Ironing out some namespace stuff

DESCRIPTION

@@ -1,24 +1,23 @@
 Package: deform
 Type: Package
-Title: Crustal deformation tools in R
-Version: 0.0-2
-Date: 2014-11-04
+Title: Crustal deformation modeling tools in R
+Version: 0.0-4
+Date: 2014-11-07
 Author: Andrew J. Barbour; some of these tools were
-    adapted from Matlab code by Brendan Crowell (UW),
+    adapted from Matlab codes by Brendan Crowell (UW),
     and Francois Beauducel (IPGP).
 Maintainer: A.J.Barbour <[email protected]>
-Description: Crustal deformation tools.
-License: GPL3
+Description: Crustal deformation modeling tools.
+License: GPL
 Imports:
     Rcpp (>= 0.11.2)
 Depends:
-    RCurl,
     rgdal,
     sp,
-    maptools,
-    plyr,
-    reshape2,
-    abind
+    maptools
 Suggests:
-    maps
+    RColorBrewer,
+    TeachingDemos,
+    maps,
+    plyr
 LinkingTo: Rcpp

NAMESPACE

@@ -21,5 +21,9 @@ export(timevarying_fluidmass)
 export(timevarying_porepressure)
 export(timevarying_surface_displacement)
 exportPattern("^[[:alpha:]]+")
+importFrom(RCurl,getURL)
+importFrom(RCurl,url.exists)
 importFrom(Rcpp,evalCpp)
+importFrom(abind,abind)
+importFrom(plyr,mutate)
 useDynLib(deform)

NOBUILD/Sandbox/segall.R

@@ -1,6 +1,7 @@
-library(deform)
 library(kook)
+library(plyr)
 library(TeachingDemos)
+library(deform)
 
 .x. <- sort(unique(c(-7:-3, seq(-3.90,3.90,by=0.15), 3:7)))
 su <- surface_displacement(.x.*1e3, C.=1e13, z_src=0.7e3)
@@ -58,31 +59,32 @@ F3 <- function(){
   matplot(.x.km., zz2*1e3, type="l", col="black", main="Subsidence, mm, Segall 1985, Fig 8B", sub=Sys.time())
 }
 
+try(F3())
+
 F3t <- function(){
   #matplot(.time./yr, t(zz2t), type="l")
-  matplot(.x.km., zz2t, type="l", col="black")
+  matplot(.x.km., zz2t*1e6, type="l", col="black", main="Tilt")
 }
 
-#try(F3())
-#try(F3t())
-
+try(F3t())
 
 zz3 <- timevarying_fluidmass(.x.km.*1e3, .time., .Vdot., .L., .t., .c., phi.=.phi.)
 
 F4 <- function(){
   #matplot(.time./yr, t(zz3)*1e2, type="l")
-  matplot(.x.km., zz3*1e2, type="l", col="black")
+  matplot(.x.km., zz3*1e2, type="l", col="black", main="t.v. Fluid mass change")
 }
 
-#try(F4())
+try(F4())
 
-zzp <- timevarying_porepressure(.x.km.*1e3, .z.km.*1e3, .time., .Vdot., .B., .L., .D., .c., .t., .mu., Pt.Sources.x=.TwoSources.x.)
+redo <- FALSE
+if (!exists("zzp") | redo) zzp <- timevarying_porepressure(.x.km.*1e3, .z.km.*1e3, .time., .Vdot., .B., .L., .D., .c., .t., .mu., Pt.Sources.x=.TwoSources.x.)
 
 F5 <- function(do.log=FALSE){
   #matplot(.time./yr, t(zz3)*1e2, type="l")
   X<- zzp[,,length(.time.)]
   if (do.log) X <- log10(abs(X))
-  matplot(x=.x.km., X, col=NA)
+  matplot(x=.x.km., X, col=NA, main="t.v. Pore pressure")
   aaply(zzp, 3, .fun = function(X) {
     if (do.log) X <- log10(abs(X))
     matplot(x=.x.km., X, type="l", add=TRUE)
@@ -95,14 +97,17 @@ try(F5())
 
 
 F5c <- function(){
-  #matplot(.time./yr, t(zz3)*1e2, type="l")
-  #contour(x=.x.km., y=.z.km., zzp[,,length(.time.)], col=NA)
+  layout(matrix(seq_len(dim(zzp)[3]), nrow=1))
   aaply(zzp, 3, .fun = function(X) {
-    image(x=.x.km., y=.z.km., X, ylim=c(12,0), col = brewerRamp())
-    contour(x=.x.km., y=.z.km., X, ylim=c(12,0), add = TRUE)
+    image(x=.x.km., y=.z.km., X, ylim=c(6,0), col = brewerRamp())
+    contour(x=.x.km., y=.z.km., X, ylim=c(6,0), add = TRUE)
+    abline(v=.TwoSources.x./1e3, col="grey", lwd=2)
+    abline(h=(.D.+c(-1*.t.,.t.)/2)/1e3, col="grey", lwd=2)
     return("x")
     })
+
   invisible()
+  layout(matrix(1))
 }
 
-#try(F5c())
+try(F5c())

R/deform-package.R

@@ -3,9 +3,15 @@
 #' 
 #' @name deform
 #' @docType package
+#' 
 #' @useDynLib deform
+#' 
 #' @exportPattern "^[[:alpha:]]+"
+#' 
 #' @importFrom Rcpp evalCpp
+#' @importFrom abind abind
+#' @importFrom plyr mutate
+#' @importFrom RCurl url.exists getURL
 #' 
 #' @seealso \code{\link{segall85}} for deformation associated with fluid extraction
 NULL

R/deform-utilities.R

@@ -8,21 +8,21 @@ erf <- function(x){
 #' @rdname erf
 #' @export
 erfc <- function(x){
-  2 * pnorm(x * sqrt(2), lower = FALSE)
+  2 * pnorm(x * sqrt(2), lower.tail = FALSE)
 }
 
 #' @rdname erf
 #' @export
 ierf <- function (x){
-  qnorm((1 + x)/2)/sqrt(2)
+  qnorm((1 + x) / 2) / sqrt(2)
 }
 
 #' @rdname erf
 #' @export
 ierfc <- function (x){
-  qnorm(x/2, lower = FALSE)/sqrt(2)
+  qnorm(x/2, lower.tail = FALSE) / sqrt(2)
 }
 
 ierfc2 <- function(x){
-  exp(-1*x^2)/sqrt(pi) - x*erfc(x)
+  exp(-1 * x^2) / sqrt(pi) - x * erfc(x)
 }

R/epsg.R

@@ -72,8 +72,8 @@ getEPSG <- function(ref.id=4326, verbose=TRUE, agency=NULL){
   #http://spatialreference.org/ref/epsg/4326/proj4/
   ref.url <- sprintf("%s/%s/proj4/", agency.root(agency), ref.id)
   if (verbose) message(ref.url)
-  stopifnot(RCurl::url.exists(ref.url))
-  prj <- RCurl::getURL(ref.url)
+  stopifnot(url.exists(ref.url))
+  prj <- getURL(ref.url)
   return(prj)
 }