consider data with columns x1, y1, x2, and y2. Suppose xColumns = c("x1", "x2") and yColumns = c("y1", "y2"). The result will contain nrow(data) polygons. Each one will have two vertices, (x1, y1) and (x2, y2) and POS values 1 and 2, respectively. If data includes an SID column, so will the result.

If data contains an EID and not a PID column, the function uses the EIDs as PIDs.

If data contains both PID and EID columns, the function assumes it is PolyData and ignores the EID column.

Value

PolySet with the same PIDs as those given in data. If data has an SID column, the result will include it.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addPoints, plotPoints.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create sample PolyData
  polyData <- data.frame(PID=c(1, 2, 3),
     x1=c(1, 3, 5), y1=c(1, 3, 2),
     x2=c(1, 4, 5), y2=c(2, 4, 1),
     x3=c(2, 4, 6), y3=c(2, 3, 1))
  #--- print PolyData
  print(polyData)
  #--- make a PolySet from PolyData
  polys <- convDP(polyData,
    xColumns=c("x1", "x2", "x3"),
    yColumns=c("y1", "y2", "y3"))
  #--- print and plot the PolySet
  print(polys)
  plotLines(polys, xlim=c(0,7), ylim=c(0,5), col=2)
  par(oldpar)
})

Convert Polylines into a Polygon

Description

Convert two polylines into a polygon.

Usage

convLP (polyA, polyB, reverse = TRUE)

Arguments

Details

The resulting PolySet contains all the vertices from polyA in their original order. If reverse = TRUE, this function appends the vertices from polyB in the reverse order (nrow(polyB):1). Otherwise, it appends them in their original order. The PID column equals the PID of polyA. No SID column appears in the result. The resulting polygon is an exterior boundary.

Value

PolySet with a single PID that is the same as polyA. The result contains all the vertices in polyA and polyB. It has the same projection and zone attributes as those in the input PolySets. If an input PolySet's attributes equal NULL, the function uses the other PolySet's. If the PolySet attributes conflict, the result's attribute equals NULL.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addLines, appendPolys, closePolys, convCP, joinPolys, plotLines.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create two polylines
  polyline1 <- data.frame(PID=rep(1,2),POS=1:2,X=c(1,4),Y=c(1,4))
  polyline2 <- data.frame(PID=rep(1,2),POS=1:2,X=c(2,5),Y=c(1,4))
  #--- create two plots to demonstrate the effect of `reverse'
  par(mfrow=c(2, 1))
  plotPolys(convLP(polyline1, polyline2, reverse=TRUE), col=2)
  plotPolys(convLP(polyline1, polyline2, reverse=FALSE), col=3)
  par(oldpar)
})

Convert Coordinates between UTM and Lon/Lat

Description

Convert coordinates between UTM and Lon/Lat.

Usage

convUL (xydata, km=TRUE, southern=NULL)

Arguments

Details

The object xydata must possess a projection attribute that identifies the current projection. If the data frame contains UTM coordinates, it must also have a zone attribute equal to a number between 1 and 60 (inclusive). If it contains geographic (longitude/latitude) coordinates and the zone attribute is missing, the function computes the mean longitude and uses that value to determine the zone. The longitude range of zone i is -186 + 6 i^\circ < x \le -180 + 6 i^\circ.

This function converts the X and Y columns of xydata from "LL" to "UTM" or vice-versa. If the data span more than one zone to the right or left of the intended central zone, the underlying algorithm may produce erroneous results. This limitation means that the user should use the most central zone of the mapped region, or allow the function to determine the central zone when converting from geographic to UTM coordinates. After the conversion, this routine adjusts the data frame's attributes accordingly.

Value

A data frame identical to xydata, except that the X and Y columns contain the results of the conversion, and the projection attribute matches the new projection.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB
Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Regional Headquarters, Vancouver BC
Last modified Rd: 2022-09-06

References

Ordnance Survey. (2020) A guide to coordinate systems in Great Britain. Copyright Ordnance Survey 2018 (v3.6). Southampton, UK.

See Also

closePolys, fixBound.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data
  data(nepacLL,envir=.PBSmapEnv)
  #--- set the zone attribute
  #--- use a zone that is most central to the mapped region
  attr(nepacLL, "zone") <- 6
  #--- convert and plot the result
  nepacUTM <- convUL(nepacLL)
  plotMap(nepacUTM)
  par(oldpar)
})

Divide a Single Polygon into Several Polygons

Description

Divide a single polygon (with several outer-contour components) into several polygons, a polygon for each outer contour, by modifying the PID and SID indices.

Usage

dividePolys (polys)

Arguments

Details

Given the input PolySet, this function renumbers the PID and SID indices so that each outer contour has a unique PID and is followed by all of its holes, identifying them with SIDs greater than one.

Value

PolySet, possibly with the addition of an SID column if it did not already exist. The function may also reorder columns such that PID, SID, POS, X and Y appear first, in that order.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2007-06-06

See Also

combinePolys.

Run PBSmapping Example Figures

Description

Run built-in example figures for PBSmapping.

Usage

.PBSfigs(nfigs=1:10, wait=TRUE)
.PBSfig01()
.PBSfig02()
.PBSfig03()
.PBSfig04()
.PBSfig05()
.PBSfig06()
.PBSfig07()
.PBSfig08()
.PBSfig09()
.PBSfig10()

Arguments

Details

The wrapper function '.PBSfigs' displays pre-defined figures from 1 to 10, depending on the numbers that the user specifies. User can also call each figure directly, e.g., '.PBSfig05()'.

Value

NULL

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB
Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Offsite, Vancouver BC
Last modified Rd: 2023-10-30

Examples

.PBSfigs(nfigs=1:3, wait=FALSE)

PBSmapping Environment

Description

An environment set aside for PBSmapping.

Usage

.PBSmapEnv

Format

A new environment with a .GlobalEnv parent.

Details

The environment is created in 'zzz.r' and can be used by PBSmodelling functions 'lisp', 'tget', 'tput', 'tprint', and 'tcall', if this package has be loaded.

Currently, '.PBSmapEnv' is only used in '.validateData' (in the namespace), and by a set of print functions specific to PBSmapping.

Source

Generated by a call to the base function new.env().

See Also

In PBSmapping:
print.EventData, print.LocationSet, print.PolyData, print.PolySet, print.summary.PBS
In PBSmodelling:
lisp, tget, packList

Add Items to Plots

Description

Routines to add various items to existing plots.

Usage

.addAxis(xlim, ylim, tckLab, tck, tckMinor, ...)
.addAxis2(side=1:2, xlim, ylim, tckLab, tck, tckMinor, ...)
.addBubblesLegend(radii.leg, usr.xdiff, usr.ydiff, symbol.zero, symbol.fg, symbol.bg,
   legend.pos, legend.breaks, legend.type, legend.title, legend.cex, ...)
.addCorners(polys, ptSummary)
.addFeature(feature, data, polyProps, isEventData, cex=NULL, col=NULL, font=NULL,
   pch=NULL, ...)
.addLabels(projection=NULL, ...)
.addProps(type, polyProps, ...)

Arguments

Details

Internal functions add features to an existing map plot.

Value

Nothing in particular.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
plotMap, addBubbles, addPolys, addLabels, addStipples

Calculate Things

Description

Calculate distance and/or orientation.

Usage

.calcDist(polys)
.calcOrientation(polys)

Arguments

Details

.calcdist : Equatorial radius 6,378.14 km; Polar radius 6,356.78 km; Mean radius 6,371.3 km

.calcOrientation : Calls C code 'calcOrientation' using .C().

Value

.calcdist : distance vector (distances between each point)

.calcOrientation : data frame with 'orientation' column (-1 when counter-clockwise; 0 when N/A; +1 when clockwise) or NULL if no rows in output

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
calcLength, placeHoles, thickenPolys

Check Stuff

Description

Auxiliary (dot) functions to check various attributes of PBmapping objects.

Usage

.checkClipLimits(limits)
.checkProjection(projectionPlot, projectionPoly)
.checkRDeps(caller="unspecified", requires=NULL)

Arguments

Details

Auxiliary dot functions to facilitate the machinations of PBSmapping.

Value

.checkClipLimits : nada; just a limit checker
.checkProjection : nada; just a projection checker
.checkRDeps : nada; just a package checker

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
.checkClipLimits used by:
importGSHHS
.checkProjection used by:
addLabels, addLines, addPoints, addPolys, addStipples
.checkRDeps used by:
calcVoronoi, importShapefile (temporarily unavailable)

Create Indices for PolySets

Description

Create indices for indexing map data structures (PolySets).

Usage

.createIDs(x, cols, fastIDdig=NULL)
.createFastIDdig(polysA, polysB=NULL, cols)
.createGridIDs(d, addSID, byrow)

Arguments

Details

.createIDs : create IDs (or IDX) column from its input.

.createFastIDdig : determine the maximum number of digits in the second column of a data frame. If given two data frames ('polysA' and 'polysB'), determine the maximum between the two data frames.

.createGridIDs : Create IDs for a grid according to the addSID and byrow arguments.

Value

.createIDs : a vector of integer or real-number indices.

.createFastIDdig : maximum number of digits to use in real-number index.

.createGridIDs : a modified grid PolySet.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-25

See Also

In package PBSmapping:
plotMap, addBubbles, addPolys, addLabels, addStipples

Fix Things

Description

Fix things like GSHHSWorld.

Usage

.fixGSHHSWorld(world)

Arguments

Details

Determine PID of Antarctica, which is used to extract the current Antarctica. The continent is rebuilt from left to right, creating a new, very wide Antarctica. It is then clipped and merged into the existing world (with other polygons).

Value

A revised PolySet of the world with a peeled version of Antarctica.

Note

This function is not called by any PBSmapping functions. It can be used after 'importGSHHS' uses ylim=c(-90,90).

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
importGSHHS, clipPolys

Examples

## Not run: 
worldLL =
importGSHHS("gshhs_l.b",xlim=c(-20,360),ylim=c(-90,90),level=1,n=15,xoff=0)
worldLL = .fixGSHHSWorld(worldLL)

## End(Not run)

Get Stuff

Description

Routines to get various attributes from PBmapping objects.

Usage

.getBasename(fn, ext)
.getGridPars(polys, fullValidation=TRUE)

Arguments

Details

Auxiliary dot functions to facilitate the machinations of PBSmapping.

Value

.getBasename : base name of a shapefile set (usually with multiple extensions).
.getGridPars : PBSmapping grid object attributes.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
importShapefile (temporarily unavailable), makeGrid, is.PolySet

Are Points in Polygons?

Description

Determines which points (EventData) are located inside a polygon (PolySet).

Usage

.is.in(events, polys, use.names=TRUE)

Arguments

Details

Taps into the PBSmapping C code for 'findPolys'.

Value

Reports events inside the polygon, outside the polygon, and whether all events are inside, outside, or on the boundary of the polygon.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-03-11

See Also

In PBSmapping:
findPolys, as.EventData, is.PolySet, findPolys

Convert Matrix to Data Frame

Description

Convert PBS matrices to data frames, preserving certain attributes.

Usage

.mat2df(data)

Arguments

Details

Converts a PBS matrix object to a PBS data frame. Preserves PBS class objects 'EventData', 'LocationSet', 'PolyData', 'PolySet', if any of them exist in the matrix.

Value

Transformed data object (from matrix to data frame).

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addPoints, .addFeature, .validateData

Validate PBSmapping Data Structures

Description

Routines to validate data structures (e.g., required field names, attributes) that are passed to package functions.

Usage

.validateData(data, className, requiredCols=NULL, requiredAttr=NULL, 
   noFactorCols=NULL, noNACols=NULL, keyCols=NULL, numericCols=NULL)
.validateEventData(EventData)
.validateLocationSet(LocationSet)
.validatePolyData(PolyData)
.validatePolyProps(polyProps, parCols=NULL)
.validatePolySet(polys)
.validateXYData(xyData)

Arguments

Details

Internal functions check the validity of data objects used by PBSmapping. The primary function is '.validateData'; other dot validate functions are wrappers for the four main data structures: 'PolySet', 'PolyData', 'EventData', and 'LocationSet'.

Value

The data object that is validated.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
PolySet, PolyData, EventData, LocationSet

Extract PolyData from a PolySet

Description

Extract PolyData from a PolySet. Columns for the PolyData include those other than PID, SID, POS, oldPOS, X, and Y.

Usage

extractPolyData (polys)

Arguments

Details

This function identifies the PolySet's extra columns and determines if those columns contain unique values for each (PID, SID). Where they do, the (PID, SID) will appear in the PolyData output with that unique value. Where they do not, the extra column will contain NAs for that (PID, SID).

Value

PolyData with columns PID, SID, and any extra columns.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

makeProps, PolyData, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  #--- create a PolySet with an extra column
  polys <- data.frame(PID = c(rep(1, 10), rep(2, 10)),
    POS = c(1:10, 1:10),
    X = c(rep(1, 10), rep(1, 10)),
    Y = c(rep(1, 10), rep(1, 10)),
    colour = (c(rep("green", 10), rep("red", 10))))
  #--- extract the PolyData
  print(extractPolyData(polys))
})

Find Grid Cells that Contain Events

Description

Find the grid cells in a PolySet that contain events specified in EventData. Similar to findPolys, except this function requires a PolySet resulting from makeGrid. This restriction allows this function to calculate the result with greater efficiency.

Usage

findCells (events, polys, includeBdry=NULL)

Arguments

Details

The resulting data frame, a LocationSet, contains the columns EID, PID, SID (if in polys), and Bdry, where an event (EID) occurs in a polygon (PID, SID). The Boolean (0,1) variable Bdry indicates whether an event lies on a polygon's edge. Note that if an event lies properly outside of all the polygons, then a record with (EID, PID, SID) does not occur in the output. It may happen, however, that an event occurs in multiple polygons (i.e., on two or more boundaries). Thus, the same EID can occur more than once in the output.

If an event happens to lie at the boundary intersection of four (or two) grid cells then one EID will be associated with four (or two) grid cells. A user can choose to manipulate this result by setting the argument includeBdry to a numeric value that constrains the association of a boundary event to 0 or 1 grid cell (see argument description above).

Value

LocationSet that links events with polygons.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2014-12-15

See Also

findPolys, makeGrid, combineEvents, locateEvents, locatePolys, LocationSet.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create some EventData: points in a diagonal line
  events <- data.frame(EID=1:11, X=seq(0, 2, length=11),
     Y=seq(0, 2, length=11))
  events <- as.EventData(events, projection=1);
  #--- create a PolySet (a grid)
  polys <- makeGrid (x=seq(0, 2, by=0.50), y=seq(0, 2, by=0.50), projection=1)
  #--- show a picture
  plotPolys(polys, xlim=range(polys$X)+c(-0.1, 0.1),
    ylim=range(polys$Y)+c(-0.1, 0.1), projection=1)
  addPoints(events, col=2)
  #--- run findCells and print the results
  fc <- findCells(events, polys)
  fc <- fc[order(fc$EID, fc$PID, fc$SID), ]
  fc$label <- paste(fc$PID, fc$SID, sep=", ")
  print (fc)
  #--- add labels to the graph
  addLabels(as.PolyData(fc[!duplicated(paste(fc$PID,fc$SID)), ],
    projection=1), placement="CENTROID", 
    polys=as.PolySet(polys, projection=1), col=4)
  par(oldpar)
})

Find Polygons that Contain Events

Description

Find the polygons in a PolySet that contain events specified in EventData.

Usage

findPolys (events, polys, maxRows = 1e+05, includeBdry=NULL)

Arguments

Details

The resulting data frame, a LocationSet, contains the columns EID, PID, SID (if in polys), and Bdry, where an event (EID) occurs in a polygon (PID, SID) and SID does not correspond to an inner boundary. The Boolean variable Bdry indicates whether an event lies on a polygon's edge. Note that if an event lies properly outside of all the polygons, then a record with (EID, PID, SID) does not occur in the output. It may happen, however, that an event occurs in multiple polygons. Thus, the same EID can occur more than once in the output.

If an event happens to lie at the boundary intersection of two or more polygons then one EID will be associated with two or more polygons. A user can choose to manipulate this result by setting the argument includeBdry to a numeric value that constrains the association of a boundary event to 0 or 1 polygon (see argument description above).

Value

LocationSet that links events with polygons.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2014-12-15

See Also

combineEvents, findCells, locateEvents, locatePolys, LocationSet, makeGrid.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create some EventData: a column of points at X = 0.5
  events <- data.frame(EID=1:10, X=.5, Y=seq(0, 2, length=10))
  events <- as.EventData(events, projection=1)
  #--- create a PolySet: two squares with the second above the first
  polys <- data.frame(PID=c(rep(1, 4), rep(2, 4)), POS=c(1:4, 1:4),
    X=c(0, 1, 1, 0, 0, 1, 1, 0),
    Y=c(0, 0, 1, 1, 1, 1, 2, 2))
  polys <- as.PolySet(polys, projection=1)
  #--- show a picture
  plotPolys(polys, xlim=range(polys$X)+c(-0.1, 0.1),
    ylim=range(polys$Y)+c(-0.1, 0.1), projection=1);
  addPoints(events, col=2);
  #--- run findPolys and print the results
  print(findPolys(events, polys))
  par(oldpar)
})

Fix the Boundary Points of a PolySet

Description

The ranges of a PolySet's X and Y columns define its boundary. This function fixes a PolySet's vertices by moving vertices near a boundary to the actual boundary.

Usage

fixBound (polys, tol)

Arguments

Details

When moving vertices to a boundary, the function moves them strictly horizontally or vertically, as appropriate.

Value

PolySet identical to the input, except for possible changes in the X and Y columns.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

closePolys, fixPOS, isConvex, isIntersecting, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- set up a long horizontal and long vertical line to extend the plot's
  #--- limits, and then try fixing the bounds of a line in the top-left
  #--- corner and a line in the bottom-right corner
  polys <- data.frame(PID=c(1, 1, 2, 2,  3, 3, 4, 4),
    POS=c(1, 2, 1, 2,  1, 2, 1, 2),
    X = c(0, 10, 5, 5, 0.1, 4.9, 5.1, 9.9),
    Y = c(5, 5, 0, 10, 5.1, 9.9, 0.1, 4.9))
  polys <- fixBound(polys, tol=0.0100001)
  plotLines(polys)
  par(oldpar)
})

Fix the POS Column of a PolySet

Description

Fix the POS column of a PolySet by recalculating it using sequential integers.

Usage

fixPOS (polys, exteriorCCW = NA)

Arguments

Details

This function recalculates the POS values of each (PID, SID) as either 1 to N or N to 1, depending on the order of POS (ascending or descending) in the input data. POS values in the input must be properly ordered (ascending or descending), but they may contain fractional values. For example, POS = 2.5 might correspond to a point manually added between POS = 2 and POS = 3. If exteriorCCW = NA, all other columns remain unchanged. Otherwise, it orders the X and Y columns according to exteriorCCW.

Value

PolySet with the same columns as the input, except for possible changes to the POS, X, and Y columns.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

closePolys, fixBound, isConvex, isIntersecting, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  #--- create a PolySet with broken POS numbering
  polys <- data.frame(PID = c(rep(1, 10), rep(2, 10)),
    POS = c(seq(2, 10, length = 10), seq(10, 2, length = 10)),
    X = c(rep(1, 10), rep(1, 10)),
    Y = c(rep(1, 10), rep(1, 10)))
  #--- fix the POS numbering
  polys <- fixPOS(polys)
  #--- print the results
  print(polys)
})

Import EventData from a Text File

Description

Import a text file and convert into EventData.

Usage

importEvents(EventData, projection=NULL, zone=NULL)

Arguments

Value

An imported EventData.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2023-10-30

See Also

importPolys, importLocs, importGSHHS

Import Data from a GSHHS Database

Description

Import data from a GSHHS database and convert data into a PolySet with a PolyData attribute. The database was originally called ‘Global Self-consistent, Hierarchical, High-resolution Shoreline’ (GSHHS, Wessel and Smith 1996), but ‘Shoreline’ was subsequently expanded to include more ‘Geography’ (GSHHG).

Usage

importGSHHS(gshhsDB, xlim, ylim, maxLevel=4, n=0, useWest=FALSE)

Arguments

Details

This routine requires a binary GSHHG (Global Self-consistent, Hierarchical, High-resolution Geography) database file. The GSHHG database has been released in the public domain.
(www.soest.hawaii.edu/pwessel/gshhg)
At the time of writing, the most recent binary database was the archive file called gshhg-bin-2.3.7.zip.

The archive contains multiple binary files that contain geographical coordinates for shorelines (gshhs), rivers (wdb_rivers), and borders (wdb_borders). The latter two come from World DataBank II (WDBII). The five resolutions available are: full (f), high (h), intermediate (i), low (l), and coarse (c).

This routine returns a PolySet object with an associated PolyData attribute. The attribute contains four fields: (a) PID, (b) SID, (c) Level, and (d) Source. Each record corresponds to a line/polygon in the PolySet. The Level indicates the line's/polygon's level (1=land, 2=lake, 3=island, 4=pond). The Source identifies the data source (1=WVS, 0=CIA (WDBII)).

Value

A PolySet with a PolyData attribute.

Note

The function calls a C routine, also called importGSHHS, which returns a set of map coordinates that is not always predictably laid out. This issue stems from how the world is divided at the Greenwich meridian and at the International Date Line. The unpredictability occurs when user-specified X-limits span either of the longitudinal meridians – (0^\circ, 360^\circ) or (-180^\circ, 180^\circ).

This version of the R function attempts to stitch together the overlapping edges of gshhs that run from -20^\circ to 360^\circ (see example map 5 below). At present, no attempt has been made to deal with the overlap at the International Date Line where Russia overlaps the Aleutian Islands of Alaska. To some extent, the C-code can deal with this, but not in all cases.

Therefore, the user will likely experience some limitations when using importGSHHS. The solution is to import the whole dataset with this function using xlim=c(0,360), and then apply the function refocusWorld with user-desired X-limits. The Y-limits are generally not problematic unless the user wants to focus on either pole.

Author(s)

Nicholas M. Boers, Senior Software Engineer
Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Offsite, Vancouver BC
Last modified Rd: 2024-09-25

References

Wessel, P., and Smith, W.H.F. (1996) A Global Self-consistent, Hierarchical, High-resolution Shoreline Database. J. Geophys. Res. 101 8741-8743.
(www.soest.hawaii.edu/pwessel/gshhg/Wessel+Smith_1996_JGR.pdf)

See Also

In package PBSmapping:
importEvents, importLocs, importPolys

Examples

## Not run: 
useWest=FALSE
useVers=c("2.2.0","2.2.3","2.3.0","2.3.4") # GSHHG versions
mapswitch = 5
for (i in c("land","rivers","borders"))
  if (exists(i)) eval(parse(text=paste0("rm(",i,")")))
switch( mapswitch,
 # 1. Canada------------------------------------------------
      {vN=4; useWest=T; xlim=c(-150,-50)+360;ylim=c(40,75)},
 # 2. NW Canada & America-----------------------------------
      {vN=4; useWest=T;xlim=c(-136,-100)+360;ylim=c(40,75)},
 # 3. Black Sea (user Ivailo)-------------------------------
      {vN=4; xlim=c(27.5, 34.3); ylim=c(40.9, 46.7)},
 # 4. W Europe, NW Africa (user Uli)------------------------
      {vN=4; xlim=c(-20,10); ylim=c(20,50)},
 # 5. W Europe + Iceland------------------------------------
      {vN=4; xlim=c(-25, 20); ylim=c(40, 68)},
 # 6. New Zealand-------------------------------------------
      {vN=4; xlim=c(163, 182); ylim=c(-48,-34)},
 # 7. Australia---------------------------------------------
      {vN=4; xlim=c(112,155); ylim=c(-44,-10)},
 # 8. Japan-------------------------------------------------
      {vN=4; xlim=c(127,148); ylim=c(30,47)},
 # 9. Central America---------------------------------------
      {vN=4; useWest=T; xlim=c(-95,-60)+360;ylim=c(-10,25)},
 #10. North Pacific-----------------------------------------
      {vN=4; useWest=T; xlim=c(150,220); ylim=c(45,80)},
 #11. Pacific Ocean-----------------------------------------
      {vN=4; xlim=c(112,240); ylim=c(-48,80)},
 #12. North Atlantic (world coordinates)--------------------
      {vN=4; xlim=c(285,360); ylim=c(40,68)},
 #13. North Atlantic (western hemisphere coordinates)-------
      {vN=4; xlim=c(-75,0); ylim=c(40,68)},
 #14. Atlantic Ocean----------------------------------------
      {vN=4; xlim=c(285,380); ylim=c(-50,68)},
 #15. Northern hemisphere-----------------------------------
      {vN=4; xlim=c(-180,180); ylim=c(0,85)},
 #16. Asia--------------------------------------------------
      {vN=4; xlim=c(0,180); ylim=c(0,80)},
 #17. North America-----------------------------------------
      {vN=4; xlim=c(-180,0); ylim=c(0,80)},
 #18. International date line-------------------------------
      {vN=4; xlim=c(45,315); ylim=c(0,80)},
 #19. Indian Ocean------------------------------------------
      {vN=4; xlim=c(20,130); ylim=c(-40,40)},
 #20. Moose County ("400 miles north of everywhere")--------
      {vN=4; xlim=c(272.5,280.5); ylim=c(43,47.5)}
)
db=paste0("gshhg-bin-",useVers[vN])        # database version folder
gshhg   = paste0("C:/Ruser/GSHHG/",db,"/") # directory with binary files
land    = importGSHHS(paste0(gshhg,"gshhs_i.b"),
          xlim=xlim,ylim=ylim,maxLevel=4,useWest=useWest)
rivers  = importGSHHS(paste0(gshhg,"wdb_rivers_i.b"),
          xlim=xlim,ylim=ylim,useWest=useWest)
borders = importGSHHS(paste0(gshhg,"wdb_borders_i.b"),
          xlim=xlim,ylim=ylim,useWest=useWest,maxLevel=1)
if(exists("land")){
  plotMap(land,xlim=xlim-ifelse(useWest,360,0),ylim=ylim,
    col="lemonchiffon",bg="aliceblue")
  if(!is.null(rivers)) addLines(rivers,col="blue")
  if(!is.null(borders)) addLines(borders,col="red",lwd=2)
}

## End(Not run)

Import LocationSet from Text File

Description

Import a text file and convert it into a LocationSet.

Usage

importLocs(LocationSet)

Arguments

Value

An imported LocationSet.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2023-10-30

See Also

importPolys, importEvents, importGSHHS

Import PolySet from Text File

Description

Import a text file and convert it into a PolySet with optional PolyData attribute.

Usage

importPolys(PolySet, PolyData=NULL, projection=NULL, zone=NULL)

Arguments

Value

An imported PolySet with optional PolyData attribute.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2023-10-30

See Also

importEvents, importLocs, importGSHHS

Determine Whether Polygons are Convex

Description

Determine whether polygons found in a PolySet are convex.

Usage

isConvex (polys)

Arguments

Details

Convex polygons do not self-intersect. In a convex polygon, only the first and last vertices may share the same coordinates (i.e., the polygons are optionally closed).

The function does not give special consideration to holes. It returns a value for each unique (PID, SID), regardless of whether a contour represents a hole.

Value

PolyData with columns PID, SID (may be missing), and convex. Column convex contains Boolean values.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

isIntersecting, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- calculate then print the polygons that are convex
  p <- isConvex(nepacLL);
  #--- nepacLL actually contains no convex polygons
  print(p[p$convex,])
})

Determine Whether Polygons are Self-Intersecting

Description

Determine whether polygons found in a PolySet are self-intersecting.

Usage

isIntersecting (polys, numericResult = FALSE)

Arguments

Details

When numericResult = TRUE, this function counts intersections as the algorithm processes them. It counts certain types (i.e., those involving vertices and those where an edge retraces over an edge) more than once.

The function does not give special consideration to holes. It returns a value for each unique (PID, SID), regardless of whether a contour represents a hole.

Value

PolyData with columns PID, SID (may be missing), and intersecting. If numericResult is TRUE, intersecting contains the number of intersections. Otherwise, it contains a Boolean value.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

isConvex, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
  data(nepacLL,envir=.PBSmapEnv)
  #--- calculate then print the polygons that are self-intersecting
  p <- isIntersecting(nepacLL, numericResult = FALSE)
  print(p[p$intersecting,])
})

Join One or Two PolySets using a Logic Operation

Description

Join one or two PolySets using a logic operation.

Usage

joinPolys(polysA, polysB=NULL, operation="INT")

Arguments

Details

This function interfaces with the first version of the Clipper Library, specifically version 6.2.1 released 2014-10-31, developed by Angus Johnson. Angus now offers Clipper 2 Library. Prior to 2013-03-23, 'joinPolys' used the General Polygon Clipper library by Alan Murta at the University of Manchester. We keep this historic reference to GPC because 'joinPolys' remains faithful to Murta's definition of a generic polygon, which we describe below.

Murta (2004) defines a generic polygon (or polygon set) as zero or more disjoint boundaries of arbitrary configuration. He relates a boundary to a contour, where each may be convex, concave or self-intersecting. In a PolySet, the polygons associated with each unique PID loosely correspond to a generic polygon, as they can represent both inner and outer boundaries. Our use of the term generic polygon includes the restrictions imposed by a PolySet. For example, the polygons for a given PID cannot be arranged arbitrarily.

If 'polysB' is NULL, this function sequentially applies the logic 'operation' between the generic polygons in 'polysA'. For example, suppose 'polysA' contains three generic polygons (A, B, C). The function outputs the PolySet containing ((A op B) op C).

If 'polysB' is not NULL, this function applies the logic 'operation' between each generic polygon in 'polysA' and each one in 'polysB'. For example, suppose 'polysA' contains two generic polygons (A, B) and 'polysB' contains two generic polygons (C, D). The function's output is the concatenation of A op C, B op C, A op D, B op D, with PIDs 1 to 4, respectively. Generally there are n times m comparisons, where n = number of polygons in 'polysA' and m = number of polygons in 'polysB'. If 'polysB' contains only one generic polygon, the function maintains the PIDs from 'polysA'. It also maintains them when 'polysA' contains only one generic polygon and the 'operation' is "DIFF" (difference). Otherwise, if 'polysA' contains only one generic polygon, it maintains the PIDs from 'polysB'.

Value

If 'polysB' is NULL, the resulting PolySet contains a single generic polygon (one PID), possibly with several components (SIDs). The function recalculates the PID and SID columns.

If 'polysB' is not NULL, the resulting PolySet contains one or more generic polygons (PIDs), each with possibly several components (SIDs). The function recalculates the SID column, and depending on the input, it may recalculate the PID column.

Author(s)

C code: Angus Johnson, Computer Programmer

Implementation: Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

References

Murta, A. (2004) A General Polygon Clipping Library. Accessed: Jul 29, 2004.

Johnson, A. (2014) Clipper – an open source freeware library for clipping and offsetting lines and polygons. Accessed: Oct 31, 2014.

See Also

In package PBSmapping:
addPolys, appendPolys, clipPolys, closePolys, fixBound, fixPOS, locatePolys, plotMap, plotPoints, thickenPolys, thinPolys

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)

  ### Example 1. Cut a triangle out of Vancouver Island
  par(mfrow=c(1,1))
  #--- create a triangle to use in clipping
  polysB <- data.frame(PID=rep(1, 3), POS=1:3,
    X=c(-127.5, -124.5, -125.6), Y = c(49.2, 50.3, 48.6))
  #--- intersect nepacLL with the single polygon, and plot the result
  plotMap(joinPolys(nepacLL, polysB), col="cyan")
  #--- add nepacLL in a different line type to emphasize the intersection
  addPolys(nepacLL, border="purple", lty=3, density=0)
  box()

  ### Example 2. Cut Texada and Lasqueti Islands out of Boxes
  xlim = list(box1=c(-124.8,-124),box2=c(-124,-123.9))
  ylim = list(box1=c(49.4,49.85), box2=c(49.85,49.9))
  Xlim = extendrange(xlim); Ylim=extendrange(ylim)
  polyA = as.PolySet(data.frame(
    PID = rep(1:2,each=4), POS = rep(1:4,2),
    X = as.vector(sapply(xlim,function(x){x[c(1,1,2,2)]})),
    Y = as.vector(sapply(ylim,function(x){x[c(1,2,2,1)]}))
    ), projection="LL")
  data(nepacLLhigh,envir=.PBSmapEnv)
  polyB = nepacLLhigh[is.element(nepacLLhigh$PID,c(736,1912)),]
  polyC = joinPolys(polyA, polyB, "DIFF")
  par(mfrow=c(2,2),cex=1,mgp=c(2,0.5,0))
  plotMap(polyA,col="lightblue",xlim=Xlim,ylim=Ylim)
  addPolys(polyB,col="gold");
  text(mean(Xlim)-0.05,Ylim-0.04,"Boxes (A,B)  and  Isles (C,D)")
  labs = calcCentroid(polyA)
  labs[1,c("X","Y")] = labs[2,c("X","Y")]+c(-0.1,-0.05)
  text(labs[,"X"],labs[,"Y"],c("A","B"),font=2)
  plotMap(polyC[is.element(polyC$PID,1),],col="pink",xlim=Xlim,ylim=Ylim)
  text(mean(Xlim)-0.05,Ylim-0.04,"Box A  \"DIFF\"  Isle C")
  plotMap(polyC[is.element(polyC$PID,3),],col="green",xlim=Xlim,ylim=Ylim)
  text(mean(Xlim)-0.05,Ylim-0.04,"Box A  \"DIFF\"  Isle D")
  plotMap(polyC[is.element(polyC$PID,c(1,3)),],col="cyan",xlim=Xlim,ylim=Ylim)
  text(mean(Xlim)-0.05,Ylim-0.04,"Box A  \"DIFF\"  Isles (C,D)")
  par(oldpar)
})

Locate Events on the Current Plot

Description

Locate events on the current plot (using the locator function).

Usage

locateEvents (EID, n = 512, type = "p", ...)

Arguments

Details

This function allows its user to define events with mouse clicks on the current plot via the locator function. The arguments n and type are the usual parameters of the locator function. If EID is not missing, then n = length(EID).

On exit from locator, suppose the user defined m events. If EID was missing, then the output data frame will contain m events. However, if EID exists, then the output data frame will contain length(EID) events, and both X and Y will be NA for events EID[(m+1):n]. The na.omit function can remove rows with NAs.

Value

EventData with columns EID, X, and Y, and projection attribute equal to the map's projection. The function does not set the zone attribute.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2007-06-06

See Also

addPoints, combineEvents, convDP, EventData, findCells, findPolys, plotPoints.

Examples

#--- define five events on the current plot, numbering them 10 to 14
## Not run: events <- locateEvents(EID = 10:14)

Locate Polygons on the Current Plot

Description

Locate polygons on the current plot (using the locator function).

Usage

locatePolys (pdata, n = 512, type = "o", ...)

Arguments

Details

This function allows its user to define polygons with mouse clicks on the current plot via the locator function. The arguments n and type are the usual parameters for the locator function, but the user can specify them for each individual (PID, SID) in a pdata object.

If a pdata object exists, the function ignores columns other than PID, SID, n, and type. If pdata includes n, then an outer boundary has n > 0 and an inner boundary has n < 0.

On exit from locator, suppose the user defined m vertices for a given polygon. For that polygon, the X and Y columns will contain NAs where POS = (m+1):n for outer-boundaries and POS = (|n|-m):1 for inner-boundaries. The na.omit function can remove rows with NAs.

If a pdata object does not exist, the output contains only one polygon with a PID equal to 1. One inner-boundary polygon (POS goes from n to 1) can be generated by supplying a negative n.

If type = "o" or type = "l", the function draws a line connecting the last and first vertices.

Value

PolySet with projection attribute equal to the map's projection. The function does not set the zone attribute.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2007-06-06

See Also

addPolys, appendPolys, clipPolys, closePolys, findCells, findPolys, fixPOS, joinPolys, plotMap, plotPolys, thickenPolys, thinPolys.

Examples

#--- define one polygon with up to 5 vertices on the current plot
## Not run: polys <- locatePolys(n = 5)

Make a Grid of Polygons

Description

Make a grid of polygons, using PIDs and SIDs according to the input arguments.

Usage

makeGrid(x, y, byrow=TRUE, addSID=TRUE, 
   projection=NULL, zone = NULL, type="rectangle")

Arguments

Details

This function makes a grid of polygons, labeling them according to byrow and addSID.

For rectangular tesselations (grid cells), the variables i and j indicate column and row numbers, respectively, where the lower-left cell of the grid is (1, 1):

• byrow = TRUE and addSID = FALSE implies PID = i + (j - 1) \times (m - 1)

• byrow = FALSE and addSID = FALSE implies PID = j + (i - 1) \times (n - 1)

• byrow = TRUE and addSID = TRUE implies PID = i, SID = j

• byrow = FALSE and addSID = TRUE implies PID = j, SID = i

For hexagonal tesselations (grid cells), i indicates columns for flat-topped hexagons and rows for pointy-topped hexagons. The reverse is true for j. Stemming from their six-sided nature, hexagons will adjoin along a long-edge by row when their orientation is such that one vertex is higher than all the others. Hexagons will adjoin along a long-edge by column when their orientation shows two uppermost vertices.

Value

PolySet with columns PID, SID (if addSID=TRUE), POS, X, and Y.
The PolySet is a set of rectangular grid cells when type='rectangle', with vertices:
(x_{i}, y_{j}), (x_{i+1}, y_{j}), (x_{i+1}, y_{j+1}), (x_{i}, y_{j+1}).
The PolySet is a set of hexagonal grid cells when type='hexagon'.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Institute of Ocean Sciences (IOS), Sidney BC
Last modified Rd: 2019-01-04

See Also

addPolys, clipPolys, combineEvents, findCells, findPolys, thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  ##--- make a 10 x 10 grid
  polyGrid <- makeGrid(x=0:10, y=0:10)
  ##--- plot the grid
  plotPolys(polyGrid, density=0, projection=1)
  par(oldpar)
})

Make Polygon Properties

Description

Append a column for a polygon property (e.g., border or lty) to PolyData based on measurements in the PolyData's Z column.

Usage

makeProps(pdata,breaks,propName="col",propVals=1:(length(breaks)-1))

Arguments

Details

This function acts like the cut function to produce PolyData suitable for the polyProps plotting argument (see addLabels, addLines, addPoints, addPolys, addStipples, plotLines, plotMap,plotPoints, and plotPolys). The Z column of pdata is equivalent to the data vector x of the cut function.

Value

PolyData with the same columns as pdata plus an additional column propName.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addLabels, addLines, addPoints, addPolys, addStipples, plotLines, plotMap, plotPoints, plotPolys, PolyData, PolySet.

Examples

local(envir=.PBSmapEnv,expr={
  #--- create a PolyData object
  pd <- data.frame(PID=1:10, Z=1:10)

  #--- using 3 intervals, create a column named `col' and populate it with
  #--- the supplied values
  makeProps(pdata=pd, breaks=3, propName="col", propVals=c(1:3))
})

Make Topography Data from Online Source

Description

Make topography data suitable for the 'graphics::contour' and 'grDevices::contourLines' functions using freely available global seafloor topography data.

Usage

makeTopography (dat, digits=2, func=NULL)

Arguments

Details

Suitable data can be obtained through the Topex acquisition form. The function 'utils::read.table' will import dowloaded ASCII files into R, creating objects suitable for the argument 'dat' in 'makeTopography'.

When creating data for regions with longitude values spanning -180^\circ to 0^\circ, consider subtracting 360 from the result's longitude coordinates (x).

When creating bathymetry data, consider negating the result's elevations (z) to give depths positive values.

Combinations of (x,y) do not need to be complete (z[x,y]=NA) or unique (z[x,y] = func(z[x,y])).

Value

List with elements x, y, and z. Elements x and y are vectors, while z is a matrix with rownames x and colnames y. The functions 'graphics::contour' and 'grDevices::contourLines' expect data conforming to this list format.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Institute of Ocean Sciences (IOS), Sidney BC
Last modified Rd: 2021-01-11

See Also

In package graphics:
contour
In package grDevices:
contourLines
In package PBSmapping:
convCP

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- Example 1: Sample data frame and conversion.
  file <- data.frame(X=c(1,1,2,2),Y=c(3,4,3,4),Z=c(5,6,7,8))
  print(makeTopography(file))

  #--- Example 2: Aleutian Islands bathymetry
  isob <- c(100,500,1000,2500,5000)
  icol <- rgb(0,0,seq(255,100,len=length(isob)),max=255)
  afile <- paste(system.file(package="PBSmapping"),
    "/Extra/aleutian.txt",sep="")
  aleutian <- read.table(afile, header=FALSE, col.names=c("x","y","z"))
  aleutian$x <- aleutian$x - 360
  aleutian$z <- -aleutian$z
  alBathy <- makeTopography(aleutian)
  alCL <- contourLines(alBathy,levels=isob)
  alCP <- convCP(alCL)
  alPoly <- alCP$PolySet
  attr(alPoly,"projection") <- "LL"
  plotMap(alPoly, type="n", cex.axis=1.2, cex.lab=1.5)
  addLines(alPoly,col=icol)
  data(nepacLL,envir=.PBSmapEnv)
  addPolys(nepacLL,col="gold")
  legend(x="topleft",bty="n",col=icol,lwd=2,legend=as.character(isob))
  par(oldpar)
})

Data: Shorelines of the NE Pacific Ocean and of the World

Description

PolySet of polygons for the shorelines of the northeast Pacific Ocean and of the world, both in normal and high resolution.

Usage

  data(nepacLL)
  data(nepacLLhigh)
  data(worldLL)
  data(worldLLhigh)

Format

Data frame consisting of 4 columns: PID = primary polygon ID, POS = position of each vertex within a given polygon, X = longitude coordinate, and Y = latitude coordinate. Attributes: projection = "LL".

Note

In R, the data must be loaded using the data function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2023-10-30

Source

Polygon data from the GSHHG (Global Self-consistent, Hierarchical, High-resolution Geography) Database.
Download the native binary files of shoreline polygons, rivers, and borders contained in the latest zip archive (version 2.3.4 ) at
(www.soest.hawaii.edu/pwessel/gshhg).

nepacLL <- importGSHHS("gshhs_h.b", xlim=c(-190,-110), ylim=c(34,72), 
           level=1, n=15, xoff=-360)

nepacLLhigh <- importGSHHS("gshhs_f.b", xlim=c(-190,-110),
               ylim=c(34,72), level=1, n=0, xoff=-360)
nepacLLhigh <- thinPolys(nepacLLhigh, tol=0.1, filter=3)

worldLL <- importGSHHS("gshhs_l.b", xlim=c(-20,360), ylim=c(-90,90), 
           level=1, n=15, xoff=0)
worldLL <- PBSmapping:::.fixGSHHSWorld(worldLL)

worldLLhigh <- importGSHHS("gshhs_i.b", xlim=c(-20,360),
               ylim=c(-90,90), level=1, n=15, xoff=0)
worldLLhigh <- PBSmapping:::.fixGSHHSWorld(worldLLhigh)

References

Wessel, P. and Smith, W.H.F. (1996) A global, self-consistent, hierarchical, high-resolution shoreline database. Journal of Geophysical Research 101, 8741–8743.
(www.soest.hawaii.edu/pwessel/gshhg/Wessel+Smith_1996_JGR.pdf)

See Also

Data:
bcBathymetry, surveyData, towData

Functions:
importGSHHS, plotMap, plotPolys, addPolys, clipPolys, refocusWorld, thickenPolys, thinPolys

Place Holes Under Solids

Description

Place secondary polygons identified as holes (inner contours) under primary polygons identified as solids (outer contours) if the vertices of the holes lie completely within the vertices of the solids. This operation is performed for each primary polygon until all holes have been assigned.

Usage

placeHoles(polyset, minVerts=3, 
   orient=FALSE, show.progress=FALSE, unique.pid=FALSE)

Arguments

Details

The algorithm identifies outer contours (solids) and inner contours (holes) using either the default PBSmapping method (solids = increasing "POS", holes = decreasing "POS") or the rotational direction of the polygons (solids = clockwise, holes = counter-clockwise).

It then systematically starts matching holes with solids based on their vertices being completely within the boundaries of the solid. If a hole happens to match a current solid completley (all vertices on the boundary), then the hole is not matched to this solid because it is a hole in another solid that creates space for the current solid.

To facilitate computation, the algorithm assumes that once a hole is located in a solid, it will not occur in any other solid. This means that for each successive solid, the number of candidate holes will either decrease or stay the same.

This function makes use of the PBSmapping hidden function ".is.in" which uses the C code "findPolys". The latter only returns events found in a polygon (or on the boundary) but .is.in evaluates all events and returns a list containing:
"e.in" – events within the polygon,
"e.out" – events outside the polygon,
"all.in" – logical value of whether all events are in the polygon,
"all.out" – logical value of whether all events are outside the polygon,
"all.bdry" – logical value of whether all events occur on the boundary of the polygon

Value

Returns the input PolySet where holes have been arranged beneath appropriate solids for each PID (original or redefined).

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Offsite, Vancouver BC
Last modified Rd: 2023-10-30

See Also

In package PBSmapping:
findPolys, is.PolySet, dot-is.in

Plot a PolySet as Polylines

Description

Plot a PolySet as polylines.

Usage

plotLines (polys, xlim = NULL, ylim = NULL, projection = FALSE,
           plt = c(0.11, 0.98, 0.12, 0.88), polyProps = NULL,
           lty = NULL, col = NULL, bg = 0, axes = TRUE,
           tckLab = TRUE, tck = 0.014, tckMinor = 0.5 * tck, ...)

Arguments

Details

This function plots a PolySet, where each unique (PID, SID) describes a polyline. It does not connect each polyline's last vertex to its first. Unlike plotMap, the function ignores the aspect ratio. It clips polys to xlim and ylim before plotting.

The function creates a blank plot when polys equals NULL. In this case, the user must supply both xlim and ylim arguments. Alternatively, it accepts the argument type = "n" as part of ..., which is equivalent to specifying polys = NULL, but requires a PolySet. In both cases, the function's behaviour changes slightly. To resemble the plot function, it plots the border, labels, and other parts according to par parameters such as col.

For additional help on the arguments lty and col, please see par.

Value

PolyData consisting of the PolyProps used to create the plot.

Note

To satisfy the aspect ratio, this plotting routine resizes the plot region. Consequently, par parameters such as plt, mai, and mar will change. When the function terminates, these changes persist to allow for additions to the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addLines, calcLength, clipLines, closePolys, convLP, fixBound, fixPOS,

locatePolys, thinPolys, thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a PolySet to plot
  polys <- data.frame(PID=rep(1,4),POS=1:4,X=c(0,1,1,0),Y=c(0,0,1,1))
  #--- plot the PolySet
  plotLines(polys, xlim=c(-.5,1.5), ylim=c(-.5,1.5))
  par(oldpar)
})

Plot a PolySet as a Map

Description

Plot a PolySet as a map, using the correct aspect ratio.

Usage

plotMap(polys, xlim = NULL, ylim = NULL, projection = TRUE,
        plt = c(0.11, 0.98, 0.12, 0.88), polyProps = NULL,
        border = NULL, lty = NULL, col = NULL, colHoles = NULL,
        density = NA, angle = NULL, bg = 0, axes = TRUE,
        tckLab = TRUE, tck = 0.014, tckMinor = 0.5 * tck, ...)

.plotMaps(polys, xlim, ylim, projection, plt, polyProps,
          border, lty, col, colHoles, density, angle, bg,
          axes, tckLab, tck, tckMinor, isType, ...)

.initPlotRegion(projection, xlim, ylim, plt)

Arguments

Details

This function plots a PolySet, where each unique (PID, SID) describes a polygon. It connects each polygon's last vertex to its first. The function supports both borders (border, lty) and fills (col, density, angle). When supplied with the appropriate arguments, it can draw only borders or only fills . Unlike plotLines and plotPolys, it uses the aspect ratio supplied in the projection attribute of polys. If this attribute is missing, it attempts to use its projection argument. In the absence of both, it uses a default aspect ratio of 1:1. It clips polys to xlim and ylim before plotting.

The function creates a blank plot when polys equals NULL. In this case, the user must supply both xlim and ylim arguments. Alternatively, it accepts the argument type = "n" as part of ..., which is equivalent to specifying polys = NULL, but requires a PolySet. In both cases, the function's behaviour changes slightly. To resemble the plot function, it plots the border, labels, and other parts according to par parameters such as col.

For additional help on the arguments border, lty, col, density, and angle, please see polygon and par.

Value

PolyData consisting of the PolyProps used to create the plot.

Note

To satisfy the aspect ratio, this plotting routine resizes the plot region. Consequently, par parameters such as plt, mai, and mar will change. When the function terminates, these changes persist to allow for additions to the plot.

Auxiliary dot function '.initPlotRegion' initialises the plot region, accounting for the aspect ratio.

Author(s)

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-09-03

See Also

In package PBSmapping:
addLabels, addPolys, addStipples, clipPolys, closePolys, fixBound, fixPOS, locatePolys, plotLines, plotPoints, thinPolys, thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a PolySet to plot
  polys <- data.frame(PID=rep(1,4),POS=1:4,X=c(0,1,1,0),Y=c(0,0,1,1))
  #--- plot the PolySet
  plotMap(polys,xlim=c(-.5,1.5),ylim=c(-.5,1.5),density=0,projection=1)
  par(oldpar)
})

Plot EventData/PolyData as Points

Description

Plot EventData/PolyData, where each unique EID or (PID, SID) describes a point.

Usage

plotPoints (data, xlim = NULL, ylim = NULL, projection = FALSE,
            plt = c(0.11, 0.98, 0.12, 0.88), polyProps = NULL,
            cex = NULL, col = NULL, pch = NULL, axes = TRUE,
            tckLab = TRUE, tck = 0.014, tckMinor = 0.5 * tck, ...)

Arguments

Details

This function clips data to xlim and ylim before plotting. It only adds PolyData containing X and Y columns.

The function creates a blank plot when polys equals NULL. In this case, the user must supply both xlim and ylim arguments. Alternatively, it accepts the argument type = "n" as part of ..., which is equivalent to specifying polys = NULL, but requires a PolySet. In both cases, the function's behaviour changes slightly. To resemble the plot function, it plots the border, labels, and other parts according to par parameters such as col.

For additional help on the arguments cex, col, and pch, please see par.

Value

PolyData consisting of the PolyProps used to create the plot.

Note

To satisfy the aspect ratio, this plotting routine resizes the plot region. Consequently, par parameters such as plt, mai, and mar will change. When the function terminates, these changes persist to allow for additions to the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addPoints, combineEvents, convDP, findPolys, locateEvents.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,surveyData,envir=.PBSmapEnv)
  #--- plot a map
  plotMap(nepacLL, xlim=c(-136, -125), ylim=c(48, 57))
  #--- add events
  addPoints(surveyData, col=1:7)
  par(oldpar)
})

Plot a PolySet as Polygons

Description

Plot a PolySet as polygons.

Usage

plotPolys (polys, xlim = NULL, ylim = NULL, projection = FALSE,
           plt = c(0.11, 0.98, 0.12, 0.88), polyProps = NULL,
           border = NULL, lty = NULL, col = NULL, colHoles = NULL,
           density = NA, angle = NULL, bg = 0, axes = TRUE,
           tckLab = TRUE, tck = 0.014, tckMinor = 0.5 * tck, ...)

Arguments

Details

This function plots a PolySet, where each unique (PID, SID) describes a polygon. It connects each polygon's last vertex to its first. The function supports both borders (border, lty) and fills (col, density, angle). When supplied with the appropriate arguments, it can draw only borders or only fills. Unlike plotMap, it ignores the aspect ratio. It clips polys to xlim and ylim before plotting.

This function creates a blank plot when polys equals NULL. In this case, the user must supply both xlim and ylim arguments. Alternatively, it accepts the argument type = "n" as part of ..., which is equivalent to specifying polys = NULL, but requires a PolySet. In both cases, the function's behaviour changes slightly. To resemble the plot function, it plots the border, labels, and other parts according to par parameters such as col.

For additional help on the arguments border, lty, col, density, and angle, please see polygon and par.

Value

PolyData consisting of the PolyProps used to create the plot.

Note

To satisfy the aspect ratio, this plotting routine resizes the plot region. Consequently, par parameters such as plt, mai, and mar will change. When the function terminates, these changes persist to allow for additions to the plot.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

addLabels, addPolys, addStipples, clipPolys, closePolys, fixBound, fixPOS, locatePolys, plotLines, plotMap, plotPoints, thinPolys, thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- create a PolySet to plot
  polys <- data.frame(PID=rep(1,4),POS=1:4,X=c(0,1,1,0),Y=c(0,0,1,1))
  #--- plot the PolySet
  plotPolys(polys, xlim=c(-.5,1.5), ylim=c(-.5,1.5), density=0)
  par(oldpar)
})

Print PBS Mapping Objects

Description

This function displays information about a PBS Mapping object.

Functions 'summary.EventData', 'summary.LocationSet', 'summary.PolyData', and 'summary.PolySet' produce an object with class 'summary.PBS'.

Usage

## S3 method for class 'EventData'
print(x, ...)
## S3 method for class 'LocationSet'
print(x, ...)
## S3 method for class 'PolyData'
print(x, ...)
## S3 method for class 'PolySet'
print(x, ...)
## S3 method for class 'summary.PBS'
print(x, ...)

Arguments

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2019-03-14

See Also

In package PBSmapping:
Data structures: EventData, LocationSet, PolyData, PolySet
Functions: PBSprint, summary

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- change to summary printing style
  PBSprint <- TRUE
  #--- print the PolySet
  print(nepacLL)
})

Data: Pythagoras' Theorem Diagram PolySet

Description

PolySet of shapes to prove Pythagoras' Theorem: a^2 + b^2 = c^2.

Usage

data(pythagoras)

Format

4 column data frame: PID = primary polygon ID, POS = position of each vertex within a given polyline, X = X-coordinate, and Y = Y-coordinate. Attributes: projection = 1.

Note

In R, the data must be loaded using the data function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2022-09-06

Source

An artificial construct to illustrate the proof of Pythagoras' Theorem using trigonometry.

See Also

addPolys, plotPolys, plotMap, PolySet.

Refocus the worldLL/worldLLhigh Data Sets

Description

Refocus the worldLL/worldLLhigh data sets, e.g., refocus them so that Eastern Canada appears to the west of Western Europe.

Usage

refocusWorld (polys, xlim=NULL, ylim=NULL, clip.AN=TRUE)

Arguments

Details

This function accepts a PolySet containing one or more polygons with X-coordinates that collectively span approximately 360 degrees. The function effectively joins the PolySet into a cylinder and then splits it at an arbitrary longitude according to the user-specified limits. Modifications in the resulting PolySet are restricted to shifting X-coordinates by +/- multiples of 360 degrees, and instead of clipping polygons, the return value simply omits out-of-range polygons.

Value

PolySet, likely a subset of the input PolySet, which retains the same PID/SID values.

Note

The Antarctic polygon is treated as a special case in that it is expanded longitudinally by duplicating it to the West and East of the base polygon. The expanded Antarctica is then clipped to the limits of the plot, or not if 'clip.NA=FALSE'.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Institute of Ocean Sciences (IOS), Sidney BC
Last modified Rd: 2018-10-26

See Also

joinPolys

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load appropriate data
  data(worldLL,envir=.PBSmapEnv)
  #--- set limits
  xlim <- c(-100,25)
  ylim <- c(0,90)
  #--- refocus and plot the world
  polys <- refocusWorld(worldLL, xlim, ylim)
  plotMap(polys, xlim, ylim)
  par(oldpar)
})

Rotate Polygons and Events

Description

Rotate a PolySet (or an EventData set) clockwise by a specified angle around a fixed point.

Usage

rotatePolys(polys, angle=40, centroid=c(500,5700),
   proj.out, zone, xlim=c(-135,-121.5), ylim=c(47,56),
   plot=FALSE, keep.extra=FALSE, ...)

rotateEvents(data, angle=40, centroid=c(500,5700),
   proj.out, zone, plot=FALSE, keep.extra=FALSE, ...)

Arguments

Details

Map rotation returns coordinates that are no longer meaningful with respect to the original coordinate system. When displaying rotated maps, the user might wish to turn off axis labels using xaxt="n" and yaxt="n".

Value

Rotated PolySet or EventData set where 'X' and 'Y' are the rotated coordinates in the projection specified by 'proj.out'. The returned object has an attribute list object named 'rotation' that contains:

• angle – angle of clockwise rotation in degrees

• radian – angle of rotation in radians: pi * (-angle)/180

• centroid – fixed point in UTM coordinates (km) around which map is rotated in UTM projection

• R – rotation matrix (2-dimensional)

• xylim – list object to keep track of 'xlim', 'ylim' and a bounding box 'xybox'.

• projection – projection of the rotated PolySet or EventData set

• zone – zone of the rotated PolySet or EventData set

When keep.extra=TRUE, the returned object will contain additional fields calculated by the rotational algorithm:

• (X0,Y0) – original coordinates of the input PolySet | EventData set

• (uX0,uY0) – original coordinates converted to UTM (only if original projection is 'LL')

• (aX,aY) – UTM coordinates adjusted by subtracting the UTM centroid

• (tX,tY) – adjusted UTM coordinates transformed by multiplying the rotational matrix

• (rX,rY) – rotated UTM coordinates re-centered by adding the UTM centroid

Note:
If proj.out="UTM", the coordinates c(rX, rY) are used as the final rotated coordinates. If proj.out="LL", the coordinates c(rX, rY) are transformed back into projection 'LL' as the final rotated coordinates.

Additionally, 'xylim' in the 'rotation' list attribute contains intermediary bounding box objects. For instance, if the input PolySet | EventData object has projection 'LL', the 'xylim' object contains:

• LL – original (X,Y) limits ('xlim', 'ylim', 'xybox')

• UTM – original (X,Y) limits transformed to UTM coordinates

• rot – rotated UTM (X,Y) limits

• out – final projection (X,Y) limits

Note

The map rotation algorithm is not heavily tested at this time. Report any issues to the package maintainer.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Institute of Ocean Sciences (IOS), Sidney BC
Last modified Rd: 2019-03-14

References

Academo – 2D Rotation about a point

Wikipedia – Rotation matrix

See Also

In package PBSmapping:
as.PolySet in PolySet, clipPolys, nepacLL, plotMap, plotPoints, refocusWorld, surveyData

Summarize PBS Mapping Objects

Description

summary method for PBS Mapping classes.

Usage

## S3 method for class 'EventData'
summary(object, ...)
## S3 method for class 'LocationSet'
summary(object, ...)
## S3 method for class 'PolyData'
summary(object, ...)
## S3 method for class 'PolySet'
summary(object, ...)

Arguments

Details

After creating a list of summary statistics, this function assigns the class 'summary.PBS' to the output in order to accomplish formatted printing via print.summary.PBS.

Value

A list of summary statistics.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2019-03-14

See Also

In package PBSmapping:
EventData, LocationSet, PolyData, PolySet, PBSprint

Examples

local(envir=.PBSmapEnv,expr={
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(surveyData,envir=.PBSmapEnv)
  print(summary(surveyData))
})

Data: Tow Information from Pacific Ocean Perch Survey

Description

EventData of Pacific ocean perch (POP) tow information (1966-89).

Usage

data(surveyData)

Format

Data frame consisting of 9 columns: PID = primary polygon ID, POS = position of each vertex within a given polygon, X = longitude coordinate, Y = latitude coordinate, trip = trip ID, tow = tow number in trip, catch = catch of POP (kg), effort = tow effort (minutes), depth = fishing depth (m), and year = year of survey trip. Attributes: projection = "LL", zone = 9.

Note

In R, the data must be loaded using the data function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2008-09-03

Source

The GFBio database, maintained at the Pacific Biological Station (Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7), archives catches and related biological data from commercial groundfish fishing trips and research/assessment cruises off the west coast of British Columbia (BC).

The POP (Sebastes alutus) survey data were extracted from GFBio. The data extraction covers bottom trawl surveys that focus primarily on POP biomass estimation: 1966-89 for the central BC coast and 1970-85 for the west coast of Vancouver Island. Additionally, a 1989 cruise along the entire BC coast concentrated on the collection of biological samples. Schnute et al. (2001) provide a more comprehensive history of POP surveys including the subset of data presented here.

References

Schnute, J.T., Haigh, R., Krishka, B.A. and Starr, P. (2001) Pacific ocean perch assessment for the west coast of Canada in 2001. Canadian Science Advisory Secretariat, Research Document 2001/138, 90 pp.

See Also

addPoints, combineEvents, EventData, findPolys, makeGrid, plotPoints.

Thicken a PolySet of Polygons

Description

Thicken a PolySet, where each unique (PID, SID) describes a polygon.

Usage

thickenPolys (polys, tol = 1, filter = 3, keepOrig = TRUE,
              close = TRUE)

Arguments

Details

This function thickens each polygon within polys according to the input arguments.

If keepOrig = TRUE, all of the original vertices appear in the result. It calculates the distance between two sequential original vertices, and if that distance exceeds tol, it adds a sufficient number of vertices spaced evenly between the two original vertices so that the distance between vertices no longer exceeds tol. If close = TRUE, it adds intermediate vertices between the last and first vertices when necessary.

If keepOrig = FALSE, only the first vertex of each polygon is guaranteed to appear in the results. From this first vertex, the algorithm walks the polygon summing the distance between vertices. When this cumulative distance exceeds tol, it adds a vertex on the line segment under inspection. After doing so, it resets the distance sum, and walks the polygon from this new vertex. If close = TRUE, it will walk the line segment from the last vertex to the first.

Value

PolySet containing the thickened data. The function recalculates the POS values for each polygon.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

thinPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- plot Vancouver Island
  plotMap(nepacLL[nepacLL$PID == 33, ])
  #--- calculate a thickened version using a 30 kilometres tolerance,
  #--- without keeping the original points
  p <- thickenPolys(nepacLL[nepacLL$PID == 33, ], tol = 30, keepOrig = FALSE)
  #--- convert the PolySet to EventData by dropping the PID column and
  #--- renaming POS to EID
  p <- p[-1]; names(p)[1] <- "EID"
  #--- convert the now invalid PolySet into a data frame, and then into
  #--- EventData
  p <- as.EventData(as.data.frame(p), projection="LL")
  #--- plot the results
  addPoints(p, col=2, pch=19)
  par(oldpar)
})

Thin a PolySet of Polygons

Description

Thin a PolySet, where each unique (PID, SID) describes a polygon.

Usage

thinPolys (polys, tol = 1, filter = 3)

Arguments

Details

This function executes the Douglas-Peuker line simplification algorithm on each polygon within polys.

Value

PolySet containing the thinned data. The function recalculates the POS values for each polygon.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2013-04-10

See Also

thickenPolys.

Examples

local(envir=.PBSmapEnv,expr={
  oldpar = par(no.readonly=TRUE)
  #--- load the data (if using R)
  if (!is.null(version$language) && (version$language=="R"))
    data(nepacLL,envir=.PBSmapEnv)
  #--- plot a thinned version of Vancouver Island (3 km tolerance)
  plotMap(thinPolys(nepacLL[nepacLL$PID == 33, ], tol = 3))
  #--- add the original Vancouver Island in a different line type to
  #--- emphasize the difference
  addPolys(nepacLL[nepacLL$PID == 33, ], border=2, lty=8, density=0)
  par(oldpar)
})

Data: Tow Information from Longspine Thornyhead Survey

Description

PolyData of tow information for a longspine thornyhead survey (2001).

Usage

data(towData)

Format

Data frame consisting of 8 columns: PID = primary polygon ID, POS = position of each vertex within a given polygon, X = longitude coordinate, Y = latitude coordinate, depth = fishing depth (m), effort = tow effort (minutes), distance = tow track distance (km), catch = catch of longspine thornyhead (kg), and year = year of survey. Attributes: projection = "LL", zone = 9.

Note

In R, the data must be loaded using the data function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2008-09-03

Source

The GFBio database, maintained at the Pacific Biological Station (Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7), archives catches and related biological data from commercial groundfish fishing trips and research/assessment cruises off the west coast of British Columbia (BC). The longspine thornyhead (Sebastolobus altivelis) survey data were extracted from GFBio. Information on the first 45 tows from the 2001 survey (Starr et al. 2002) are included here. Effort is time (minutes) from winch lock-up to winch release.

References

Starr, P.J., Krishka, B.A. and Choromanski, E.M. (2002) Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island, September 15 - October 2, 2001. Canadian Technical Report of Fisheries and Aquatic Sciences 2421, 60 pp.

See Also

makeProps, PolyData, towTracks.

Data: Tow Track Polylines from Longspine Thornyhead Survey

Description

PolySet of geo-referenced polyline tow track data from a longspine thornyhead survey (2001).

Usage

data(towTracks)

Format

Data frame consisting of 4 columns: PID = primary polygon ID, POS = position of each vertex within a given polyline, X = longitude coordinate, and Y = latitude coordinate. Attributes: projection = "LL", zone = 9.

Note

In R, the data must be loaded using the data function.

Author(s)

Nicholas M. Boers, Staff Software Engineer
Jobber, Edmonton AB
Last modified Rd: 2008-09-03

Source

The longspine thornyhead (Sebastolobus altivelis) tow track spatial coordinates are available at the Pacific Biological Station (Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7). The geo-referenced coordinates of the first 45 tows from the 2001 survey (Starr et al. 2002) are included here. Coordinates are recorded once per minute between winch lock-up and winch release.

References

Starr, P.J., Krishka, B.A. and Choromanski, E.M. (2002) Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island, September 15 - October 2, 2001. Canadian Technical Report of Fisheries and Aquatic Sciences 2421, 60 pp.

See Also

addLines, calcLength, clipLines, plotLines, PolySet, towData.