Merge pull request #44 from MindTheGap-ERC/dev

Dev

NAMESPACE

@@ -76,6 +76,7 @@ S3method(time_to_strat,phylo)
 export(L_axis_lab)
 export(T_axis_lab)
 export(add_adm_to_multiadm)
+export(anchor)
 export(condensation)
 export(condensation_fun)
 export(flux_const)

NEWS.md

@@ -1,10 +1,12 @@
 # admtools (development version)
 
+* added anchoring of age-depth models via `anchor`
+
 # admtools 0.3.1
 
 * more options for sedimentation rate generator `sed_rate_from_matrix`
 
-* abstracted exctraction of tie points
+* abstracted extraction of tie points
 
 * added utility functions for S3 class `sac`
 

R/anchor.R

@@ -0,0 +1,63 @@
+anchor = function(x, index = "last", t_anchor = NULL, n = 1000L){
+  #' @export
+  #' 
+  #' @title anchor age-depth model
+  #' 
+  #' @param x age-depth model
+  #' @param index "last" or "first", specifying at which tie point the age-depth model will be anchored
+  #' @param t_anchor time at which the adm is anchored. must be a function that takes no arguments and returns the timing of the tie point. see example or vignettes for details
+  #' @param n integer, number of samples drawn from the tie point
+  #' 
+  #' @description
+    #' anchors a deterministic age-depth model (adm object) at a tie point that is associated with uncertainty. 
+    #' 
+    #' 
+  #' 
+  #' @returns a collection of age-depth models (a multiadm object)
+  #' 
+  #' @examples
+    #' t_anchor = function() rnorm(1) # normally distributed uncertainty
+    #' x = tp_to_adm(t = c(1,2), h = c(2,3)) # simple age-depth model
+    #' m = anchor(x, index = "last", t_anchor = t_anchor, n = 100) # anchor age-depth model
+    #' plot(m)
+    #' 
+  if (! index %in% c("last", "first")){
+    stop("can only anchor at first or last tie point")
+  }
+
+  if (! (is.function(t_anchor))){
+    stop("expect functions as inputs for t_anchor")
+  }
+  adm_list = list()
+  if (index == "last"){
+    t_ref = max_time(x)
+  }
+  if (index == "first"){
+    t_ref = min_time(x)
+  }
+
+  for (i in seq_len(n)){
+    t_offset = t_anchor()
+    t = get_T_tp(x) - t_ref + t_offset
+    h = get_L_tp(x)
+    L_unit = get_L_unit(x)
+    T_unit = get_T_unit(x)
+    adm_list[[i]] = tp_to_adm(t, h, T_unit, L_unit)
+  }
+
+  multiadm = list("t" = list(),
+                  "h" = list(),
+                  "destr" = list(),
+                  "no_of_entries" = length(adm_list),
+                  "T_unit" = get_T_unit(x),
+                  "L_unit" = get_L_unit(x))
+
+  for (i in seq_along(adm_list)){
+    adm = adm_list[[i]]
+    multiadm[["t"]][[i]] = adm$t
+    multiadm[["h"]][[i]] = adm$h
+    multiadm[["destr"]][[i]] = adm$destr
+  }
+  class(multiadm) = "multiadm"
+  return(multiadm)
+}

R/merge_adm_to_multiadm.R

@@ -20,11 +20,11 @@ merge_adm_to_multiadm = function(...){
                   "L_unit" = NULL)
   T_units = unlist(sapply(adm_list, get_T_unit))
   L_units = unlist(sapply(adm_list, get_L_unit))
-  
-  if (any(rep(T_units[1], length(adm_list)) != T_units)){
-    stop("Inconsistent time units, can not merge adms")
+
+   if (any(rep(T_units[1], length(adm_list)) != T_units)){
+     stop("Inconsistent time units, can not merge adms")
   }
-  if (any(rep(L_units[1], length(adm_list)) != L_units)){
+   if (any(rep(L_units[1], length(adm_list)) != L_units)){
     stop("Inconsistent length units, can not merge adms")
   }
 

R/tp_helpers.R

@@ -91,7 +91,7 @@ tp_time_det = function(times){
   #' 
   #' @seealso [tp_height_det()] for deterministic tie points in height, [tp_time_norm()] for tie points following a normal distribution 
   #' 
-  #' @returns a function for usage with _strat_cont_to_multiadm_ and_sedrate_to_mulitadm_ as t_tp input
+  #' @returns a function for usage with _strat_cont_to_multiadm_ and _sedrate_to_mulitadm_ as t_tp input
   #' 
   if (is.unsorted(times, strictly = TRUE)){
     stop("Need strictly increasing times")

R/tp_to_adm.R

@@ -11,8 +11,8 @@ tp_to_adm = function(t, h, T_unit = NULL, L_unit = NULL){
   #' 
   #' @param t Vector, tie points in time
   #' @param h Vector, tie points in height
-  #' @param T_unit time unit
-  #' @param L_unit length unit
+  #' @param T_unit character, time unit
+  #' @param L_unit character, length unit
   #' 
   #' @details
     #' by default, intervals with no sediment accumulation are marked as destructive.
@@ -26,11 +26,11 @@ tp_to_adm = function(t, h, T_unit = NULL, L_unit = NULL){
   #'
   #'
   #' @examples
-    #' \dontrun{
+    #' 
     #' my_adm = tp_to_adm(t = 1:4, h = c(1,2,2,3), T_unit = "kyr", L_unit = "m")
     #' plot(my_adm)
     #' # see vignette("admtools") for other examples
-    #' }
+    #' 
     #'  
   #' 
 

tests/testthat/test_anchor.R

@@ -0,0 +1,13 @@
+test_that("incorrect input for index paramter is caught", {
+  t_anchor = function() rnorm(n = 1)
+  x = tp_to_adm(c(0,1), c(0,1), "Myr", "m")
+  expect_no_condition(anchor(x, index = "last", t_anchor, n = 10))
+  expect_no_condition(anchor(x, index = "first", t_anchor, n = 10))
+  expect_error(anchor(x, index = 2, t_anchor, n = 10))
+})
+
+test_that("incorrect input for t_anchor parameter is caught", {
+  x = tp_to_adm(c(0,1), c(0,1), "Myr", "m")
+  t_anchor = 2
+  expect_error(anchor(x, "last", t_anchor, n = 10))
+})

vignettes/admtools_doc.Rmd

@@ -101,6 +101,7 @@ The following functions transform `adm` objects into other S3 classes:
 
 -   `merge_adm_to_multiadm` into `multiamd`
 -   `add_adm_to_multiadm` to add `adm` to `multiadm`
+-   `anchor` to transform anchor `adm` at a tie point with uncertainty, resulting in a `multiadm`
 
 ### S3 class `sac`
 
@@ -177,7 +178,8 @@ The S3 class `multiadm` represents **multi**ple **a**ge **d**epth **m**odels.. S
 
 The following functions construct `multiadm` objects:
 
--   `merge_adm_to_multiadm` to contruct `multiadm` from `adm` objects
+-   `anchor` to construct `multiadm` from uncertain tie points and `adm` objects.
+-   `merge_adm_to_multiadm` to construct `multiadm` from `adm` objects
 -   `sedrate_to_multiadm` construct `multiadm` from info on sedimentation rates, see `vignette("adm_from_sedrate")`
 -   `strat_cont_to_multiadm` construct `multiadm` from tracer information, see `vignette("adm_from_trace_cont")`