abstract extraction of tie points

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: admtools
 Title: Estimate and Manipulate Age-Depth Models
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: 
     person("Niklas", "Hohmann", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))

NAMESPACE

@@ -2,9 +2,13 @@
 
 S3method(condensation,adm)
 S3method(condensation,multiadm)
+S3method(get_L_tp,adm)
+S3method(get_L_tp,sac)
 S3method(get_L_unit,adm)
 S3method(get_L_unit,multiadm)
 S3method(get_L_unit,sac)
+S3method(get_T_tp,adm)
+S3method(get_T_tp,sac)
 S3method(get_T_unit,adm)
 S3method(get_T_unit,multiadm)
 S3method(get_T_unit,sac)
@@ -68,7 +72,9 @@ export(condensation_fun)
 export(flux_const)
 export(flux_linear)
 export(flux_quad)
+export(get_L_tp)
 export(get_L_unit)
+export(get_T_tp)
 export(get_T_unit)
 export(get_completeness)
 export(get_data_from_eTimeOpt)

NEWS.md

@@ -1,4 +1,8 @@
-# admtools (development version)
+# admtools 0.3.1
+
+* more options for sedimentation rate generator `sed_rate_from_matrix`
+
+* abstracted exctraction of tie points
 
 # admtools 0.3.0
 

R/get_L_tp.R

@@ -0,0 +1,29 @@
+get_L_tp = function(x, ...){
+  #' @export
+  #' 
+  #' @title get height/length tie point
+  #' 
+  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
+  #' @param ... other options, currently not used
+  #' 
+  #' @description
+    #' extracts the height/length time points from an age-depth model or sediment accumulation curve
+    #' 
+  #' @returns numeric vector of the time/length tie points
+  #' 
+  #' @seealso [get_T_tp()] to extract time tie points
+  #' 
+  UseMethod("get_L_tp")
+}
+
+get_L_tp.adm = function(x, ...){
+  #' @export
+  #' 
+  return(x$h)
+}
+
+get_L_tp.sac = function(x, ...){
+  #' @export
+  #' 
+  return(x$h)
+}

R/get_T_tp.R

@@ -0,0 +1,27 @@
+get_T_tp = function(x, ...){
+  #' @export
+  #' 
+  #' @title extract time tie points
+  #' 
+  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
+  #' @param ... other options, currently unused
+  #' 
+  #' @description
+    #' Extracts the time tie points from an age-depth model or sediment accumulation curve
+    #' 
+  #' @returns a vector, containing the time tie points
+  #' 
+  #' @seealso [get_L_tp()] to extract length/height tie points
+  #' 
+  UseMethod("get_T_tp")
+}
+
+get_T_tp.adm = function(x, ...){
+  #' @export
+  return(x$t)
+}
+
+get_T_tp.sac = function(x, ...){
+  #' @export
+  return(x$t)
+}

R/tp_to_adm.R

@@ -22,7 +22,7 @@ tp_to_adm = function(t, h, T_unit = NULL, L_unit = NULL){
   #' 
   #' @returns object of class `adm`
   #' 
-  #' @seealso [is_adm()] to check validity of `adm` objects
+  #' @seealso [is_adm()] to check validity of `adm` objects, [get_T_tp()] and [get_L_tp()] to extract time and height/length tie points
   #'
   #'
   #' @examples

R/tp_to_sac.R

@@ -12,6 +12,8 @@ tp_to_sac = function(t, h, T_unit = NULL, L_unit = NULL){
   #' @param L_unit length unit
   #' 
   #' @returns a _sac_ object reflecting a sediment accumulation curve
+  #' 
+  #' @seealso [sac_to_adm()] to transform sediment accumulation curves into age-depth models,  [get_T_tp()] and [get_L_tp()] to extract time and height/length tie points
 
   li = list(t = t,
             h = h,

tests/testthat/test_get_L_tp.R

@@ -0,0 +1,10 @@
+test_that("correct heights are returned",{
+  h = 1:4
+  t = 1:4
+  adm = tp_to_adm(t, h)
+  expect_equal(get_L_tp(adm), h)
+
+  h = rev(h)
+  sac = tp_to_sac(t, h)
+  expect_equal(get_L_tp(sac), h)
+})

tests/testthat/test_get_T_tp.R

@@ -0,0 +1,10 @@
+test_that("correct times are returned",{
+  h = 1:4
+  t = 1:4
+  adm = tp_to_adm(t, h)
+  expect_equal(get_T_tp(adm), t)
+
+  h = rev(h)
+  sac = tp_to_sac(t, h)
+  expect_equal(get_T_tp(sac), t)
+})

vignettes/admtools.Rmd

@@ -141,7 +141,7 @@ If you want to inspect the insides of the object, use `str`:
 str(my_adm)
 ```
 
-You can manually manipulate the fields of the `adm` object by treating it like a list. I do not recommend doing so, as it might result in unexpected downstream behavior.
+You can manually manipulate the fields of the `adm` object by treating it like a list. I do not recommend doing so, as it might result in unexpected downstream behavior. If you want to extract tie points use `get_L_tp` and `get_T_tp`.
 
 You can plot `adm` objects via the standard `plot` function. Here, I use the option to highlight hiatuses in red, and increase the linw width of the conservative ( = non-destructive) intervals.
 

vignettes/admtools_doc.Rmd

@@ -92,7 +92,8 @@ The following functions extract information from `adm` objects:
 -   `max_height.adm` extracts highest stratigraphic point in adm
 -   `min_height.adm` extracts lowest stratigaphic point in adm
 -   `min_time.adm` extracts timing of first tie point in adm
-_   `max_time.adm` extracts timing of last tie point in adm
+-    `max_time.adm` extracts timing of last tie point in adm
+-   `get_L_tp` and `get_T_tp` to extract tie points.
 
 #### Transformation into other S3 classes
 
@@ -144,6 +145,7 @@ The following functions modify `sac` objects:
 The following functions extract information from `sac` objects:
 
 -   `get_L_unit` and `get_T_unit` to extract units
+-   `get_T_tp` and `get_L_tp` to extract tie points
 
 #### Transformation into other S3 classes