travis

.Rbuildignore

@@ -0,0 +1,4 @@
+.gitignore
+.git
+.RS_Store
+.travis.yml

.travis.yml

@@ -0,0 +1,32 @@
+# Sample .travis.yml for R projects.
+#
+# See the r-travis repo and its wiki 
+#   https://github.com/craigcitro/r-travis/wiki
+
+language: c
+
+env:
+  global:
+    - R_BUILD_ARGS="--no-build-vignettes --no-manual"
+    - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran"
+
+before_install:
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+
+install:
+  - ./travis-tool.sh install_r testthat knitr
+
+script: 
+  - ./travis-tool.sh run_tests
+
+after_script:
+  - ./travis-tool.sh dump_logs
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+

DESCRIPTION

@@ -11,7 +11,7 @@ Authors@R: person("Baptiste", "Auguie", email = "[email protected]",
     source listed in the help file.")
 Description: Physical constants. Gold, silver and glass permittivities,
     together with spline interpolation functions.
-Version: 0.2.2
+Version: 0.2.3
 Date: 2012-03-04
 Depends:
     R (>= 2.13),

NAMESPACE

@@ -2,4 +2,4 @@ export(dielectric2plot)
 export(drude)
 export(epsAg)
 export(epsAu)
-export(fitDrude)
+export(fit_drude)

NEWS

@@ -1,3 +1,8 @@
+
+dielectric 0.2.3 (2013-11-08)
+
+* silly typo in Au_JC demo
+
 dielectric 0.2.2 (2013-05-18)
 
 * cleaning examples for CRAN

R/drude.r

@@ -2,41 +2,46 @@
 ##'
 ##' a bacground contribution eps_inf is assumed for the core electrons
 ##' @title drude
-##' @param wavelength wavelength in m
-##' @param omega angular frequency in rad/s
+##' @param wavelength wavelength in nm
 ##' @param p vector of 3 parameters
+##' @param omega angular frequency in rad/s
 ##' @param omega_p plasma frequency in rad/s
 ##' @param gamma_p damping constant, in rad/s
 ##' @param epsilon_inf background dielectric function
 ##' @param ... not used
-##' @return a data.frame with wavelength in microns and complex dielectric function
+##' @return a data.frame with wavelength in nm and complex dielectric function
 ##' @author Baptiste Auguie
 ##' @export
-drude <- function(wavelength, omega=NULL, p=c(1e16, 1e14, 1),
+drude <- function(wavelength=633, p=c(1e16, 1e14, 1), 
+                  omega=2*pi*1e9 * 2.99792458e8 / wavelength, 
                   omega_p = p[1], gamma_p = p[2], epsilon_inf = p[3], ...){
-    cel <- 2.99792458e8
-    if(is.null(omega))
-      omega <- 2*pi * cel / wavelength
-    data.frame(wavelength=wavelength *1e6,
-               epsilon = epsilon_inf -  omega_p^2 / (omega^2 +  (0+1i) * omega * gamma_p))
-
+
+  if(missing(wavelength))
+    wavelength <- 2*pi*1e9 * 2.99792458e8 / omega
+
+  data.frame(wavelength=wavelength,
+             epsilon = epsilon_inf -  omega_p^2 / (omega^2 +  (0+1i) * omega * gamma_p))
+
 }
+
 ##' Objective function for the Drude model
 ##'
 ##' Used to fit a Drude model to a material
-##' @title fitFDrude
+##' @title fit_drude
 ##' @param p parameters vector (3)
-##' @param material data.frame with wavelength in microns and complex epsilon
-##' @param ... passed to Drude
+##' @param material data.frame with wavelength in nm and complex epsilon
+##' @param ... passed to drude
 ##' @return sum of squares
 ##' @author Baptiste Auguie
 ##' @export
-fitDrude <- function(p, material, ...){
-
-  res <- drude(material$wavelength*1e-9, omega_p=p[1], gamma_p=p[2], epsilon_inf=p[3], ...)
-
-  sos.real <- sum((Re(res$epsilon) - Re(material$epsilon))^2) / sum(Re(material$epsilon)^2)
-  sos.imag <- sum((Im(res$epsilon) - Im(material$epsilon))^2) / sum(Im(material$epsilon)^2)
+fit_drude <- function(p, material, ...){
+
+  res <- drude(material[['wavelength']], p, ...)
+
+  sos.real <- sum((Re(res[['epsilon']]) - Re(material[['epsilon']]))^2) / 
+    sum(Re(material[['epsilon']])^2)
+  sos.imag <- sum((Im(res[['epsilon']]) - Im(material[['epsilon']]))^2) / 
+    sum(Im(material[['epsilon']])^2)
 
   sos.real + sos.imag
 }

demo/AuJC.r

@@ -6,9 +6,9 @@ data(AuJC)
 
 AuJC$set_span(300, 800)
 raw <- dielectric2plot(AuJC$raw())
-silver <- AuJC$predict(n=300, all.knots=TRUE)
+gold <- AuJC$predict(n=300, all.knots=TRUE)
 
-d <- dielectric2plot(silver)
+d <- dielectric2plot(gold)
 
 ggplot(d, aes(wavelength, value)) + geom_path() +
   facet_grid(variable~., scales="free") +

man/drude.Rd

@@ -2,17 +2,18 @@
 \alias{drude}
 \title{drude}
 \usage{
-  drude(wavelength, omega = NULL, p = c(1e+16, 1e+14, 1),
+  drude(wavelength = 633, p = c(1e+16, 1e+14, 1),
+    omega = 2 * pi * 1e+09 * 299792458/wavelength,
     omega_p = p[1], gamma_p = p[2], epsilon_inf = p[3],
     ...)
 }
 \arguments{
-  \item{wavelength}{wavelength in m}
-
-  \item{omega}{angular frequency in rad/s}
+  \item{wavelength}{wavelength in nm}
 
   \item{p}{vector of 3 parameters}
 
+  \item{omega}{angular frequency in rad/s}
+
   \item{omega_p}{plasma frequency in rad/s}
 
   \item{gamma_p}{damping constant, in rad/s}
@@ -22,8 +23,8 @@
   \item{...}{not used}
 }
 \value{
-  a data.frame with wavelength in microns and complex
-  dielectric function
+  a data.frame with wavelength in nm and complex dielectric
+  function
 }
 \description{
   Drude model for the dielectric function of good (governed

man/fitDrude.Rd → man/fit_drude.Rd

@@ -1,16 +1,16 @@
-\name{fitDrude}
-\alias{fitDrude}
-\title{fitFDrude}
+\name{fit_drude}
+\alias{fit_drude}
+\title{fit_drude}
 \usage{
-  fitDrude(p, material, ...)
+  fit_drude(p, material, ...)
 }
 \arguments{
   \item{p}{parameters vector (3)}
 
-  \item{material}{data.frame with wavelength in microns and
+  \item{material}{data.frame with wavelength in nm and
   complex epsilon}
 
-  \item{...}{passed to Drude}
+  \item{...}{passed to drude}
 }
 \value{
   sum of squares