Dev

NAMESPACE

@@ -3,11 +3,13 @@
 S3method(condensation,adm)
 S3method(condensation,multiadm)
 S3method(get_L_tp,adm)
+S3method(get_L_tp,multiadm)
 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,multiadm)
 S3method(get_T_tp,sac)
 S3method(get_T_unit,adm)
 S3method(get_T_unit,multiadm)
@@ -30,14 +32,20 @@ S3method(get_time,adm)
 S3method(get_time,multiadm)
 S3method(get_total_duration,adm)
 S3method(get_total_duration,multiadm)
+S3method(get_total_duration,sac)
 S3method(get_total_thickness,adm)
 S3method(get_total_thickness,multiadm)
+S3method(get_total_thickness,sac)
 S3method(is_destructive,adm)
 S3method(is_destructive,multiadm)
 S3method(max_height,adm)
+S3method(max_height,sac)
 S3method(max_time,adm)
+S3method(max_time,sac)
 S3method(min_height,adm)
+S3method(min_height,sac)
 S3method(min_time,adm)
+S3method(min_time,sac)
 S3method(plot,adm)
 S3method(plot,multiadm)
 S3method(plot,sac)
@@ -61,6 +69,7 @@ S3method(strat_to_time,numeric)
 S3method(strat_to_time,phylo)
 S3method(summary,adm)
 S3method(summary,multiadm)
+S3method(summary,sac)
 S3method(time_to_strat,list)
 S3method(time_to_strat,numeric)
 S3method(time_to_strat,phylo)

NEWS.md

@@ -4,11 +4,13 @@
 
 * abstracted exctraction of tie points
 
+* added utility functions for S3 class `sac`
+
 # admtools 0.3.0
 
 * removed dependency from `ape` package
 
-* defined S3 class `timelist` and `stratlist` for data assiciated with time/height
+* defined S3 class `timelist` and `stratlist` for data associated with time/height
 
 * unified syntax for time-depth transformation
 

R/get_L_tp.R

@@ -3,7 +3,7 @@ get_L_tp = function(x, ...){
   #' 
   #' @title get height/length tie point
   #' 
-  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
+  #' @param x age-depth model (adm/multiadm) or sediment accumulation curve (sac)
   #' @param ... other options, currently not used
   #' 
   #' @description
@@ -26,4 +26,10 @@ get_L_tp.sac = function(x, ...){
   #' @export
   #' 
   return(x$h)
+}
+
+get_L_tp.multiadm = function(x, ...){
+  #' @export
+  #' 
+  return(x$h)
 }

R/get_T_tp.R

@@ -3,7 +3,7 @@ get_T_tp = function(x, ...){
   #' 
   #' @title extract time tie points
   #' 
-  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
+  #' @param x age-depth model (adm/multiadm) or sediment accumulation curve (sac)
   #' @param ... other options, currently unused
   #' 
   #' @description
@@ -24,4 +24,9 @@ get_T_tp.adm = function(x, ...){
 get_T_tp.sac = function(x, ...){
   #' @export
   return(x$t)
+}
+
+get_T_tp.multiadm = function(x, ...){
+  #' @export
+  return(x$t)
 }

R/get_total_duration.R

@@ -1,14 +1,45 @@
-get_total_duration = function(x){
+get_total_duration = function(x, ...){
 
   #' @export
   #' 
   #' @title Total duration covered 
   #' 
-  #' @param x an adm object
+  #' @param x age-depth model (adm/multiadm) or sediment accumulation curve (sac)
+  #' @param ... other options, currently unused
   #' 
-  #' @returns numeric vector, total duration covered by the age-depth models
+  #' @returns numeric, total duration covered by the age-depth models/sediment accumulation curve
   #' 
   #' @seealso [min_time()] and [max_time()] to extract the first/last tie point in time
   #' 
   UseMethod("get_total_duration")
 }
+
+get_total_duration.adm = function(x, ...){
+
+  #'
+  #' @export
+  #' 
+  adm = x
+  return(diff(range(adm$t)))
+}
+
+get_total_duration.multiadm = function(x, ...){
+  #'
+  #' @export
+  #' 
+
+  multiadm = x
+
+  adm_list = split_multiadm(multiadm)
+
+  durations  = sapply(adm_list, function(x) get_total_duration(x))
+  return(durations)
+
+}
+
+get_total_duration.sac = function(x, ...){
+  #' @export
+  #' 
+  t = get_T_tp(x)
+  return(diff(range(t)))
+}

R/get_total_thickness.R

@@ -1,16 +1,56 @@
-get_total_thickness = function(x){
+get_total_thickness = function(x, ...){
 
   #' 
   #' 
   #' @export
   #' 
-  #' @title get thickness
+  #' @title get total thickness
   #' 
-  #' @param x an adm object
+  #' @param x an age-depth model (adm/multiadm) or a sediment accumulation curve (sac)
+  #' @param ... other options, currently unused
   #' 
-  #' @returns numeric vector containing total sediment thickness accumulated
+  #' @returns numeric, total sediment thickness accumulated
+  #' 
+  #' @description
+    #' for sediment accumulation curves, returns the difference between the highest and lowest point of the curve. For age-depth models, returns the total thickness of sediment accumulated.
+    #' 
   #' 
   #' @seealso [max_height()] and [min_height()] to extract the highest/lowest stratigraphic point
   #' 
   UseMethod("get_total_thickness")
-}
+}
+
+get_total_thickness.multiadm = function(x, ...){
+
+  #'
+  #' @export
+  #' 
+
+  multiadm = x
+
+  adm_list = split_multiadm(multiadm)
+
+  thicknesses  = sapply(adm_list, function(x) get_total_thickness(x))
+  return(thicknesses)
+
+
+}
+
+
+get_total_thickness.adm = function(x, ...){
+
+  #' 
+  #' @export
+  #' 
+  #' 
+
+  adm = x
+  return(diff(range(adm$h)))
+}
+
+get_total_thickness.sac = function(x, ...){
+  #' @export
+  #' 
+  h = get_L_tp(x)
+  return(diff(range(h)))
+}

R/max_heigth.R

@@ -1,11 +1,11 @@
 max_height = function(x){
   #' @export
   #' 
-  #' @title get highest stratigraphic position in an adm
+  #' @title get highest stratigraphic tie point
   #' 
-  #' @param x an age-depth model
+  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
   #' 
-  #' @returns a scalar
+  #' @returns number, stratigraphic position of the highest stratigraphic tie point
   #' 
   #' @seealso [min_height()], [get_total_thickness()]
   #' 
@@ -14,6 +14,13 @@ max_height = function(x){
 
 max_height.adm = function(x){
   #' @export
-
-  return(max(x$h))
+  h = get_L_tp.adm(x)
+  return(max(h))
+}
+
+max_height.sac = function(x){
+  #' @export
+  #' 
+  h = get_L_tp.sac(x)
+  return(max(h))
 }

R/max_time.R

@@ -1,11 +1,11 @@
 max_time = function(x){
   #' @export
   #' 
-  #' @title extract earliest time from adm
+  #' @title last time tie point
   #' 
-  #' @param x age-depth model
+  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
   #' 
-  #' @returns a scalar, timing of earliest tie point in the adm
+  #' @returns number, last time tie point of the age-depth model/sediment accumulation curve
   #' 
   #' @seealso [min_time()], [get_total_duration()]
   #' 
@@ -15,5 +15,12 @@ max_time = function(x){
 max_time.adm = function(x){
   #' @export
   #' 
-  return(max(x$t))
+  t = get_T_tp.adm(x)
+  return(max(t))
+}
+
+max_time.sac = function(x){
+  #' @export
+  t = get_T_tp.sac(x)
+  return(max(t))
 }

R/min_height.R

@@ -2,9 +2,11 @@ min_height = function(x){
 
   #' @export
   #' 
-  #' @title get lowest stratigraphic position in an adm
+  #' @title get lowest stratigraphic tie point
   #' 
-  #' @param x an age-depth model
+  #' @param x an age-depth model (adm) or sediment accumulation curve (sac)
+  #' 
+  #' @returns number, stratigraphic position of lowest tie poin
   #' 
   #' @seealso [get_total_thickness()], [max_height()]
   #' 
@@ -15,6 +17,12 @@ min_height = function(x){
 min_height.adm = function(x){
 
   #' @export
-
-  return(min(x$h))
+  h = get_L_tp.adm(x)
+  return(min(h))
+}
+
+min_height.sac = function(x){
+  #' @export
+  h = get_L_tp.sac(x)
+  return(min(h))
 }

R/min_time.R

@@ -1,11 +1,11 @@
 min_time = function(x){
   #' @export
   #' 
-  #' @title extract last time from adm
+  #' @title first time tie point
   #' 
-  #' @param x age-depth model
+  #' @param x age-depth model (adm) or sediment accumulation curve (sac)
   #' 
-  #' @returns a scalar, timing of last tie point in the adm
+  #' @returns number, timing of first tie point of the age-depth model/sediment accumulation curve
   #' 
   #' @seealso [max_time()], [get_total_duration()]
   #' 
@@ -15,5 +15,13 @@ min_time = function(x){
 min_time.adm = function(x){
   #' @export
   #' 
-  return(min(x$t))
+  t = get_T_tp.adm(x)
+  return(min(t))
+}
+
+min_time.sac = function(x){
+  #' @export
+  #' 
+  t = get_T_tp.sac(x)
+  return(min(t))
 }