Install R package - SvenGastauer/scatmod GitHub Wiki

This page provides guidance on how to install R functionality of scatmod.

devtools - Requirement to install from Github

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scatmod can be installed form GitHub. This requires the devtools package.

If you don't have devtools installed yet:

# The package can be installed from Github:
# install.packages("devtools")

Install from Github using devtools

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devtools changed the syntax to install from Github after the release of devtools 2.0. Please check which version of devtools you have currently installed:

packageVersion("devtools")

If you use devtools > 2.0:

#Install the package from github with vignettes
# Latest devtools syntax
#no vignettes
devtools::install_github("AustralianAntarcticDivision/ZooScatR")
#with vignettes
devtools::install_github("AustralianAntarcticDivision/ZooScatR", build_opts = c("--no-manual"))## For devtools v < 2.0

If you use devtools < 2.0:

# devtools::install_github("SvenGastauer/scatmod", build_vignettes = TRUE, force_deps=TRUE)

Dependencies

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scatmod currently depends on:

• ggplot2 - for nicer plots

These dependencies should be installed automatically, if unavailable when scatmod is installed. If not, the missing libraries can be installed through:

packages <- c("ggplot2")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
  install.packages(setdiff(packages, rownames(installed.packages())))}

If you get a message such as:
WARNING: Rtools is required to build R packages, but is not currently installed.
Install Rtools by downloading the required binary package from cran:

• Windows users
• Linux users
• MacOsX
• MacOs

Usage - Quick Start

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For a quick start, a minimal example:

## Simulate the TS of a weakly scattering sphere for 1 and multiple frequencies
#define the variables
c_w = 1500 
freqs = np.arange(.1,300,0.1)*1000
f = 200 * 1000
Range = 10
Radius = 0.01
Rho_w = 1026
g = 1.0025
h = 1.0025

# Simulation for 1 frequency
TS <- as.numeric(sapply(freqs,TS.sphere2,r=Range,a=Radius,c=c_w,h=h,g=g,rho=Rho_w))
# Simulation for a range of frequencies
TS_R <- as.numeric(sapply(freqs,TS.sphere2,r=Range,a=Radius,c=c_w,h=h,g=g,rho=Rho_w))

#create data frame with numeric values for easy plotting in ggplot
tsdat <- data.frame(cbind(freq=freqs,TS=TS_R))
tsdat$freq =  as.numeric(tsdat$freq)
tsdat$TS =  as.numeric(tsdat$TS)

#plot results with ggplot
ggplot(data=tsdat,aes(x=freq/1000,y=TS))+
    geom_path(lwd=1,col="orange")+
    xlab("Frequency [kHz]")+
    ylab( expression(paste("TS [dB re 1", m^{2},"]")))+
    ggtitle(paste("TS for a sphere with a =", round(a*100,2), "cm @ range =", round(r,1),"m"))+
    theme_classic()+
    theme(text = element_text(size=16))