diff --git a/NAMESPACE b/NAMESPACE
index 506ad19..14b36ae 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.0): do not edit by hand
+# Generated by roxygen2 (4.0.1.99): do not edit by hand
 
 export(La)
 export(alpha_kuwata)
diff --git a/R/dispersion.r b/R/dispersion.r
index e3af964..c35d279 100644
--- a/R/dispersion.r
+++ b/R/dispersion.r
@@ -11,6 +11,7 @@
 ##' @param polarisation linear or circular polarisation
 ##' @param progress logical, display progress bar
 ##' @return data.frame
+##' @note The incident wavevector is along the z direction.
 ##' @export
 ##' @family user_level cda
 ##' @author baptiste Auguie
diff --git a/inst/doc/CD-theory.pdf b/inst/doc/CD-theory.pdf
deleted file mode 100644
index 556e028..0000000
Binary files a/inst/doc/CD-theory.pdf and /dev/null differ
diff --git a/man/G0.Rd b/man/G0.Rd
index 2d0d551..2f81316 100644
--- a/man/G0.Rd
+++ b/man/G0.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{G0}
 \alias{G0}
@@ -11,12 +10,10 @@
    \item{\code{Gxx}}{ A complex vector}
  }}
 \description{
-Converged lattice sum G0 for an infinite 2D array of
-dipoles at normal incidence
+Converged lattice sum G0 for an infinite 2D array of dipoles at normal incidence
 }
 \details{
-The calculation was made using code from Prof. J. G. de
-Abajo (CSIC, Spain)
+The calculation was made using code from Prof. J. G. de Abajo (CSIC, Spain)
 }
 \examples{
 data(G0)
diff --git a/man/La.Rd b/man/La.Rd
index e264966..2937ace 100644
--- a/man/La.Rd
+++ b/man/La.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{La}
 \alias{La}
 \title{La}
@@ -7,11 +6,11 @@
 La(a = 50, b = a, c = a)
 }
 \arguments{
-  \item{a}{semi-axis in nm}
+\item{a}{semi-axis in nm}
 
-  \item{b}{semi-axis in nm}
+\item{b}{semi-axis in nm}
 
-  \item{c}{semi-axis in nm}
+\item{c}{semi-axis in nm}
 }
 \value{
 shape factor along a
@@ -26,9 +25,9 @@ calculates the shape factor for a general ellipsoid
 baptiste Auguie
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{alpha_kuwata}},
-\code{\link{inverse_polarizability}},
-\code{\link{polarizability_ellipsoid}}
+Other user_level polarizability: \code{\link{Kuwata.A}},
+  \code{\link{Kuwata.B}}, \code{\link{alpha_kuwata}};
+  \code{\link{inverse_polarizability}};
+  \code{\link{polarizability_ellipsoid}}
 }
 
diff --git a/man/alpha_kuwata.Rd b/man/alpha_kuwata.Rd
index 8c00a1a..2be856d 100644
--- a/man/alpha_kuwata.Rd
+++ b/man/alpha_kuwata.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{alpha_kuwata}
 \alias{Kuwata.A}
 \alias{Kuwata.B}
@@ -9,17 +8,17 @@
 alpha_kuwata(wavelength, epsilon, V, axis, L, medium = 1.33)
 }
 \arguments{
-  \item{wavelength}{wavelength}
+\item{wavelength}{wavelength}
 
-  \item{epsilon}{permittivity}
+\item{epsilon}{permittivity}
 
-  \item{V}{volume}
+\item{V}{volume}
 
-  \item{axis}{semi-axis along incident field}
+\item{axis}{semi-axis along incident field}
 
-  \item{L}{shape factor}
+\item{L}{shape factor}
 
-  \item{medium}{refractive index}
+\item{medium}{refractive index}
 }
 \value{
 polarizability
@@ -34,13 +33,11 @@ prescription from Kuwata
 baptiste Auguie
 }
 \references{
-Kuwata et al. Resonant light scattering from metal
-nanoparticles: Practical analysis beyond Rayleigh
-approximation Appl. Phys. Lett. 83, 22 (2003)
+Kuwata et al. Resonant light scattering from metal nanoparticles: Practical analysis beyond Rayleigh approximation Appl. Phys. Lett. 83, 22 (2003)
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{inverse_polarizability}}, \code{\link{La}},
-\code{\link{polarizability_ellipsoid}}
+Other user_level polarizability: \code{\link{La}};
+  \code{\link{inverse_polarizability}};
+  \code{\link{polarizability_ellipsoid}}
 }
 
diff --git a/man/array.Rd b/man/array.Rd
index 4528397..0c25aff 100644
--- a/man/array.Rd
+++ b/man/array.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{array}
 \alias{array}
@@ -8,8 +7,9 @@
 Exposes a C++ calculation of the array factor.
 }
 \details{
-\itemize{ \item{array_factor}{ Truncated lattice sum for a
-finite 2D square array} }
+\itemize{
+ \item{array_factor}{ Truncated lattice sum for a finite 2D square array}
+}
 }
 \examples{
 show( array )
diff --git a/man/array_factor.Rd b/man/array_factor.Rd
index 02900ff..1fb9711 100644
--- a/man/array_factor.Rd
+++ b/man/array_factor.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{array_factor}
 \alias{array_factor}
 \title{array factor}
@@ -7,11 +6,11 @@
 array_factor(wavelength, N, pitch)
 }
 \arguments{
-  \item{wavelength}{wavelength in nm}
+\item{wavelength}{wavelength in nm}
 
-  \item{N}{half number of dipoles along one side}
+\item{N}{half number of dipoles along one side}
 
-  \item{pitch}{pitch in nm}
+\item{pitch}{pitch in nm}
 }
 \value{
 S
@@ -20,8 +19,7 @@ S
 C++ calculation of the array factor
 }
 \details{
-Brute-force numerical evaluation of the truncated 2D sum of
-dipole fields
+Brute-force numerical evaluation of the truncated 2D sum of dipole fields
 }
 \examples{
 S <- array_factor(seq(400, 600),  10,  500)
diff --git a/man/cd.Rd b/man/cd.Rd
index 5055e4b..ddbb000 100644
--- a/man/cd.Rd
+++ b/man/cd.Rd
@@ -1,18 +1,15 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{cd}
 \alias{cd}
 \title{Rcpp module: cd}
 \description{
-Exposes a calculation of orientation-averaged circular
-dichroism within the coupled-dipole approximation.
+Exposes a calculation of orientation-averaged circular dichroism within the coupled-dipole approximation.
 }
 \details{
-\itemize{ \item{average_spectrum}{ Loop over wavelengths
-and calculate the orientation averaging of the difference
-in extinction, absorption, scattering for left/right
-circularly polarised light} }
+\itemize{
+ \item{average_spectrum}{ Loop over wavelengths and calculate the orientation averaging of the difference in extinction, absorption, scattering for left/right circularly polarised light}
+}
 }
 \examples{
 show( cd )
diff --git a/man/cda-package.Rd b/man/cda-package.Rd
index b964106..84f89b2 100644
--- a/man/cda-package.Rd
+++ b/man/cda-package.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{package}
 \name{cda-package}
 \alias{cda-package}
@@ -8,52 +7,31 @@
 Coupled dipole approximation in electromagnetic scattering
 }
 \details{
-Solves the electromagnetic problem of coupled-dipoles
-(scattering and absorption by a cluster of subwavelength
-particles in arbitrary 3D configuration) by direct
-inversion of the interaction matrix. Functions are provided
-for linear polarisation with varying angle of incidence, as
-well as circular polarisation with angular averaging
-(optical activity). Retardation is included in the
-interaction.
+Solves the electromagnetic problem of coupled-dipoles (scattering and absorption by a cluster of subwavelength particles in arbitrary 3D configuration) by direct inversion of the interaction matrix. Functions are provided for linear polarisation with varying angle of incidence, as well as circular polarisation with angular averaging (optical activity). Retardation is included in the interaction.
 }
 \author{
 baptiste Auguie
 }
 \references{
-Draine BT. The discrete-dipole approximation and its
-application to interstellar graphite grains. Astrophysical
-Journal. 1988.
+Draine BT. The discrete-dipole approximation and its application to interstellar graphite grains. Astrophysical Journal. 1988.
 
-Schatz GC, Duyne RP. Discrete dipole approximation for
-calculating extinction and Raman intensities for small
-particles with arbitrary shapes. Journal of Chemical
-Physics. 1995.
+Schatz GC, Duyne RP. Discrete dipole approximation for calculating extinction and Raman intensities for small particles with arbitrary shapes. Journal of Chemical Physics. 1995.
 
-Gunnarsson L, Zou S, Schatz GC, et al. Confined plasmons in
-nanofabricated single silver particle pairs: Experimental
-observations of strong interparticle interactions. Journal
-of Physical Chemistry B. 2005.
+Gunnarsson L, Zou S, Schatz GC, et al. Confined plasmons in nanofabricated single silver particle pairs: Experimental observations of strong interparticle interactions. Journal of Physical Chemistry B. 2005.
 
-## Any one of the following references should be used to
-cite and acknowledge the use of this package.
+## Any one of the following references should be used to cite and acknowledge the use of this package.
 
 Circular dichroism:
 
-B. Auguie, J.L. Alonso-Gomez, A. Guerrero-Martinez, L.M.
-Liz-Marzan. Fingers crossed: circular dichroism with a
-dimer of plasmonic nanorods. J. Phys. Chem. Lett. 2, (2011)
+B. Auguie, J.L. Alonso-Gomez, A. Guerrero-Martinez, L.M. Liz-Marzan. Fingers crossed: circular dichroism with a dimer of plasmonic nanorods. J. Phys. Chem. Lett. 2, (2011)
 
 Linear extinction:
 
-B. Auguie, W.L. Barnes. Diffractive coupling in gold
-nanoparticle arrays and the effect of disorder. Optics
-Letters (2009)
+B. Auguie, W.L. Barnes. Diffractive coupling in gold nanoparticle arrays and the effect of disorder. Optics Letters (2009)
 
 Array factor (infinite case):
 
-B. Auguie, W.L. Barnes. Collective resonances in gold
-nanoparticle arrays. Physical Review Letters (2008)
+B. Auguie, W.L. Barnes. Collective resonances in gold nanoparticle arrays. Physical Review Letters (2008)
 }
 \keyword{package}
 \keyword{packagelibrary}
diff --git a/man/cda.Rd b/man/cda.Rd
index 5a4c27d..02c48cf 100644
--- a/man/cda.Rd
+++ b/man/cda.Rd
@@ -1,24 +1,22 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{cda}
 \alias{cda}
 \title{Rcpp module: cda}
 \description{
-Exposes basic C++ functions used in the coupled-dipole
-approximation.
+Exposes basic C++ functions used in the coupled-dipole approximation.
 }
 \details{
-\itemize{ \item{absorption}{ Absorption cross-section}
-\item{extinction}{ Extinction cross-section }
-\item{axis_rotation}{ 3D rotation matrix parametrized by
-axis + angle} \item{euler}{ 3D rotation matrix parametrized
-by Euler angles } \item{interaction_matrix}{ Build the
-coupled-dipole interaction matrix } \item{block_diagonal}{
-Diagonal blocks of the coupled-dipole interaction matrix }
-\item{incident_field}{ Construct the incident fields for
-specific Euler angles} \item{multiple_incident_field}{
-Construct the incident fields for specific axes+angles} }
+\itemize{
+  \item{absorption}{ Absorption cross-section}
+  \item{extinction}{ Extinction cross-section }
+  \item{axis_rotation}{ 3D rotation matrix parametrized by axis + angle}
+  \item{euler}{ 3D rotation matrix parametrized by Euler angles }
+  \item{interaction_matrix}{ Build the coupled-dipole interaction matrix }
+  \item{block_diagonal}{ Diagonal blocks of the coupled-dipole interaction matrix }
+  \item{incident_field}{ Construct the incident fields for specific Euler angles}
+  \item{multiple_incident_field}{ Construct the incident fields for specific axes+angles}
+}
 }
 \examples{
 show( cda )
diff --git a/man/circular_dichroism_spectrum.Rd b/man/circular_dichroism_spectrum.Rd
index 0aa8dd8..7410a79 100644
--- a/man/circular_dichroism_spectrum.Rd
+++ b/man/circular_dichroism_spectrum.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{circular_dichroism_spectrum}
 \alias{circular_dichroism_spectrum}
 \title{circular_dichroism_spectrum}
@@ -10,37 +9,31 @@ circular_dichroism_spectrum(cluster, material, medium = 1.33, Nquad = 100,
   progress = FALSE, verbose = TRUE, result.matrix = FALSE)
 }
 \arguments{
-  \item{cluster}{cluster (list)}
+\item{cluster}{cluster (list)}
 
-  \item{material}{material}
+\item{material}{material}
 
-  \item{medium}{refractive index medium}
+\item{medium}{refractive index medium}
 
-  \item{Nquad}{number of integration points}
+\item{Nquad}{number of integration points}
 
-  \item{averaging}{averaging method, using either Gauss
-  Legendre quadrature (default), Quasi Monte Carlo, regular
-  grid, or "cheap" (3 axes)}
+\item{averaging}{averaging method, using either Gauss Legendre quadrature (default), Quasi Monte Carlo, regular grid, or "cheap" (3 axes)}
 
-  \item{iterative}{logical, increase N until convergence
-  (QMC only)}
+\item{iterative}{logical, increase N until convergence (QMC only)}
 
-  \item{precision}{relative diff between two runs (QMC
-  only)}
+\item{precision}{relative diff between two runs (QMC only)}
 
-  \item{Nmax}{maximum N if convergence not attained (QMC
-  only)}
+\item{Nmax}{maximum N if convergence not attained (QMC only)}
 
-  \item{dN}{iterative increase in N (QMC only)}
+\item{dN}{iterative increase in N (QMC only)}
 
-  \item{full}{logical use full (retarded) dipolar field}
+\item{full}{logical use full (retarded) dipolar field}
 
-  \item{progress}{print progress lines}
+\item{progress}{print progress lines}
 
-  \item{verbose}{display messages}
+\item{verbose}{display messages}
 
-  \item{result.matrix}{logical return the results as a
-  matrix}
+\item{result.matrix}{logical return the results as a matrix}
 }
 \description{
 Simulate a CD spectrum
@@ -52,9 +45,6 @@ CD spectrum
 baptiste Auguie
 }
 \references{
-Y. Okada, Efficient numerical orientation averaging of
-light scattering properties with a quasi-Monte-Carlo
-method, Journal of Quantitative Spectroscopy and Radiative
-Transfer, Volume 109, Issue 9, June 2008, Pages 1719-1742.
+Y. Okada, Efficient numerical orientation averaging of light scattering properties with a quasi-Monte-Carlo method, Journal of Quantitative Spectroscopy and Radiative Transfer, Volume 109, Issue 9, June 2008, Pages 1719-1742.
 }
 
diff --git a/man/cluster_chain.Rd b/man/cluster_chain.Rd
index a2c3df4..d5ee141 100644
--- a/man/cluster_chain.Rd
+++ b/man/cluster_chain.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{cluster_chain}
 \alias{cluster_chain}
 \title{cluster_chain}
@@ -7,18 +6,18 @@
 cluster_chain(N, pitch = 500, a = 50, b = 30, c = b)
 }
 \arguments{
-  \item{N}{number of rods}
+\item{N}{number of rods}
 
-  \item{pitch}{pitch}
+\item{pitch}{pitch}
 
-  \item{a}{semi axis}
+\item{a}{semi axis}
 
-  \item{b}{semi axis}
+\item{b}{semi axis}
 
-  \item{c}{semi axis}
+\item{c}{semi axis}
 }
 \value{
-list with r, sizes, angles
+list with r,  sizes, angles
 }
 \description{
 cluster_chain
@@ -30,9 +29,9 @@ linear chain of parallel nanorods
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_dimer}},
-\code{\link{cluster_dimer_end}},
-\code{\link{cluster_helix}}, \code{\link{equal_angles}},
-\code{\link{equal_sizes}}, \code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_dimer}}; \code{\link{cluster_helix}};
+  \code{\link{equal_angles}}; \code{\link{equal_sizes}};
+  \code{\link{helix}}
 }
 
diff --git a/man/cluster_dimer.Rd b/man/cluster_dimer.Rd
index 7bd4560..7996602 100644
--- a/man/cluster_dimer.Rd
+++ b/man/cluster_dimer.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{cluster_dimer}
 \alias{cluster_dimer}
 \title{cluster_dimer}
@@ -8,35 +7,36 @@ cluster_dimer(d = a, dihedral = 0, alpha1 = 0, alpha2 = 0, a = 0.035,
   b = 0.012)
 }
 \arguments{
-  \item{d}{center-to-center distance}
+\item{d}{center-to-center distance}
 
-  \item{dihedral}{dihedral angle}
+\item{dihedral}{dihedral angle}
 
-  \item{alpha1}{angle first rod}
+\item{alpha1}{angle first rod}
 
-  \item{alpha2}{angle second rod}
+\item{alpha2}{angle second rod}
 
-  \item{a}{semi axis}
+\item{a}{semi axis}
 
-  \item{b}{semi axis}
+\item{b}{semi axis}
 }
 \value{
-list with r, sizes, angles
+list with r,  sizes,  angles
 }
 \description{
 cluster_dimer
 }
 \details{
-cluster with two nanorods first rod along x at (0, 0, -d/2)
+cluster with two nanorods
+first rod along x at (0, 0, -d/2)
 second rod at (0, 0, d/2)
 }
 \author{
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer_end}},
-\code{\link{cluster_helix}}, \code{\link{equal_angles}},
-\code{\link{equal_sizes}}, \code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_helix}}; \code{\link{equal_angles}};
+  \code{\link{equal_sizes}}; \code{\link{helix}}
 }
 
diff --git a/man/cluster_dimer_end.Rd b/man/cluster_dimer_end.Rd
index bfaf9d1..ee7fd65 100644
--- a/man/cluster_dimer_end.Rd
+++ b/man/cluster_dimer_end.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{cluster_dimer_end}
 \alias{cluster_dimer_end}
 \title{cluster_dimer_end}
@@ -8,34 +7,34 @@ cluster_dimer_end(d = a, dihedral = 0, a = 0.035, b = 0.012,
   rescale = TRUE)
 }
 \arguments{
-  \item{d}{end-to-end distance}
+\item{d}{end-to-end distance}
 
-  \item{dihedral}{dihedral angle}
+\item{dihedral}{dihedral angle}
 
-  \item{a}{semi axis}
+\item{a}{semi axis}
 
-  \item{b}{semi axis}
+\item{b}{semi axis}
 
-  \item{rescale}{logical, rescale the z coordinates so that
-  d is the center-to-center distance}
+\item{rescale}{logical, rescale the z coordinates so that d is the center-to-center distance}
 }
 \value{
-list with r, sizes, angles
+list with r,  sizes,  angles
 }
 \description{
 cluster_dimer_end
 }
 \details{
-cluster with two nanorods first rod along x at (0, 0, -d/2)
+cluster with two nanorods
+first rod along x at (0, 0, -d/2)
 second rod at (0, 0, d/2)
 }
 \author{
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer}}, \code{\link{cluster_helix}},
-\code{\link{equal_angles}}, \code{\link{equal_sizes}},
-\code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer}}; \code{\link{cluster_helix}};
+  \code{\link{equal_angles}}; \code{\link{equal_sizes}};
+  \code{\link{helix}}
 }
 
diff --git a/man/cluster_helix.Rd b/man/cluster_helix.Rd
index afe9e9b..37374a1 100644
--- a/man/cluster_helix.Rd
+++ b/man/cluster_helix.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{cluster_helix}
 \alias{cluster_helix}
 \title{cluster_helix}
@@ -9,29 +8,29 @@ cluster_helix(N = 5, R0 = 12, pitch = 15, delta = pi/2, delta0 = 0,
   "fixed"), seed = 123, ...)
 }
 \arguments{
-  \item{N}{number of particles}
+\item{N}{number of particles}
 
-  \item{R0}{radius of helix}
+\item{R0}{radius of helix}
 
-  \item{pitch}{pitch of helix}
+\item{pitch}{pitch of helix}
 
-  \item{delta}{angle between particles}
+\item{delta}{angle between particles}
 
-  \item{delta0}{initial angle}
+\item{delta0}{initial angle}
 
-  \item{right}{logical, helicity}
+\item{right}{logical, helicity}
 
-  \item{a}{ellipsoid semi-axis}
+\item{a}{ellipsoid semi-axis}
 
-  \item{b}{ellipsoid semi-axis}
+\item{b}{ellipsoid semi-axis}
 
-  \item{c}{ellipsoid semi-axis}
+\item{c}{ellipsoid semi-axis}
 
-  \item{angles}{type of angular orientation}
+\item{angles}{type of angular orientation}
 
-  \item{seed}{random seed for reproducibility}
+\item{seed}{random seed for reproducibility}
 
-  \item{...}{extra arguments (ignored)}
+\item{...}{extra arguments (ignored)}
 }
 \value{
 list
@@ -46,10 +45,9 @@ helical cluster of ellipsoids
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer}},
-\code{\link{cluster_dimer_end}},
-\code{\link{equal_angles}}, \code{\link{equal_sizes}},
-\code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_dimer}}; \code{\link{equal_angles}};
+  \code{\link{equal_sizes}}; \code{\link{helix}}
 }
 
diff --git a/man/curve_povray.Rd b/man/curve_povray.Rd
index b88a2e5..7944adc 100644
--- a/man/curve_povray.Rd
+++ b/man/curve_povray.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{curve_povray}
 \alias{curve_povray}
 \title{curve_povray}
@@ -7,13 +6,13 @@
 curve_povray(positions, size = 0.005, radius, out = "positions.pov")
 }
 \arguments{
-  \item{positions}{matrix of positions}
+\item{positions}{matrix of positions}
 
-  \item{size}{radius of particles}
+\item{size}{radius of particles}
 
-  \item{radius}{radius of inner cylinder}
+\item{radius}{radius of inner cylinder}
 
-  \item{out}{output filename}
+\item{out}{output filename}
 }
 \value{
 side-effect only (note append=TRUE)
diff --git a/man/dispersion.Rd b/man/dispersion.Rd
index d53e3ad..e1b5d5c 100644
--- a/man/dispersion.Rd
+++ b/man/dispersion.Rd
@@ -1,22 +1,16 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \docType{data}
 \name{dispersion}
 \alias{dispersion}
 \title{Rcpp module: dispersion}
 \description{
-Exposes C++ calculation of scattering and absorption of
-dipolar particles by linearly polarised light in fixed
-orientation.
+Exposes C++ calculation of scattering and absorption of dipolar particles by linearly polarised light in fixed orientation.
 }
 \details{
-\itemize{ \item{dispersion}{ Returns absorption, scattering
-and extinction cross-sections for two orthogonal
-polarisations at multiple angles of incidence, fixed
-wavelength (subroutine)} \item{dispersion_spectrum}{
-Returns absorption, scattering and extinction spectra for
-two orthogonal polarisations at multiple angles of
-incidence} }
+\itemize{
+  \item{dispersion}{ Returns absorption, scattering and extinction cross-sections for two orthogonal polarisations at multiple angles of incidence, fixed wavelength (subroutine)}
+  \item{dispersion_spectrum}{ Returns absorption, scattering and extinction spectra for two orthogonal polarisations at multiple angles of incidence}
+}
 }
 \examples{
 show( dispersion )
diff --git a/man/dispersion_spectrum.Rd b/man/dispersion_spectrum.Rd
index 0242cec..8eeee6c 100644
--- a/man/dispersion_spectrum.Rd
+++ b/man/dispersion_spectrum.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{dispersion_spectrum}
 \alias{dispersion_spectrum}
 \title{dispersion_spectrum}
@@ -8,20 +7,19 @@ dispersion_spectrum(cluster, material, medium = 1.33, angles = 0,
   axes = "z", polarisation = c("linear", "circular"), progress = FALSE)
 }
 \arguments{
-  \item{cluster}{list describing a cluster}
+\item{cluster}{list describing a cluster}
 
-  \item{material}{list}
+\item{material}{list}
 
-  \item{medium}{medium refractive index}
+\item{medium}{medium refractive index}
 
-  \item{angles}{of incident field in radians}
+\item{angles}{of incident field in radians}
 
-  \item{axes}{of incident field rotation character vector
-  from ('x', 'y', 'z')}
+\item{axes}{of incident field rotation character vector from ('x', 'y', 'z')}
 
-  \item{polarisation}{linear or circular polarisation}
+\item{polarisation}{linear or circular polarisation}
 
-  \item{progress}{logical, display progress bar}
+\item{progress}{logical, display progress bar}
 }
 \value{
 data.frame
@@ -32,6 +30,9 @@ dispersion spectrum
 \details{
 dispersion spectrum
 }
+\note{
+The incident wavevector is along the z direction.
+}
 \author{
 baptiste Auguie
 }
diff --git a/man/equal_angles.Rd b/man/equal_angles.Rd
index 585c0de..b053224 100644
--- a/man/equal_angles.Rd
+++ b/man/equal_angles.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{equal_angles}
 \alias{equal_angles}
 \title{equal_angles}
@@ -7,13 +6,13 @@
 equal_angles(phi = 0, theta = 0, psi = 0, N)
 }
 \arguments{
-  \item{phi}{phi}
+\item{phi}{phi}
 
-  \item{theta}{theta}
+\item{theta}{theta}
 
-  \item{psi}{psi}
+\item{psi}{psi}
 
-  \item{N}{N}
+\item{N}{N}
 }
 \value{
 matrix Nx3
@@ -28,10 +27,9 @@ generate a matrix of equal angles
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer}},
-\code{\link{cluster_dimer_end}},
-\code{\link{cluster_helix}}, \code{\link{equal_sizes}},
-\code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_dimer}}; \code{\link{cluster_helix}};
+  \code{\link{equal_sizes}}; \code{\link{helix}}
 }
 
diff --git a/man/equal_sizes.Rd b/man/equal_sizes.Rd
index 6c0d93e..ef62fb5 100644
--- a/man/equal_sizes.Rd
+++ b/man/equal_sizes.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{equal_sizes}
 \alias{equal_sizes}
 \title{equal_sizes}
@@ -7,13 +6,13 @@
 equal_sizes(a, b, c, N)
 }
 \arguments{
-  \item{a}{a}
+\item{a}{a}
 
-  \item{b}{b}
+\item{b}{b}
 
-  \item{c}{c}
+\item{c}{c}
 
-  \item{N}{N}
+\item{N}{N}
 }
 \value{
 matrix Nx3
@@ -28,10 +27,9 @@ generate a matrix of equal particle sizes
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer}},
-\code{\link{cluster_dimer_end}},
-\code{\link{cluster_helix}}, \code{\link{equal_angles}},
-\code{\link{helix}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_dimer}}; \code{\link{cluster_helix}};
+  \code{\link{equal_angles}}; \code{\link{helix}}
 }
 
diff --git a/man/helix.Rd b/man/helix.Rd
index 1998481..4116039 100644
--- a/man/helix.Rd
+++ b/man/helix.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{helix}
 \alias{helix}
 \title{helix}
@@ -8,24 +7,22 @@ helix(R0 = 500, pitch = 600, N = 5, delta = pi/8, delta0 = pi/2,
   n.smooth = 100 * N, right = TRUE)
 }
 \arguments{
-  \item{R0}{radius in nm}
+\item{R0}{radius in nm}
 
-  \item{pitch}{pitch in nm}
+\item{pitch}{pitch in nm}
 
-  \item{N}{number of particles}
+\item{N}{number of particles}
 
-  \item{delta}{twist angle between two particles}
+\item{delta}{twist angle between two particles}
 
-  \item{delta0}{angle shift at origin}
+\item{delta0}{angle shift at origin}
 
-  \item{n.smooth}{number of interpolation points (for
-  plotting purposes)}
+\item{n.smooth}{number of interpolation points (for plotting purposes)}
 
-  \item{right}{logical, handedness}
+\item{right}{logical, handedness}
 }
 \value{
-list with r, sizes, invalpha, angles, R0 and smooth interp.
-points
+list with r,  sizes,  invalpha,  angles, R0 and smooth interp. points
 }
 \description{
 helix curve
@@ -48,10 +45,9 @@ rgl.ellipsoids(cl$positions, sizes, cl$angles, col="gold")
 baptiste Auguie
 }
 \seealso{
-Other user_level cluster: \code{\link{cluster_chain}},
-\code{\link{cluster_dimer}},
-\code{\link{cluster_dimer_end}},
-\code{\link{cluster_helix}}, \code{\link{equal_angles}},
-\code{\link{equal_sizes}}
+Other user_level cluster: \code{\link{cluster_chain}};
+  \code{\link{cluster_dimer_end}};
+  \code{\link{cluster_dimer}}; \code{\link{cluster_helix}};
+  \code{\link{equal_angles}}; \code{\link{equal_sizes}}
 }
 
diff --git a/man/inverse_polarizability.Rd b/man/inverse_polarizability.Rd
index 55dbe62..0ec8bd2 100644
--- a/man/inverse_polarizability.Rd
+++ b/man/inverse_polarizability.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{inverse_polarizability}
 \alias{inverse_polarizability}
 \title{inverse_polarizability}
@@ -8,32 +7,29 @@ inverse_polarizability(cluster, material,
   polarizability_fun = polarizability_ellipsoid, ...)
 }
 \arguments{
-  \item{cluster}{cluster}
+\item{cluster}{cluster}
 
-  \item{material}{material}
+\item{material}{material}
 
-  \item{polarizability_fun}{polarizability function}
+\item{polarizability_fun}{polarizability function}
 
-  \item{...}{additional arguments passed to
-  polarizability_fun}
+\item{...}{additional arguments passed to polarizability_fun}
 }
 \value{
-matrix with each row being the 3 principal values of each
-polarizability tensor
+matrix with each row being the 3 principal values of each polarizability tensor
 }
 \description{
 inverse polarizability tensors
 }
 \details{
-calculates and formats the principal polarizability of
-several particles
+calculates and formats the principal polarizability of several particles
 }
 \author{
 Baptiste Auguie
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{alpha_kuwata}}, \code{\link{La}},
-\code{\link{polarizability_ellipsoid}}
+Other user_level polarizability: \code{\link{Kuwata.A}},
+  \code{\link{Kuwata.B}}, \code{\link{alpha_kuwata}};
+  \code{\link{La}}; \code{\link{polarizability_ellipsoid}}
 }
 
diff --git a/man/particles_povray.Rd b/man/particles_povray.Rd
index 833853a..c14380d 100644
--- a/man/particles_povray.Rd
+++ b/man/particles_povray.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{particles_povray}
 \alias{particles_povray}
 \title{particles_povray}
@@ -7,13 +6,13 @@
 particles_povray(positions, angles, sizes, out = "positions.pov")
 }
 \arguments{
-  \item{positions}{matrix of positions}
+\item{positions}{matrix of positions}
 
-  \item{angles}{matrix of Euler angles in radians}
+\item{angles}{matrix of Euler angles in radians}
 
-  \item{sizes}{matrix of particle sizes}
+\item{sizes}{matrix of particle sizes}
 
-  \item{out}{output filename}
+\item{out}{output filename}
 }
 \value{
 side-effect only
diff --git a/man/polarizability_ellipsoid.Rd b/man/polarizability_ellipsoid.Rd
index 48d8582..2fdcf01 100644
--- a/man/polarizability_ellipsoid.Rd
+++ b/man/polarizability_ellipsoid.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{polarizability_ellipsoid}
 \alias{polarizability_ellipsoid}
 \title{polarizability_ellipsoid}
@@ -8,47 +7,40 @@ polarizability_ellipsoid(wavelength, epsilon, a = 50, b = 30, c = b,
   medium = 1.33, kuwata = TRUE)
 }
 \arguments{
-  \item{wavelength}{wavelength in nm}
+\item{wavelength}{wavelength in nm}
 
-  \item{epsilon}{complex permittivity}
+\item{epsilon}{complex permittivity}
 
-  \item{a}{semi-axis in nm}
+\item{a}{semi-axis in nm}
 
-  \item{b}{semi-axis in nm}
+\item{b}{semi-axis in nm}
 
-  \item{c}{semi-axis in nm}
+\item{c}{semi-axis in nm}
 
-  \item{medium}{surrounding medium}
+\item{medium}{surrounding medium}
 
-  \item{kuwata}{logical, use Kuwata or Clausius Mossotti
-  prescription, see Details}
+\item{kuwata}{logical, use Kuwata or Clausius Mossotti prescription, see Details}
 }
 \value{
 matrix of polarizability
 }
 \description{
-principal polarizability components for an ellipsoidal
-particle
+principal polarizability components for an ellipsoidal particle
 }
 \details{
 uses the Kuwata prescription (see references)
 
-The Kuwata version includes semi-empirical terms of
-radiative correction and dynamic depolarisation to better
-match the fully retarded dipolar response in a reasonable
-range of (subwavelength) sizes and aspect ratios.
+The Kuwata version includes semi-empirical terms of radiative correction and dynamic depolarisation to better match the fully retarded dipolar response in a reasonable range of (subwavelength) sizes and aspect ratios.
 }
 \author{
 baptiste Auguie
 }
 \references{
-Kuwata et al. Resonant light scattering from metal
-nanoparticles: Practical analysis beyond Rayleigh
-approximation Appl. Phys. Lett. 83, 22 (2003)
+Kuwata et al. Resonant light scattering from metal nanoparticles: Practical analysis beyond Rayleigh approximation Appl. Phys. Lett. 83, 22 (2003)
 }
 \seealso{
-Other user_level polarizability:
-\code{\link{alpha_kuwata}},
-\code{\link{inverse_polarizability}}, \code{\link{La}}
+Other user_level polarizability: \code{\link{Kuwata.A}},
+  \code{\link{Kuwata.B}}, \code{\link{alpha_kuwata}};
+  \code{\link{La}}; \code{\link{inverse_polarizability}}
 }
 
diff --git a/man/rgl.ellipsoid.Rd b/man/rgl.ellipsoid.Rd
index 9635d42..6a1a1ca 100644
--- a/man/rgl.ellipsoid.Rd
+++ b/man/rgl.ellipsoid.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{rgl.ellipsoid}
 \alias{rgl.ellipsoid}
 \title{rgl.ellipsoid}
@@ -8,29 +7,29 @@ rgl.ellipsoid(x = 0, y = 0, z = 0, a = 1, b = 1, c = 1, phi = 0,
   theta = 0, psi = 0, subdivide = 3, smooth = TRUE, ...)
 }
 \arguments{
-  \item{x}{x}
+\item{x}{x}
 
-  \item{y}{y}
+\item{y}{y}
 
-  \item{z}{z}
+\item{z}{z}
 
-  \item{a}{axis}
+\item{a}{axis}
 
-  \item{b}{axis}
+\item{b}{axis}
 
-  \item{c}{axis}
+\item{c}{axis}
 
-  \item{phi}{phi}
+\item{phi}{phi}
 
-  \item{theta}{theta}
+\item{theta}{theta}
 
-  \item{psi}{psi}
+\item{psi}{psi}
 
-  \item{subdivide}{subdivision}
+\item{subdivide}{subdivision}
 
-  \item{smooth}{smoothing}
+\item{smooth}{smoothing}
 
-  \item{...}{additional params}
+\item{...}{additional params}
 }
 \value{
 an rgl mesh
@@ -49,7 +48,7 @@ shapelist3d(ee) }
 baptiste Auguie
 }
 \seealso{
-Other user_level rgl: \code{\link{rgl_annotate}},
-\code{\link{rgl.ellipsoids}}
+Other user_level rgl: \code{\link{rgl.ellipsoids}};
+  \code{\link{rgl_annotate}}
 }
 
diff --git a/man/rgl.ellipsoids.Rd b/man/rgl.ellipsoids.Rd
index f48339e..2c52abd 100644
--- a/man/rgl.ellipsoids.Rd
+++ b/man/rgl.ellipsoids.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{rgl.ellipsoids}
 \alias{rgl.ellipsoids}
 \title{rgl.ellipsoids}
@@ -7,13 +6,13 @@
 rgl.ellipsoids(positions, sizes, angles, ...)
 }
 \arguments{
-  \item{positions}{matrix of positions}
+\item{positions}{matrix of positions}
 
-  \item{sizes}{matrix of axis lengths}
+\item{sizes}{matrix of axis lengths}
 
-  \item{angles}{matrix of Euler angles}
+\item{angles}{matrix of Euler angles}
 
-  \item{...}{additional params}
+\item{...}{additional params}
 }
 \value{
 rgl mesh
@@ -22,8 +21,7 @@ rgl mesh
 Create a list of rgl ellipsoids oriented in space
 }
 \details{
-each ellipsoid is specified by its position, dimensions,
-and Euler angles
+each ellipsoid is specified by its position, dimensions, and Euler angles
 }
 \examples{
 cl <- helix(0.5, 1, 36, delta=pi/6, n.smooth=1e3)
@@ -34,7 +32,7 @@ sizes <- equal_sizes(0.04,0.02,0.02,NROW(cl$positions))
 baptiste Auguie
 }
 \seealso{
-Other user_level rgl: \code{\link{rgl_annotate}},
-\code{\link{rgl.ellipsoid}}
+Other user_level rgl: \code{\link{rgl.ellipsoid}};
+  \code{\link{rgl_annotate}}
 }
 
diff --git a/man/rgl_annotate.Rd b/man/rgl_annotate.Rd
index 7c4f05d..40a4752 100644
--- a/man/rgl_annotate.Rd
+++ b/man/rgl_annotate.Rd
@@ -1,5 +1,4 @@
-% Generated by roxygen2 (4.0.0): do not edit by hand
-
+% Generated by roxygen2 (4.0.1.99): do not edit by hand
 \name{rgl_annotate}
 \alias{rgl_annotate}
 \title{rgl_annotate}
@@ -19,7 +18,7 @@ x, y, z axes
 baptiste Auguie
 }
 \seealso{
-Other user_level rgl: \code{\link{rgl.ellipsoid}},
-\code{\link{rgl.ellipsoids}}
+Other user_level rgl: \code{\link{rgl.ellipsoids}};
+  \code{\link{rgl.ellipsoid}}
 }