Merge pull request #32 from MindTheGap-ERC/dev

Dev

NAMESPACE

@@ -47,10 +47,12 @@ S3method(set_T_unit,adm)
 S3method(set_T_unit,multiadm)
 S3method(set_T_unit,sac)
 S3method(strat_to_time,list)
+S3method(strat_to_time,numeric)
 S3method(strat_to_time,phylo)
 S3method(summary,adm)
 S3method(summary,multiadm)
 S3method(time_to_strat,list)
+S3method(time_to_strat,numeric)
 S3method(time_to_strat,phylo)
 export(L_axis_lab)
 export(T_axis_lab)

R/adm_summary.R

@@ -60,7 +60,7 @@ mean_adm = function(x, h){
   for ( i in seq_along(h)){
     h_t[[i]] = sapply(h_list, function(x) x[i])
   }
-  t = sapply(h_t, function(x) base::mean(x))
+  t = sapply(h_t, function(x) base::mean(x, na.rm = TRUE))
   adm = tp_to_adm(t = t, h = h, T_unit = get_T_unit(x), L_unit = get_L_unit(x))
   return(adm)
 }

R/plot.multiadm.R

@@ -10,6 +10,19 @@ plot.multiadm = function(x, ...){
   #' 
   #' @returns a plot of the multiadm object
   #' 
+  #' @description
+    #' plots the median age (red) and the 95 % envelope (blue) of a multiadm object
+    #' 
+  #' 
+  #' @examples
+    #' \dontrun{
+    #' # see
+    #' vignette("adm_from_trace_cont")
+    #' # and 
+    #' vignette("adm_from_sedrate")
+    #' # for example plots.
+    #' }
+    #' 
 
 
 
@@ -47,10 +60,10 @@ move_multiadm_to_env = function(x, ...){
   multiadm = x
 
   no_of_entries = multiadm$no_of_entries
-  t_min = min(sapply(seq_len(no_of_entries), function(x) min(multiadm[["t"]][[x]])))
-  t_max = max(sapply(seq_len(no_of_entries), function(x) max(multiadm[["t"]][[x]])))
-  h_min = min(sapply(seq_len(no_of_entries), function(x) min(multiadm[["h"]][[x]])))
-  h_max = max(sapply(seq_len(no_of_entries), function(x) max(multiadm[["h"]][[x]])))
+  t_min = min(sapply(seq_len(no_of_entries), function(x) min(multiadm[["t"]][[x]])), na.rm = TRUE)
+  t_max = max(sapply(seq_len(no_of_entries), function(x) max(multiadm[["t"]][[x]])), na.rm = TRUE)
+  h_min = min(sapply(seq_len(no_of_entries), function(x) min(multiadm[["h"]][[x]])), na.rm = TRUE)
+  h_max = max(sapply(seq_len(no_of_entries), function(x) max(multiadm[["h"]][[x]])), na.rm = TRUE)
 
   assign(x = "adm_plot_info",
          value = list("T_unit" = x$T_unit,
@@ -59,7 +72,7 @@ move_multiadm_to_env = function(x, ...){
                       "t_range" = c(t_min, t_max),
                       "median_col" = "red",
                       "envelope_col" = "blue",
-                      "p_envelope" = 0.9,
+                      "p_envelope" = 0.95,
                       "madm" = x),
          envir = .adm_plot_env)
   return(invisible())
@@ -81,14 +94,13 @@ plot_envelope = function(){
   multiadm = list$madm
 
   h = seq(list$h_range[1], list$h_range[2], length.out = 100)
-  h_list = get_time(multiadm, h)
-  h_t= list()
-  for ( i in seq_len(100)){
-    h_t[[i]] = sapply(h_list, function(x) x[i])
-  }
-  graphics::lines(sapply(h_t, function(x) stats::quantile(x, 0.5 * (1 - list$p_envelope) , na.rm = TRUE)),h, col = list$envelope_col)
-  graphics::lines(sapply(h_t, function(x) stats::quantile(x, 0.5 * (1 - list$p_envelope) + list$p_envelope, na.rm = TRUE)),h, col = list$envelope_col)
-  graphics::lines(sapply(h_t, function(x) stats::quantile(x, 0.5, na.rm = TRUE)),h, col = list$median_col)
+
+  q1 = quantile_adm(multiadm, h, 0.025)
+  q2 = quantile_adm(multiadm, h, 0.975)
+  me = median_adm(multiadm, h)
+  graphics::lines(q1$t, q1$h, col = list$envelope_col)
+  graphics::lines(q2$t, q2$h, col = list$envelope_col)
+  graphics::lines(me$t, me$h, col = list$median_col)
 
   return(invisible())
 }

R/strat_to_time.R

@@ -7,7 +7,7 @@ strat_to_time = function(obj, x, ...){
   #' 
   #' @description
     #' Takes an object and transforms it from the time domain into the stratigraphic domain using the provided age-depth model.
-    #' Currently implemented for the "phylo" class.
+    #' Currently implemented for the "phylo", "list", and "numeric" class. Wraps around `get_time`.
     #' 
   #' 
   #' @param obj the object to be transformed
@@ -16,7 +16,7 @@ strat_to_time = function(obj, x, ...){
   #' 
   #' @returns an object of the same type as obj
   #' 
-  #' @seealso [time_to_strat()] to transform data from the time to the stratigraphic domain, [strat_to_time.phylo()] and [strat_to_time.list()] for details on how to transform phylo objects and lists
+  #' @seealso [time_to_strat()] to transform data from the time to the stratigraphic domain, [strat_to_time.phylo()], [strat_to_time.numeric()] and [strat_to_time.list()] for details on how to transform phylogenetic trees, vectors, and lists. See [get_time()] for the underlying procedure.
   #' 
 
   UseMethod("strat_to_time")

R/strat_to_time.numeric.R

@@ -0,0 +1,28 @@
+strat_to_time.numeric = function(obj, x, ...){
+
+  #' 
+  #' @export
+  #' 
+  #' @title transform numeric vectors from height to time domain
+  #' 
+  #' @description
+  #' This function transforms numeric vectors from the stratigrahpic to the time domain
+  #' Fundamentally a wrapper around get_time for consistent syntax
+  #' 
+  #' 
+  #' @param obj a numeric vector representing stratigraphic positions.
+  #' @param x an _adm_ object
+  #' @param ... options passed to `get_time`
+  #' 
+  #' @seealso [time_to_strat.numeric()] for the transformation from time to height domain, [get_time()] for the underlying procedure, [time_to_strat()] for the higher level function, [strat_to_time.list()] and [strat_to_time.phylo()] for the transformation of lists and phylogenetic trees.
+  #' 
+  #' @returns A numeric vector with times of deposition of the entries in `obj`
+  #' 
+  #' @examples
+  #' # see vignette("admtools") for an example
+  #' 
+
+  t = get_time(x, obj, ...)
+
+  return(t)
+}

R/time_to_strat.R

@@ -7,7 +7,7 @@ time_to_strat = function(obj, x, ...){
   #' 
   #' @description
     #' Takes an object and transforms it from the time domain into the stratigraphic domain using the provided age-depth model.
-    #' Currently implemented for the "phylo" class.
+    #' Currently implemented for the "phylo", "list", and "numeric" class.
     #' 
   #' 
   #' @param obj the object to be transformed
@@ -16,7 +16,7 @@ time_to_strat = function(obj, x, ...){
   #' 
   #' @returns an object of the same type as obj
   #' 
-  #' @seealso [strat_to_time()] to transform data from the stratigraphic domain to the time domain, [time_to_strat.phylo()] and [time_to_strat.list()] for details on how to transfrom phylo objects and lists
+  #' @seealso [strat_to_time()] to transform data from the stratigraphic domain to the time domain, [time_to_strat.phylo()], [time_to_strat.numeric()] and [time_to_strat.list()] for details on how to transfrom phylo objects, vectors, and lists. See [get_height()] for the underlying procedure.
   #' 
 
   UseMethod("time_to_strat")

R/time_to_strat.list.R

@@ -14,7 +14,7 @@ time_to_strat.list = function(obj, x, ...){
   #' @param x an _adm_ object
   #' @param ... options passed to _get_height_
   #' 
-  #' @seealso [strat_to_time.list()] for the transformation from height to time domain
+  #' @seealso [strat_to_time.list()] for the transformation from height to time domain, [time_to_strat.phylo()] and [time_to_strat.numeric()] for transformations of phylogenetic trees and vectors. See [get_height()] for the underlying procedure.
   #' 
   #' @returns a list with one named element "h" instead of the element "t", containing the stratigraphic positions corresponding to the times inf "t"
   #' 

R/time_to_strat.numeric.R

@@ -0,0 +1,28 @@
+time_to_strat.numeric = function(obj, x, ...){
+  #' 
+  #' @export
+  #' 
+  #' @title transform vectors from time to height domain
+  #' 
+  #' @description
+  #' This function transforms numeric vectors from the time to the stratigrahpic domain
+  #' Fundamentally a wrapper around get_height for consistent syntax
+  #' 
+  #' 
+  #' @param obj a numeric vector, interpreted as timing of events
+  #' @param x an _adm_ object
+  #' @param ... options passed to _get_height_
+  #' 
+  #' @seealso [strat_to_time.numeric()] for the transformation from height to time domain, [time_to_strat.phylo()] and [time_to_strat.list()] for transformations of phylogenetic trees and lists. See [get_height()] for the underlying procedure.
+  #' 
+  #' @returns a numberic vector - stratigraphic position of the events
+  #' 
+  #' @examples
+  #' # see vignette("admtools") for an example
+  #' 
+
+
+  h  = get_height(x, t = obj, ...)
+  return(h)
+
+}

R/time_to_strat.phylo.R

@@ -16,7 +16,7 @@ time_to_strat.phylo = function(obj, x, ...){
   #' 
   #' @returns a phylo object, representation of the tree in the strat domain
   #' 
-  #' @seealso [get_height()] for the underlying procedure, [time_to_strat()] for the higher level function, and [strat_to_time.phylo()] for the transformantion of phylo objects from strat domain to the time domain.
+  #' @seealso [get_height()] for the underlying procedure, [time_to_strat()] for the higher level function, and [strat_to_time.phylo()] for the transformantion of phylo objects from strat domain to the time domain. See [time_to_strat.list()] and [time_to_strat.numeric()] for the transformation of lists and numeric vectors 
 
   tree = obj
   adm = x

vignettes/adm_from_sedrate.Rmd

@@ -317,6 +317,12 @@ For information on estimating age-depth models from tracer contents of rocks and
 vignette("adm_from_trace_cont")
 ```
 
+For details on plotting ADMs see
+
+```{r, eval=FALSE}
+vignette("adm_plotting)
+```
+
 For an overview of the structure of the `admtools` package and the classes used therein see
 
 ```{r, eval=FALSE}

vignettes/adm_from_trace_cont.Rmd

@@ -331,6 +331,14 @@ For information on estimating age-depth models from sedimentation rates, see
 vignette("adm_from_sedrate")
 ```
 
+
+For details on plotting ADMs see
+
+```{r, eval=FALSE}
+vignette("adm_plotting)
+```
+
+
 For an overview of the structure of the `admtools` package and the classes used therein see
 
 ```{r, eval=FALSE}

vignettes/adm_plotting.Rmd

@@ -58,6 +58,9 @@ plot(adm,
 T_axis_lab(label = "Elapsed Model Time")
 L_axis_lab(label = "Stratigraphic Height")
 ```
+
 ## Multiple age-depth models (class "multiadm")
 
+By default, `multiadm` plots median ages in red and the 95 % envelope in blue. See also `?plot.multiadm`.
+
 

vignettes/admtools.Rmd

@@ -302,6 +302,10 @@ plot(x = strat_list$h,
 
 Note the jump in traits generated by the erosional interval in `my_adm`.
 
+#### Numeric vectors
+
+Numeric vectors can be transformed using `time_to_strat` and `strat_to_time` too. These are essentially high level wrappers around `get_height` and `get_time`. See functions `time_to_strat.numeric` and `strat_to_time.numeric` for details.
+
 ## Further information
 
 For an overview of the structure of the `admtools` package and the classes used therein see
@@ -310,6 +314,12 @@ For an overview of the structure of the `admtools` package and the classes used
 vignette("admtools_doc")
 ```
 
+For details on plotting ADMs see
+
+```{r, eval=FALSE}
+vignette("adm_plotting)
+```
+
 For information on estimating age-depth models from sedimentation rates, see
 
 ```{r, eval=FALSE}

vignettes/admtools_doc.Rmd

@@ -233,6 +233,11 @@ The following functions transform `multiadm` objects into other S3 classes:
 -   `strat_to_time.phylo`: Transform stratigraphic tree into time domain
 -   `time_to_strat.phylo`: Transform time tree into strat domain
 
+### Class `numeric`
+
+-   `strat_to_time.numeric`: Transform vectors from stratigraphic domain to time domain. Wrapper around `get_time`
+-   `time_to_strat.numeric`: Transform vectors from time to stratigraphic domain. Wrapper around `get_height`
+
 ## Plotting
 
 The following functions are used for plotting:
@@ -264,3 +269,7 @@ The following functions are used internally and not exposed to users. They can b
 -   `plot_acc_parts`
 
 -   `make_adm_canvas`
+
+## Vignettes
+
+-   `browseVignettes(package = "admtools")` to show a list of vignettes