Merge pull request #46 from MindTheGap-ERC/dev

Dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: admtools
 Title: Estimate and Manipulate Age-Depth Models
-Version: 0.3.1.9000
+Version: 0.3.1.9001
 Authors@R: 
     person("Niklas", "Hohmann", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))

NAMESPACE

@@ -67,12 +67,14 @@ S3method(set_T_unit,sac)
 S3method(strat_to_time,list)
 S3method(strat_to_time,numeric)
 S3method(strat_to_time,phylo)
+S3method(strat_to_time,pre_paleoTS)
 S3method(summary,adm)
 S3method(summary,multiadm)
 S3method(summary,sac)
 S3method(time_to_strat,list)
 S3method(time_to_strat,numeric)
 S3method(time_to_strat,phylo)
+S3method(time_to_strat,pre_paleoTS)
 export(L_axis_lab)
 export(T_axis_lab)
 export(add_adm_to_multiadm)

NEWS.md

@@ -1,5 +1,7 @@
 # admtools (development version)
 
+* added transformations for S3 class `pre_paleoTS` to integrate with `StratPal` and `paleoTS` package
+
 * added anchoring of age-depth models via `anchor`
 
 # admtools 0.3.1

R/is_adm.R

@@ -15,6 +15,13 @@ is_adm = function(x, quietly = TRUE){
   #' 
   #' @returns logical. Is the input a valid adm object?
   #' 
+  #' 
+  #' @examples
+    #' 
+    #' x = tp_to_adm(t = c(2,1), h = c(1,2)) # reversed order of time tie points
+    #' is_adm(x) # returns FALSE
+    #' 
+    #' 
 
 
   warning_status = getOption("warn")

R/strat_to_time.pre_paleoTS.R

@@ -0,0 +1,20 @@
+strat_to_time.pre_paleoTS = function(obj, x, ...){
+  #' @export
+  #' 
+
+  li = obj
+  adm = x
+
+  if (! "h" %in% names(li)){
+    stop("no stratigraphic information found. Expected element with name \"h\" in list")
+  }
+  if ("t" %in% names(li)){
+    warning("Found element with name \"t\" in list. Temporal information will be overwritten")
+  }
+
+  li[["t"]]  = get_time(adm, h = li[["h"]], ...)
+  li = li[names(li) != "h" ]
+  class(li) = c("pre_paleoTS" ,"timelist", "list")
+  return(li)
+
+}

R/time_to_strat.pre_paleoTS.R

@@ -0,0 +1,18 @@
+time_to_strat.pre_paleoTS = function(obj, x, ...){
+  #' @export
+
+  li = obj
+  adm = x
+
+  if (! "t" %in% names(li)){
+    stop("no time information found. Expected element with name \"t\"")
+  }
+  if ("h" %in% names(li)){
+    warning("Found element with name \"h\" in list. Height information will be overwritten")
+  }
+
+  li[["h"]]  = get_height(adm, t = li[["t"]], ...)
+  li = li[names(li) != "t" ]
+  class(li) = c("pre_paleoTS" , "stratlist", "list")
+  return(li)
+}