From 0ec2dc1ce8cfe34e234cfba2ed6afa621281e456 Mon Sep 17 00:00:00 2001
From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>
Date: Thu, 12 Sep 2024 07:59:21 +0200
Subject: [PATCH 1/3] add example

---
 R/is_adm.R    | 7 +++++++
 man/is_adm.Rd | 7 +++++++
 2 files changed, 14 insertions(+)

diff --git a/R/is_adm.R b/R/is_adm.R
index ca49a48..50e0b5a 100644
--- a/R/is_adm.R
+++ b/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")
diff --git a/man/is_adm.Rd b/man/is_adm.Rd
index aa28414..89c09a2 100644
--- a/man/is_adm.Rd
+++ b/man/is_adm.Rd
@@ -18,3 +18,10 @@ logical. Is the input a valid adm object?
 Contructors for adm objects such as \emph{tp_to_adm} do not check whether the inputs define a valid
 age-depth mode, e.g. one where the law of superposition holds. This function performs these checks
 }
+\examples{
+
+x = tp_to_adm(t = c(2,1), h = c(1,2)) # reversed order of time tie points
+is_adm(x) # returns FALSE
+
+
+}

From 00b57ff15271ec338c0622456b51204d10df0423 Mon Sep 17 00:00:00 2001
From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>
Date: Fri, 27 Sep 2024 10:52:23 +0200
Subject: [PATCH 2/3] add transformation of S3 class pre_paleoTS

---
 NAMESPACE                     |  2 ++
 NEWS.md                       |  2 ++
 R/strat_to_time.pre_paleoTS.R | 20 ++++++++++++++++++++
 R/time_to_strat.pre_paleoTS.R | 18 ++++++++++++++++++
 4 files changed, 42 insertions(+)
 create mode 100644 R/strat_to_time.pre_paleoTS.R
 create mode 100644 R/time_to_strat.pre_paleoTS.R

diff --git a/NAMESPACE b/NAMESPACE
index 191a55b..7997d31 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index feb900e..a605c58 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/strat_to_time.pre_paleoTS.R b/R/strat_to_time.pre_paleoTS.R
new file mode 100644
index 0000000..b359192
--- /dev/null
+++ b/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)
+  
+}
\ No newline at end of file
diff --git a/R/time_to_strat.pre_paleoTS.R b/R/time_to_strat.pre_paleoTS.R
new file mode 100644
index 0000000..71ee03b
--- /dev/null
+++ b/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)
+}
\ No newline at end of file

From 8c7911557b639ae97b26bd18779392f38b52921c Mon Sep 17 00:00:00 2001
From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>
Date: Fri, 27 Sep 2024 10:59:35 +0200
Subject: [PATCH 3/3] increment dev version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5ff130d..3fc7bc9 100644
--- a/DESCRIPTION
+++ b/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", , "N.H.Hohmann@uu.nl", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))