Adding prm (production rates) and Lambda (attenuation length) as built in...

Adding prm (production rates) and Lambda (attenuation length) as built in paramters accessible to the user.

DESCRIPTION

@@ -17,3 +17,5 @@ Imports:
     pracma,
     shiny,
     shinyWidgets
+Depends: 
+    R (>= 2.10)

R/data.R

+#' A set of reference parameters for SLHL production rates and decay constant
+#'
+#' 10Be, 26Al and 14C spallation production rates from Borchers et al. (2016).
+#' 10Be and 26Al muons production rates are from Braucher et al. (2011).
+#' 14C muons production rate is from Lupker et al. (2015).
+#'
+#' Borchers, B., Marrero, S., Balco, G., Caffee, M., Goehring, B., Lifton, N., Nishiizumi, K., Phillips, F., Schaefer, J., & Stone, J. (2016). Geological calibration of spallation production rates in the CRONUS-Earth project. Quaternary Geochronology, 31, 188–198. https://doi.org/10.1016/j.quageo.2015.01.009
+#'
+#' Braucher, R., Merchel, S., Borgomano, J., & Bourlès, D. L. (2011). Production of cosmogenic radionuclides at great depth: A multi element approach. Earth and Planetary Science Letters, 309(1–2), 1–9. http://dx.doi.org/10.1016/j.epsl.2011.06.036
+#'
+#' Lupker, M., Hippe, K., Wacker, L., Kober, F., Maden, C., Braucher, R., Bourlès, D., Romani, J. R. V., & Wieler, R. (2015). Depth-dependence of the production rate of in situ14C in quartz from the Leymon High core, Spain. Quaternary Geochronology, 28, 80–87. https://doi.org/10.1016/j.quageo.2015.04.004
+#'
+#' @format A matrix with nuclides in columns and production rates or decay constant in rows
+#' \describe{
+#'   \item{Pspal}{SLHL spallation production rate for scaling scheme st (at/g/a)}
+#'   \item{Pstop}{SL stopping muons production rate (at/g/a)}
+#'   \item{Pfast}{SL fast muons production rate (at/g/a)}
+#'   \item{lambda}{Decay constant (1/a)}
+#' }
+#'
+"prm"
+
+
+#' A set of attenuation lengths for cosmogenic nuclides production pathways
+#'
+#'
+#' @format A vector with 3 elements
+#' \describe{
+#'   \item{Lspal}{Spallogenic neutrons attenuation length (g/cm2)}
+#'   \item{Lstop}{Stopping muons attenuation length (g/cm2)}
+#'   \item{Lfast}{Fast muons attenuation length (g/cm2)}
+#' }
+#'
+"Lambda"
+
+
+

R/sato_muons.R

@@ -14,7 +14,7 @@
 #' @keywords
 #' @export
 #' @examples
-#' sato_muons
+#'
 sato_muons <- function(h,Rc,s) {
 
 # Sato et al. (2008) Neutron Spectrum

R/sato_neutrons_low.R

@@ -15,7 +15,7 @@
 #' @keywords
 #' @export
 #' @examples
-#' sato_neutrons_low
+#'
 sato_neutrons_low <- function(h,Rc,s,w) {
 
 #reduced version that does not do cross-sections but includes thermal and

R/utils.R

@@ -11,7 +11,7 @@
 #' @param lon2 longitude of point 2 (degrees)
 #' @keywords
 #' @examples
-#' angdist
+#'
 angdist<-function(lat1,lon1,lat2,lon2){
   lata = d2r(lat1)
   lona = d2r(lon1)
@@ -31,7 +31,7 @@ angdist<-function(lat1,lon1,lat2,lon2){
 #' @param a angle (degrees)
 #' @keywords
 #' @examples
-#' d2r
+#'
 d2r<-function(a){
   return(a/180*pi)
 }
@@ -45,7 +45,7 @@ d2r<-function(a){
 #' @param a angle (radians)
 #' @keywords
 #' @examples
-#' r2d
+#'
 r2d<-function(a){
   return(a/pi*180)
 }

devs/data/data_packaging.R

+
+# data accessible to the users ----
+
+
+# Production and decay parameters
+prm = matrix(c( 4.01  , 0.012 , 0.039  , log(2)/1.36e6,
+                27.93 , 0.84  , 0.081 , log(2)/0.717e6,
+                12.24  , 3.31  , 0     ,log(2)/5730),
+             nrow = 4,ncol=3 )
+colnames(prm) <- c("Be10","Al26","C14") # we just give names to the columns of the matrix
+rownames(prm) <- c("Pspal","Pstop","Pfast","lambda")  # we just give names to the rows of the matrix
+
+## references values for production and decay
+Lambda = c(160,1500,4320) # g/cm2
+names(Lambda) <- c("Lspal","Lstop","Lfast") # we just give names to the element of the vector
+
+## export -----
+usethis::use_data(prm,Lambda, internal = FALSE, overwrite = TRUE)
+

index.md

+
+A set of utilities for the analysis of Terrestrial Cosmogenic Nuclides (TCN) concentrations under complex exposure and erosion histories of the Earth surface
+
+## Installation
+The simplest way to install the package is using `devtools` :
+
+devtools::install_git(url = "https://gitlab.osupytheas.fr/vgodard/tcntools")
+
+## Tutorials 
+
+- [Scaling](https://people.cerege.fr/~vgodard/tcntools/TCNtools_scaling.html)
+- [Eulerian solver](https://people.cerege.fr/~vgodard/tcntools/TCNtools_eulerian_solver.html)
+- [2 nuclides plots](https://people.cerege.fr/~vgodard/tcntools/TCNtools_2_nuclides_plots.html)
+

man/Lambda.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{Lambda}
+\alias{Lambda}
+\title{A set of attenuation lengths for cosmogenic nuclides production pathways}
+\format{
+A vector with 3 elements
+\describe{
+  \item{Lspal}{Spallogenic neutrons attenuation length (g/cm2)}
+  \item{Lstop}{Stopping muons attenuation length (g/cm2)}
+  \item{Lfast}{Fast muons attenuation length (g/cm2)}
+}
+}
+\usage{
+Lambda
+}
+\description{
+A set of attenuation lengths for cosmogenic nuclides production pathways
+}
+\keyword{datasets}

man/angdist.Rd

@@ -19,5 +19,5 @@ angdist(lat1, lon1, lat2, lon2)
 Calculates angular distance theta between points on a sphere specified by latitude and longitude
 }
 \examples{
-angdist
+
 }

man/d2r.Rd

@@ -13,5 +13,5 @@ d2r(a)
 Degrees to radians conversion
 }
 \examples{
-d2r
+
 }

man/prm.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{prm}
+\alias{prm}
+\title{A set of reference parameters for SLHL production rates and decay constant}
+\format{
+A matrix with nuclides in columns and production rates or decay constant in rows
+\describe{
+  \item{Pspal}{SLHL spallation production rate for scaling scheme st (at/g/a)}
+  \item{Pstop}{SL stopping muons production rate (at/g/a)}
+  \item{Pfast}{SL fast muons production rate (at/g/a)}
+  \item{lambda}{Decay constant (1/a)}
+}
+}
+\usage{
+prm
+}
+\description{
+10Be, 26Al and 14C spallation production rates from Borchers et al. (2016).
+10Be and 26Al muons production rates are from Braucher et al. (2011).
+14C muons production rate is from Lupker et al. (2015).
+}
+\details{
+Borchers, B., Marrero, S., Balco, G., Caffee, M., Goehring, B., Lifton, N., Nishiizumi, K., Phillips, F., Schaefer, J., & Stone, J. (2016). Geological calibration of spallation production rates in the CRONUS-Earth project. Quaternary Geochronology, 31, 188–198. https://doi.org/10.1016/j.quageo.2015.01.009
+
+Braucher, R., Merchel, S., Borgomano, J., & Bourlès, D. L. (2011). Production of cosmogenic radionuclides at great depth: A multi element approach. Earth and Planetary Science Letters, 309(1–2), 1–9. http://dx.doi.org/10.1016/j.epsl.2011.06.036
+
+Lupker, M., Hippe, K., Wacker, L., Kober, F., Maden, C., Braucher, R., Bourlès, D., Romani, J. R. V., & Wieler, R. (2015). Depth-dependence of the production rate of in situ14C in quartz from the Leymon High core, Spain. Quaternary Geochronology, 28, 80–87. https://doi.org/10.1016/j.quageo.2015.04.004
+}
+\keyword{datasets}

man/r2d.Rd

@@ -13,5 +13,5 @@ r2d(a)
 Radians to degrees conversion
 }
 \examples{
-r2d
+
 }

man/sato_muons.Rd

@@ -24,5 +24,5 @@ Lifton, N., Sato, T., & Dunai, T. J. (\strong{2014}). Scaling in situ cosmogenic
 https://doi.org/10.1016/j.epsl.2013.10.052
 }
 \examples{
-sato_muons
+
 }

man/sato_neutrons_low.Rd

@@ -26,5 +26,5 @@ Lifton, N., Sato, T., & Dunai, T. J. (\strong{2014}). Scaling in situ cosmogenic
 https://doi.org/10.1016/j.epsl.2013.10.052
 }
 \examples{
-sato_neutrons_low
+
 }