swfscMisc v1.3

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Miscellaneous Functions for Southwest Fisheries Science Center

Collection of conversion, analytical, geodesic, mapping, and plotting functions. Used to support packages and code written by researchers at the Southwest Fisheries Science Center of the National Oceanic and Atmospheric Administration.

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swfscMisc

Description

swfscMisc is a collection of utility functions used at the Southwest Fisheries Science Center in La Jolla, CA. The package contains functions for geodesic calculations, commonly used mapping functions, plotting special symbols, interacting with DAS sighting data generated by the line-transect survey data entry program WinCruz, and miscellaneous analytical and conversion functions.

Installation

To install the stable version from CRAN:

install.packages('swfscMisc')

To install the latest version from GitHub:

# make sure you have Rtools installed
if (!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('ericarcher/swfscMisc')

Contact

Current functions

  • Geodesic functions:

    • bearing
    • datum
    • distance
    • circle.polygon
    • convert.angle
    • convert.distance
  • DAS file functions:

    • das.map
    • das.merge.acoustic
    • das.read
    • das.spp.freq
  • Mapping functions:

    • lat.lon.axes
    • sample.map
  • Plotting functions:

    • braces
    • color.name
    • lab.wid
    • row.col.page.fit
    • scatterdens
    • scatterhist
    • sex.symbols
  • Miscellaneous functions:

    • affin.prop
    • box.area
    • central.quantile
    • copy.tri
    • crossing.point
    • diversity
    • fisher.method.p
    • geometric.mean
    • harmonic.mean
    • isBetween
    • na.count
    • normalize
    • odds conversion (odds, invOdds, logOdds, invLogOdds)
    • one.arg
    • plotAssignments
    • pVal
    • ceiling, floor, trunc, round (.data.frame)
    • uniform.test
    • setupClusters
    • which.nearest
    • zero.pad

version 1.3 (devel)

  • fixed plotAssignments to use facets and removed grids and space around panels
  • added setupClusters

version 1.2 (on CRAN)

  • Added rounding functions for data.frames.
  • Removed NEWS.md - changelog moved to README.md
  • Added plotAssignments function.

version 1.1

  • Added autoUnits function
  • Changed default arguments for lat.range and lon.range to NULL in sample.map. If not specified, the ranges will be set to the ranges of the lat and lon.

version 1.0.9

  • Added transparent function
  • Changed distance and destination functions to accept partial matches for method of calculation, type of surface, and units

version 1.0.8

  • Fixed das.read to handle errors in position and suppress warnings about NAs during numerical conversions.
  • Fixed das.map to remove records with no position

version 1.0.7

  • Changed isBetween to accept a vector of numbers

version 1.0.6

  • Added NEWS.md
  • Added diversity function (moved from strataG package)
  • Added isBetween function to test if a number is between two numbers

Functions in swfscMisc

Name Description
box.area Area of a Box
lab.wid Label Width
crossing.point Crossing Point
isBetween Between
copy.tri Copy Matrix Triangles
das.merge.acoustic Merge DAS Data Into Acoustic Detections
harmonic.mean Harmonic Mean
datum Datum
das.map Map DAS
ggBiplot ggBiplot
row.col.page.fit Number of Rows and Columns on Page
round Rounding Numbers for Data Frames
sample.map Plot Samples on World Map
plotAssignments Plot assignment distributions
destination Destination on Sphere or Ellipsoid
fisher.method.p Fisher's Method p-value
pVal Permutation Test P-value
one.arg One Argument
na.count Count NAs
das.read Read DAS File
das.spp.freq Frequency of species from DAS file
odds Odds Conversion
distance Distance Between Coordinates
month2Season Convert Months to Seasons
lat.lon.axes Latitude and Longitude axes
diversity Unbiased Estimate of Diversity
setupClusters Setup Clusters
swfscMisc swfscMisc package
geometric.mean Geometric Mean
scatterdens Scatter Plot with Density Margins
which.nearest Which Nearest
zero.pad Zero Pad Integers
transparent Transparent Colors
uniform.test Uniform Distribution Test
sex.symbols Sex Symbols
affin.prop Affinity Propagation
autoUnits Auto Time Interval Units
bearing Calculate Bearing Between Two Positions
color.name Color Name
braces Braces
central.quantile Central Quantile
convert.angle Angle Conversion
convert.distance Distance Conversion
circle.polygon Circle Polygon (on Earth)
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Details

Type Package
URL https://github.com/EricArcher/swfscMisc
BugReports https://github.com/EricArcher/swfscMisc/issues
License GPL (>= 2)
RoxygenNote 7.0.2
NeedsCompilation no
Packaged 2020-02-20 10:44:51 UTC; ericarcher
Repository CRAN
Date/Publication 2020-02-20 11:40:02 UTC

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