shorter example times for tracelines and capzone

.Rbuildignore

@@ -8,3 +8,4 @@
 ^pkgdown$
 ^codecov\.yml$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: raem
 Title: Analytic Element Modeling of Steady Single-Layer Groundwater Flow
-Version: 0.0.0.9000
+Version: 0.1.0
 Authors@R: 
     person("Cas", "Neyens", , "[email protected]", role = c("aut", "cre", "cph"))
 Description: Analytic element modeling of steady-state, single-layer
-    groundwater flow under the Dupuit-Forchheimer assumption. Elements
-    such as wells, area-sinks and line-sinks can be placed at arbitrary 
-    locations in the flow field. Output variables include hydraulic head 
-    and the discharge vector. Tracelines can be computed numerically in 
-    three dimensions.
+    groundwater flow under the 'Dupuit-Forchheimer' assumption. Elements
+    such as wells, area-sinks and line-sinks can be placed at arbitrary
+    locations in the flow field. Output variables include hydraulic head
+    and the discharge vector. Particle traces can be computed numerically
+    in three dimensions.
 License: MIT + file LICENSE
 URL: https://github.com/cneyens/raem, https://cneyens.github.io/raem/
 BugReports: https://github.com/cneyens/raem/issues
@@ -24,6 +24,8 @@ Suggests:
     sf,
     terra,
     testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -40,4 +42,3 @@ Collate:
     'uniformflow.R'
     'utils.R'
     'well.R'
-VignetteBuilder: knitr

R/tracelines.R

@@ -188,6 +188,8 @@ outside_vertical <- function(aem, x, y, z, ...) {
 #' @export
 #' @seealso [capzone()]
 #' @examples
+#' # -------
+#' # create a model with uniform background flow
 #' k <- 10
 #' top <- 10; base <- 0
 #' n <- 0.2
@@ -199,14 +201,16 @@ outside_vertical <- function(aem, x, y, z, ...) {
 #'
 #' m <- aem(k, top, base, n = n, uf, rf)
 #'
-#' x0 <- -200; y0 <- seq(-200, 200, 50)
+#' # calculate forward particle traces
+#' x0 <- -200; y0 <- seq(-200, 200, 200)
 #' times <- seq(0, 25 * 365, 365 / 4)
 #' paths <- tracelines(m, x0 = x0, y0 = y0, z = top, times = times)
 #' endp <- endpoints(paths)
 #'
 #' xg <- seq(-500, 500, length = 100)
 #' yg <- seq(-300, 300, length = 100)
 #'
+#' # plot
 #' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
 #' plot(paths, add = TRUE, col = 'orange')
 #' points(endp[, c('x', 'y')])
@@ -215,58 +219,69 @@ outside_vertical <- function(aem, x, y, z, ...) {
 #' paths_back <- tracelines(m, x0 = x0, y0 = y0, z0 = top, times = times, R = R, forward = FALSE)
 #' plot(paths_back, add = TRUE, col = 'forestgreen', marker = 5*365, cex = 0.5)
 #'
-#' # Termination at wells and line-sinks
+#' # -------
+#' # Termination at wells, line-sinks and user-defined zone
 #' w1 <- well(200, 50, Q = 250)
 #' w2 <- well(-200, -100, Q = 450)
 #' ls <- headlinesink(x0 = -100, y0 = 100, x1 = 400, y1 = -300, hc = 7)
 #'
 #' m <- aem(k, top, base, n = n, uf, rf, w1, w2, ls)
-#' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
-#' plot(m, add = TRUE)
-#'
-#' x0 <- seq(-400, 400, 50); y0 <- 200
-#' times <- seq(0, 5 * 365, 365 / 20)
-#' paths <- tracelines(m, x0 = x0, y0 = y0, z0 = top, times = times)
-#' plot(paths, add = TRUE, col = 'orange')
 #'
 #' # User-defined termination in rectangular zone
 #' tzone <- cbind(x = c(-300, -200, -200, -300), y = c(150, 150, 100, 100))
 #' termf <- function(t, coords, parms) {
 #'   x <- coords[1]
 #'   y <- coords[2]
 #'   in_poly <- x <= max(tzone[,'x']) & x >= min(tzone[,'x']) &
-#'              y <= max(tzone[,'y']) & y >= min(tzone[,'y'])
+#'     y <= max(tzone[,'y']) & y >= min(tzone[,'y'])
 #'   return(in_poly)
 #' }
 #'
+#' x0 <- c(-300, -200, 0, 200, 300)
+#' y0 <- 200
+#' times <- seq(0, 5 * 365, 365 / 15)
 #' paths <- tracelines(m, x0 = x0, y0 = y0, z0 = top, times = times, tfunc = termf)
+#'
 #' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
 #' plot(m, add = TRUE)
 #' polygon(tzone)
 #' plot(paths, add = TRUE, col = 'orange')
 #'
+#' # -------
 #' # model with vertical flow due to area-sink
 #' as <- areasink(xc = 0, yc = 0, N = 0.001, R = 1500)
 #' m <- aem(k, top, base, n = n, uf, rf, w1, w2, as)
 #'
 #' # starting z0 locations are above aquifer top and will be reset to top with warning
+#' x0 <- seq(-400, 200, 200); y0 <- 200
+#' times <- seq(0, 5 * 365, 365 / 4)
 #' paths <- tracelines(m, x0 = x0, y0 = y0, z0 = top + 0.5, times = times)
 #'
 #' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
 #' plot(m, add = TRUE)
 #' plot(paths, add = TRUE, col = 'orange')
 #'
+#' # -------
 #' # plot vertical cross-section of traceline 4 along increasing y-axis (from south to north)
 #' plot(paths[[4]][,c('y', 'z')], type = 'l')
 #'
-#' @examplesIf parallel::detectCores() > 1
+#' # -------
 #' # parallel computing by setting ncores > 0
 #' mp <- aem(k, top, base, n = n, uf, rf)
-#'
-#' x0 <- -200; y0 <- seq(-200, 200, 50)
-#' times <- seq(0, 25 * 365, 365 / 4)
 #' pathsp <- tracelines(mp, x0 = x0, y0 = y0, z = top, times = times, ncores = 2)
 #'
+#' # -------
+#' # plot arrows
+#' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
+#' plot(paths, add = TRUE, col = 'orange', arrows = TRUE, length = 0.05)
+#'
+#' # plot point markers every 2.5 years
+#' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
+#' plot(paths, add = TRUE, col = 'orange', marker = 2.5 * 365, pch = 20)
+#'
+#' # plot point markers every 600 days
+#' plot(paths, add = TRUE, col = 'forestgreen', marker = 600, pch = 1)
+#'
 tracelines <- function(aem, x0, y0, z0, times, forward = TRUE, R = 1, tfunc = NULL, tol = 1e-3, ncores = 0, ...) {
 
   if(!is.null(tfunc) & !is.list(tfunc)) tfunc <- list(tfunc)
@@ -412,41 +427,31 @@ endpoints <- function(tracelines, ...) {
 #' @export
 #' @seealso [tracelines()]
 #' @examples
+#' # A model with vertical flow components
 #' k <- 10
 #' top <- 10; base <- 0
 #' n <- 0.3
 #'
 #' uf <- uniformflow(TR = 100, gradient = 0.001, angle = -10)
 #' rf <- constant(TR, xc = -1000, yc = 0, hc = 20)
-#' w1 = well(200, 50, Q = 250)
-#' w2 = well(-200, -100, Q = 450)
+#' w1 <- well(200, 50, Q = 250)
+#' w2 <- well(-200, -100, Q = 450)
+#' as <- areasink(0, 0, N = 0.001, R = 1500)
 #'
-#' m <- aem(k, top, base, n = n, uf, rf, w1, w2)
+#' m <- aem(k, top, base, n = n, uf, rf, w1, w2, as)
 #'
-#' # 5-year and 10-year capture zones
-#' cp5 <- capzone(m, w1, time = 5*365)
-#' cp10 <- capzone(m, w2, time = 10*365)
+#' # 5-year capture zone at two different starting levels
+#' cp5a <- capzone(m, w1, time = 5 * 365, zstart = base, npar = 6, dt = 365 / 4)
+#' cp5b <- capzone(m, w1, time = 5 * 365, zstart = 8, npar = 6, dt = 365 / 4)
 #'
 #' xg <- seq(-800, 800, length = 100)
 #' yg <- seq(-500, 500, length = 100)
-#'
-#' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
-#' plot(cp5, add = TRUE)
-#' plot(cp10, add = TRUE, col = 'orange')
-#'
-#' # model with vertical flow components
-#' as <- areasink(0, 0, N = 0.001, R = 1500)
-#' m <- aem(k, top, base, n = n, uf, rf, w1, w2, as)
-#'
-#' # two different starting levels
-#' cp5a <- capzone(m, w1, time = 5*365, zstart = base)
-#' cp5b <- capzone(m, w1, time = 5*365, zstart = 8)
-#'
 #' contours(m, xg, yg, col = 'dodgerblue', nlevels = 20)
 #' plot(cp5a, add = TRUE)
 #' plot(cp5b, add = TRUE, col = 'forestgreen') # smaller zone
 #'
 #' # plot the convex hull of the endpoints as a polygon
+#' # increase the number of particles to obtain a sharper delineation of the envelope
 #' endp <- endpoints(cp5b)
 #' hull <- chull(endp[, c('x', 'y')])
 #' polygon(endp[hull, c('x', 'y')], col = adjustcolor('forestgreen', alpha.f = 0.7))

cran-comments.md

@@ -1,16 +1,14 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+ * Reduced the elapsed time of some examples.
+
+ * Handled words flagged as possibly misspelled in DESCRIPTION. 
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
 
-* checking examples ... [32s] NOTE
-  Examples with CPU (user + system) or elapsed time > 5s
-              user system elapsed
-  capzone    16.41   0.28   17.02
-  tracelines 12.42   0.33   14.34
-
-  The underlying computations require numerical integration which is slow. 
-  Reducing the run time of the examples would require changing them in such a way that 
-  they are no longer meaningful examples.