Merge pull request #23 from MindTheGap-ERC/dev

Dev

CITATION.cff

@@ -18,6 +18,7 @@ identifiers:
     value: 10.5281/zenodo.10213587
     description: Archived version on Zenodo
 repository-code: 'https://github.com/MindTheGap-ERC/admtools'
+url: 'https://mindthegap-erc.github.io/admtools/'
 abstract: >-
   R package to estimate age-depth models and transform data
   between the time domain and the stratigraphic domain. 
@@ -26,6 +27,6 @@ keywords:
   - Age-depth modeling
   - Stratigraphy
   - Sedimentology
-license: Apache-2.0
-version: 0.1.0
-date-released: '2023-12-05'
+license: GPL-3.0
+version: 0.2.0
+date-released: '2024-03-03'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: admtools
 Title: Estimate and Manipulate Age-Depth Models
-Version: 0.1.0.9000
+Version: 0.2.0
 Authors@R: 
     person("Niklas", "Hohmann", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))

NAMESPACE

@@ -4,8 +4,10 @@ S3method(condensation,adm)
 S3method(condensation,multiadm)
 S3method(get_L_unit,adm)
 S3method(get_L_unit,multiadm)
+S3method(get_L_unit,sac)
 S3method(get_T_unit,adm)
 S3method(get_T_unit,multiadm)
+S3method(get_T_unit,sac)
 S3method(get_completeness,adm)
 S3method(get_completeness,multiadm)
 S3method(get_height,adm)
@@ -40,8 +42,10 @@ S3method(sed_rate_t,adm)
 S3method(sed_rate_t,multiadm)
 S3method(set_L_unit,adm)
 S3method(set_L_unit,multiadm)
+S3method(set_L_unit,sac)
 S3method(set_T_unit,adm)
 S3method(set_T_unit,multiadm)
+S3method(set_T_unit,sac)
 S3method(strat_to_time,list)
 S3method(strat_to_time,phylo)
 S3method(summary,adm)
@@ -59,6 +63,7 @@ export(flux_quad)
 export(get_L_unit)
 export(get_T_unit)
 export(get_completeness)
+export(get_data_from_eTimeOpt)
 export(get_height)
 export(get_hiat_duration)
 export(get_hiat_list)
@@ -70,6 +75,7 @@ export(get_total_duration)
 export(get_total_thickness)
 export(is_adm)
 export(is_destructive)
+export(is_sac)
 export(make_legend)
 export(merge_adm_to_multiadm)
 export(merge_multiadm)
@@ -78,6 +84,8 @@ export(plot_erosive_intervals)
 export(plot_sed_rate_l)
 export(plot_sed_rate_t)
 export(sac_to_adm)
+export(sed_rate_from_matrix)
+export(sed_rate_gen_from_bounds)
 export(sed_rate_l)
 export(sed_rate_l_fun)
 export(sed_rate_t)
@@ -86,7 +94,7 @@ export(sedrate_to_multiadm)
 export(set_L_unit)
 export(set_T_unit)
 export(split_multiadm)
-export(strat_cont_gen_from_proxy)
+export(strat_cont_gen_from_tracer)
 export(strat_cont_to_multiadm)
 export(strat_to_time)
 export(time_to_strat)

NEWS.md

@@ -1,10 +1,24 @@
 # admtools (development version)
 
+# admtools 0.2.0
+
+* expanded documentation of defined S3 classes
+
+* added S3 class `sac` for sediment accumulation curves
+
+* methods for objects of class `phylo` and `list`
+
+* expanded estimation procedures to multiple tie points
+
+* improved plotting
+
+* estimation of sedimentation rates
+
 # admtools 0.1.0
 
 * Updated vignettes
 
-* Added generics `time_to_strat` and `strat_to_time` to transfrom objects between time and stratigraphic domain
+* Added generics `time_to_strat` and `strat_to_time` to transform objects between time and stratigraphic domain
 
 * Added package help
 

R/T_and_L_unit_handling.R

@@ -33,6 +33,14 @@ get_L_unit.multiadm = function(x, ...){
   return(x$L_unit)
 }
 
+get_L_unit.sac = function(x, ...){
+
+  #' @export
+
+  return(x$L_unit)
+}
+
+
 set_L_unit = function(x, L_unit, ...){
 
   #' 
@@ -72,6 +80,14 @@ set_L_unit.multiadm = function(x, L_unit, ...){
   return(x)
 }
 
+set_L_unit.sac = function(x, L_unit, ...){
+
+  #' @export
+  #' 
+  x$L_unit = L_unit
+  return(x)
+}
+
 get_T_unit = function(x, ...){
 
   #'
@@ -106,6 +122,13 @@ get_T_unit.multiadm = function(x, ...){
   return(x$T_unit)
 }
 
+get_T_unit.sac = function(x, ...){
+
+  #' @export
+
+  return(x$T_unit)
+}
+
 set_T_unit = function(x, T_unit, ...){
 
   #' 
@@ -139,6 +162,14 @@ set_T_unit.adm = function(x, T_unit, ...){
 
 set_T_unit.multiadm = function(x, T_unit, ...){
 
+  #' @export
+  #' 
+  x$T_unit = T_unit
+  return(x)
+}
+
+set_T_unit.sac = function(x, T_unit, ...){
+
   #' @export
   #' 
   x$T_unit = T_unit

R/eTimeOpt_functionality.R

@@ -0,0 +1,27 @@
+get_data_from_eTimeOpt = function(res, index = 1){
+  #' @export
+  #' @title extract data from eTimeOpt results
+  #' 
+  #' @param res results generated by eTimeOpt
+  #' @param index which output should be extracted? See description for details
+  #' 
+  #' @description
+    #' Extracts data from eTimeOpt. The type of data extractecd dependes on the `output` setting used for eTimeOpt. If you want ot extract specific data, adjust the output parameter in eTimeOpt to return the correct data (e.g. 2 for r^2 envelope). See eTimeOpt documentation for details on this. Then call this function on the return variable.
+    #' 
+  #' 
+  #' @seealso [sed_rate_from_matrix()] to use define sedimentation rates based on this functions outputs, [sedrate_to_multiadm()] to estimate age-depth models from the outputs.
+  #' 
+  #' @returns a list with three entries
+    #' "sed_rate" : numeric vector, sedimentation rates
+    #' "height" : numeric vector, heights
+    #' "results" : matrix with length(height) rows and length(sed_rate) columns. results of eTimeOpt
+  r = res[[index]]
+  sedrate = r$sedrates
+  r = r[, colnames(r) != "sedrates"]
+  heights = as.numeric(sub(".", "", colnames(r)))
+  results = data.matrix(r)
+
+  return(list("sed_rate" = sedrate,
+              "heights" = heights,
+              "results" = results))
+}

R/flux_helpers.R

@@ -1,11 +1,19 @@
 flux_const = function(){
   #' @export
   #' 
-  #' @title constant deterministic proxy flux
+  #' @title constant deterministic tracer flux
   #' 
   #' @description
-    #' For usage with _strat_cont_to_multiadm_; defines constant proxy flux in the time domain
-  #' @returns a functional
+    #' For usage with _strat_cont_to_multiadm_; defines constant tracer flux in the time domain
+  #' @returns a function factory that takes no arguments
+  #' 
+  #' @examples
+  #' \dontrun{
+  #' # see this vignette for an example
+  #' vignette("adm_from_trace_cont")
+  #' }
+  #' 
+  #' @seealso [flux_linear()], [flux_quad()], [strat_cont_gen_from_tracer()]
   f = function() {stats::approxfun(x = c(0,1),
                                     y = c(1,1),
                                     rule = 2)}
@@ -15,18 +23,19 @@ flux_const = function(){
 flux_linear = function(x0 = 0, y0 = 1, x1 = 1, y1 = 2){
   #' @export
   #' 
-  #' @title linear deterministic proxy flux
+  #' @title linear deterministic tracer flux
   #' 
   #' @description
-    #' For usage with _strat_cont_to_multiadm_ : defines linear proxy flux in the time domain
-    #' Proxy flux is the linear function passing thrpugh the points (x0, y0) and (x1, y1)
+    #' For usage with _strat_cont_to_multiadm_ : defines linear tracer flux in the time domain
+    #' Tracer flux is the linear function passing through the points (x0, y0) and (x1, y1)
   #' @param x0 numeric, abscissa
   #' @param y0 numeric, ordinate
   #' @param x1 numeric, abscissa
   #' @param y1 numeric, ordinate
   #' 
-  #' @returns a functional that takes no arguments. Upon each evaluation, it returns a linear function passing thrpugh the points (x0, y0) and (x1, y1)
+  #' @returns a function factory that takes no arguments. Upon each evaluation, it returns a linear function passing through the points (x0, y0) and (x1, y1)
   #' 
+  #' @seealso [flux_const()], [flux_quad()], [strat_cont_gen_from_tracer()]
    f = function(x){
      m = (y1 - y0)/(x1 - x0)
      return( m  * (x - x0) + y0 )
@@ -37,16 +46,18 @@ flux_linear = function(x0 = 0, y0 = 1, x1 = 1, y1 = 2){
 flux_quad = function(a = 1, b = 1, c = 1){
   #' @export
   #' 
-  #' @title quadratic deterministix proxy flux
+  #' @title quadratic deterministic tracer flux
   #' 
   #' @description
-    #' For usage with _strat_cont_to_multiadm_ : defines quadratic proxy flux in the time domain
+    #' For usage with _strat_cont_to_multiadm_ : defines quadratic tracer flux in the time domain
     #' defined by the function f(x) = ax^2 + bx + c
   #' @param a numeric
   #' @param b numeric
   #' @param c numeric
   #' 
-  #' @returns a functional that takes no arguments. Upon each evaluation, it returns the quadratic function f(x) = ax^2 + bx + c
+  #' @seealso [flux_linear()], [flux_const()], [strat_cont_gen_from_tracer()]
+  #' 
+  #' @returns a function factory that takes no arguments. Upon each evaluation, it returns the quadratic function f(x) = ax^2 + bx + c
 
   f = function(x){
     return(a*x^2 + b*x +c)

R/is_sac.R

@@ -0,0 +1,28 @@
+is_sac = function(x){
+  #' @export
+  #' 
+  #' @title is valid sac objects
+  #' 
+  #' @description
+    #' checks if the object is a valid sac object
+    #' 
+  #' @param x the object to check
+  #' 
+  #' @returns logical. Is x a valid `sac` object?
+
+  if ( ! inherits(x, "sac")) { return(FALSE) }
+
+  if (! all(names(x) %in% c("t","h","T_unit","L_unit"))) { return(FALSE) }
+
+  if (length(x$t) != length(x$h)) { return(FALSE) }
+
+  if (length(x$t) < 2 ) { return(FALSE) }
+
+  if ( !(is.null(x$T_unit) | is.character(x$T_unit))) { return(FALSE) }
+  if ( !(is.null(x$L_unit) | is.character(x$L_unit))) { return(FALSE) }
+
+  if (is.unsorted(x$t, strictly = TRUE)) {return(FALSE)}
+
+  return(TRUE)
+
+}