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.

swfscMisc

Description

swfscMisc is a collection of utility functions used at the NOAA Southwest Fisheries Science Center in La Jolla, CA. The package contains functions for geodesic calculations, commonly used mapping functions, plotting special symbols, 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 devtools installed
if (!require('devtools')) install.packages('devtools')
# install from GitHub
devtools::install_github('ericarcher/swfscMisc')

Contact

• submit suggestions and bug-reports: https://github.com/ericarcher/swfscMisc/issues
• send a pull request: https://github.com/ericarcher/swfscMisc/
• e-mail: [email protected]

Current functions

• Geodesic functions:

  • bearing
  • datum
  • distance
  • circle.polygon
  • convert.angle
  • convert.distance

• Plotting functions:

  • braces
  • catSpatInterp Categorical Spatial Interpolation
  • color.name
  • lab.wid
  • lat.lon.axes
  • row.col.page.fit
  • ggBiplot
  • scatterdens
  • scatterhist
  • sex.symbols

• Distribution functions:

  • betaParams
  • central.quantile
  • distSmry
  • fisher.p
  • gammaParams
  • pVal
  • sn.params
  • uniform.test

• Miscellaneous functions:

  • affin.prop
  • autoUnits
  • box.area
  • central.quantile
  • copy.tri
  • crossing.point
  • geometric.mean
  • harmonic.mean
  • isBetween
  • month2Season
  • mcmc2list
  • na.count
  • odds conversion (odds, invOdds, logOdds, invLogOdds)
  • one.arg
  • plotAssignments
  • ceiling, floor, trunc, round (.data.frame)
  • runjags2list
  • stan2list
  • setupClusters
  • which.nearest
  • zero.pad

Changelog

version 1.7.6 (devel)

• changed usage of ggplot2::aes_string() to ggplot2::aes()
• updated ggBiplot to work with prcomp() output as well as princomp()
• changed use of modeest::mlv() to stats::density() in distSmry() because modeest is getting archived on CRAN

version 1.7 (on CRAN)

• changed maintainer email to [email protected]

version 1.6.6

• fixed bug in runjags2list() if variable in monitor vector wasn't in model
• added betaParams() and gammaParams()
• removed diversity() - now in sprex package

version 1.6.5

• removed sample.map()
• added imdo()
• added intersectingPoint()
• added ability to use modeest::mlv() to estimate mode in distSmry()
• fixed pVal() to handle NA and NaN values correctly
• deprecating diversity(). New function in sprex package.
• added runjags2list() to format posterior samples from runjags::run.jags().
• corrected package name alias documentation for CRAN

version 1.6

• reset setupClusters to choose correct function for OS
• added perpDist() and perpPt()
• added distSmry()
• added sn.params functions for computing skew normal parameters and moments

version 1.5

• removed das.* functions

version 1.4

• added catSpatInterp for Categorical Spatial Interpolation (based on code by Timo Grossenbacher)
• begin deprecation of das.* functions. to be removed in v1.5.
• change destination() to accept vectors and return a matrix.
• fixed plotAssignments() to not change class names.
• updated spatstat import

version 1.3

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

version 1.2

• 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