| Title: | Estimate and Manipulate Age-Depth Models |
| Version: | 0.6.0 |
| Description: | Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain. |
| URL: | https://github.com/MindTheGap-ERC/admtools, https://mindthegap-erc.github.io/admtools/ |
| BugReports: | https://github.com/MindTheGap-ERC/admtools/issues |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Depends: | R (≥ 4.2), |
| Imports: | ape |
| LazyData: | true |
| Suggests: | FossilSim, knitr, rmarkdown, spelling, testthat (≥ 3.0.0) |
| VignetteBuilder: | knitr |
| Config/testthat/edition: | 3 |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2025-05-20 12:56:16 UTC; hohma004 |
| Author: | Niklas Hohmann 
[aut, cre] |
| Maintainer: | Niklas Hohmann <N.H.Hohmann@uu.nl> |
| Repository: | CRAN |
| Date/Publication: | 2025-05-20 13:20:02 UTC |
admtools: Estimate and Manipulate Age-Depth Models
Description
Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.
Author(s)
Maintainer: Niklas Hohmann N.H.Hohmann@uu.nl (ORCID)
See Also
Useful links:
Report bugs at https://github.com/MindTheGap-ERC/admtools/issues
Example data from CarboCATLite
Description
Data exported from CarboCATLite model run, equivalent to scenario A from Hohmann et al. (2024). See therein for details.
Usage
CarboCATLite_data
Format
A list with the following fields:
-
time_myr : time points in Myr from the model run
-
height_2_km_offshore_m : sediment thickness accumulated 2 km from shore
-
height_4_km_offshore_m : sediment thickness accumulated 4 km from shore
-
height_6_km_offshore_m : sediment thickness accumulated 6 km from shore
-
height_8_km_offshore_m : sediment thickness accumulated 8 km from shore
-
height_10_km_offshore_m : sediment thickness accumulated 10 km from shore
-
height_12_km_offshore_m : sediment thickness accumulated 12 km from shore
-
eustatic_SL_m : eustatic sea level used for the model run.
Source
Elapsed model time, sea level, and accumulated sediment thickness taken from the scenario A model run here
References
Burgess, Peter. "CarboCAT: A cellular automata model of heterogeneous carbonate strata." Computers & geosciences 53 (2013): 129-140. doi:10.1016/j.cageo.2011.08.026
Burgess, Peter. (2023). CarboCATLite (v1.0.1). Zenodo. doi:10.5281/zenodo.8402578
Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution 24, 113. doi:10.1186/s12862-024-02287-2.
Hohmann, Niklas, Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2023. “Identification of the Mode of Evolution in Incomplete Carbonate Successions - Supporting Data.” Open Science Framework. doi:10.17605/OSF.IO/ZBPWA, published under the CC-BY 4.0 license.
plot height axis label
Description
plot height axis label
Usage
L_axis_lab(
label = "Height",
unit = TRUE,
sep = " ",
brac = c("[", "]"),
line = 2,
outer = FALSE,
at = NA,
adj = NA,
padj = NA,
cex = NA,
col = NA,
font = NA,
...
)
Arguments
label |
Axis label |
unit |
Logical or character, should unit be plotted |
sep |
separator between label and unit |
brac |
brackets surrounding unit |
line |
parameter passed to mtext, see ?mtext for details |
outer |
parameter passed to mtext, see ?mtext for details |
at |
parameter passed to mtext, see ?mtext for details |
adj |
parameter passed to mtext, see ?mtext for details |
padj |
parameter passed to mtext, see ?mtext for details |
cex |
parameter passed to mtext, see ?mtext for details |
col |
parameter passed to mtext, see ?mtext for details |
font |
parameter passed to mtext, see ?mtext for details |
... |
further graphical parameters passed to mtext, see ?mtext for details |
Value
invisible NULL
See Also
plot.adm() for plotting of adms
plot time axis label
Description
plot time axis label
Usage
T_axis_lab(
label = "Time",
unit = TRUE,
sep = " ",
brac = c("[", "]"),
line = 2,
outer = FALSE,
at = NA,
adj = NA,
padj = NA,
cex = NA,
col = NA,
font = NA,
...
)
Arguments
label |
Axis label |
unit |
Logical or character, should unit be plotted |
sep |
separator between label and unit |
brac |
brackets surrounding unit |
line |
parameter passed to mtext, see ?mtext for details |
outer |
parameter passed to mtext, see ?mtext for details |
at |
parameter passed to mtext, see ?mtext for details |
adj |
parameter passed to mtext, see ?mtext for details |
padj |
parameter passed to mtext, see ?mtext for details |
cex |
parameter passed to mtext, see ?mtext for details |
col |
parameter passed to mtext, see ?mtext for details |
font |
parameter passed to mtext, see ?mtext for details |
... |
further graphical parameters passed to mtext, see ?mtext for details |
Value
invisible NULL
See Also
plot.adm() for plotting of adms
add adm object ot multiadm object
Description
add adm object ot multiadm object
Usage
add_adm_to_multiadm(x, ...)
Arguments
x |
multiadm object |
... |
adm objects to be added to x |
Value
a multiadm object
construct depth-depth curve from age-depth models
Description
constructs a depth-depth curve from section 1 (described by adm1) to section 2 (described by adm2)
Usage
adm_to_ddc(adm1, adm2)
Arguments
adm1 |
age-depth model 1. An |
adm2 |
age-depth model 2. An |
anchor age-depth model
Description
anchors a deterministic age-depth model (adm object) at a tie point that is associated with uncertainty.
Usage
anchor(x, index = "last", t_anchor = NULL, n = 1000L)
Arguments
x |
age-depth model |
index |
"last" or "first", or an integer (marked by L, e.g. 2L), specifying at which tie point the age-depth model will be anchored. If i is passed as integer, the i-th tie point is anchored. |
t_anchor |
time at which the adm is anchored. must be a function that takes no arguments and returns the timing of the tie point. see example or vignettes for details |
n |
integer, number of samples drawn from the tie point |
Value
a collection of age-depth models (a multiadm object)
Examples
t_anchor = function() rnorm(1) # normally distributed uncertainty
x = tp_to_adm(t = c(1,2, 3), h = c(2,3, 4)) # simple age-depth model
m = anchor(x, index = "last", t_anchor = t_anchor, n = 100) # anchor age-depth model
plot(m)
m = anchor(x, index = 2L, t_anchor = t_anchor, n = 100)
plot(m)
condensation with height
Description
returns (instantaneous) condensation (time preserved per length increment) for a section
Usage
condensation(x, h, mode = "rcll", ...)
Arguments
x |
adm or multiadm object |
h |
numeric vector, positions where condensation is determined |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
if x is an adm object, a numeric vector of condensations. if x is a multiadm object, a list of condensations
condensation function
Description
returns a function that determines instantaneous condensation (time preserved per strat. increment)
Usage
condensation_fun(x, mode = "rcll", ...)
Arguments
x |
adm object |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
a function
reverse direction of depth-depth curve
Description
reverses the direction of correlation of the depth-depth curve i.e., if the original depth-depth curve maps section 1 to section 2 the flipped curve maps section 2 to section 1
Usage
flip_ddc(x, ...)
Arguments
x |
a depth-depth curve (ddc object) |
... |
other parameters, currently unused |
constant deterministic tracer flux
Description
For usage with strat_cont_to_multiadm; defines constant tracer flux in the time domain
Usage
flux_const()
Value
a function factory that takes no arguments
See Also
flux_linear(), flux_quad(), strat_cont_gen_from_tracer()
Examples
## Not run:
# see this vignette for an example
vignette("adm_from_trace_cont")
## End(Not run)
linear deterministic tracer flux
Description
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)
Usage
flux_linear(x0 = 0, y0 = 1, x1 = 1, y1 = 2)
Arguments
x0 |
numeric, abscissa |
y0 |
numeric, ordinate |
x1 |
numeric, abscissa |
y1 |
numeric, ordinate |
Value
a function factory that takes no arguments. Upon each evaluation, it returns a linear function passing through the points (x0, y0) and (x1, y1)
See Also
flux_const(), flux_quad(), strat_cont_gen_from_tracer()
quadratic deterministic tracer flux
Description
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
Usage
flux_quad(a = 1, b = 1, c = 1)
Arguments
a |
numeric |
b |
numeric |
c |
numeric |
Value
a function factory that takes no arguments. Upon each evaluation, it returns the quadratic function f(x) = ax^2 + bx + c
See Also
flux_linear(), flux_const(), strat_cont_gen_from_tracer()
get height/length tie point
Description
extracts the height/length time points from an age-depth model or sediment accumulation curve
Usage
get_L_tp(x, ...)
Arguments
x |
age-depth model (adm/multiadm) or sediment accumulation curve (sac) |
... |
other options, currently not used |
Value
numeric vector of the time/length tie points
See Also
get_T_tp() to extract time tie points
extract length unit
Description
extracts the length unit from sac, adm or multiadm object
Usage
get_L_unit(x, ...)
Arguments
x |
adm or multiadm object |
... |
other parameters |
Value
character - the length unit of x
See Also
extract length units
Description
extracts the length unit from depth-depth curves (ddc objects)
Usage
get_L_units(x, ...)
Arguments
x |
an ddc object |
... |
other parameters |
Value
character - the length unit of x
See Also
get_L_unit() set_L_unit() to extract length units from age-depth models or sediment accumulation curves
extract time tie points
Description
Extracts the time tie points from an age-depth model or sediment accumulation curve
Usage
get_T_tp(x, ...)
Arguments
x |
age-depth model (adm/multiadm) or sediment accumulation curve (sac) |
... |
other options, currently unused |
Value
a vector, containing the time tie points
See Also
get_L_tp() to extract length/height tie points
extract Time unit
Description
extracts the Time unit from sac, adm or multiadm object
Usage
get_T_unit(x, ...)
Arguments
x |
sac, adm or multiadm object |
... |
other parameters |
Value
character - the time unit of x
See Also
Determine stratigraphic (in)completeness
Description
Determine stratigraphic (in)completeness
Usage
get_completeness(x)
get_incompleteness(x)
Arguments
x |
an adm object |
Details
Stratigraphic (in)completeness is expressed as a proportion, i.e. a number between 0 and 1
Value
Number between 0 and 1, the stratigraphic (in)completeness
Examples
my_adm = tp_to_adm(t = 1:4, h = c(1,2,2,4))
get_completeness(my_adm)
get_incompleteness(my_adm)
extract data from eTimeOpt results
Description
Extracts data from eTimeOpt. The type of data extracted depends 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.
Usage
get_data_from_eTimeOpt(res, index = 1)
Arguments
res |
results generated by eTimeOpt |
index |
which output should be extracted? See description for details |
Value
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
See Also
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.
determine stratigraphic height deposited at specific time
Description
Takes an adm object and a vector of times, and returns the stratigraphic heights deposited at said times
Usage
get_height(x, t, destructive = TRUE, out_dom_val_h = "default", ...)
Arguments
x |
an adm or multiadm object |
t |
vector of times |
destructive |
logical - should destructive intervals be considered? See Details |
out_dom_val_h |
"strat_limits", "default", or a vector with one or two entries. What value is assigned to times that are not covered by the age-depth model? |
... |
parameters handed over to is_destructive |
Details
if destructive is true, NA is returned for times that coincide with destructive intervals. This is achieved by calling is_destructive with arguments passed by ....
out_dom_val specified the return value for times that are not covered by the age-depth model. For "default", NA is returned. For "strat_limits", the lowest resp. highest stratigraphic position is returned. For a vector of length one, this value is assigned to both sides. For a vector or length 2 or more, the first and second entries are assigned on the left (resp. right) side
Value
a vector with same length as t, containing the strat heights deposited
extract hiatus duration
Description
returns a vector of hiatus durations
Usage
get_hiat_duration(x)
Arguments
x |
an adm object |
Value
a vector with one element per hiatus: the duration of the hiatus
See Also
-
get_hiat_pos()to determine only stratigraphic position of hiatuses -
get_hiat_no()to determine number of hiatuses in an adm -
get_hiat_list()to get hiatus position, stat & end time
extract hiatus info
Description
returns a list with hiatus position and timing (start & end)
Usage
get_hiat_list(x)
Arguments
x |
an adm object |
Value
a list with one element per hiatus. each element is a named vector with the following entries:
"height" : stratigraphic position of hiatus
"start" : time when hiatus begins
"end" : time when hiatus ends
See Also
-
get_hiat_pos()to determine only stratigraphic position of hiatuses -
get_hiat_no()to determine number of hiatuses in an adm -
get_hiat_duration()to determine duration of hiatuses
get no. of hiatuses
Description
Determines the number of hiatuses in an age-depth model
Usage
get_hiat_no(x)
Arguments
x |
an adm object |
Value
An integer, no. of hiatuses in the age-depth model
See Also
-
get_hiat_pos()to determine stratigraphic positions of hiatuses -
get_hiat_list()to determine position and timing of hiatuses -
get_hiat_duration()to determine duration of hiatuses
Examples
my_adm = tp_to_adm(t = 1:4, h = c(1,2,2,3)) # one hiatus
get_hiat_no(my_adm)
get hiatus positions
Description
Determines stratigraphic position of hiatuses
Usage
get_hiat_pos(x)
Arguments
x |
an adm object |
Value
numeric vector with stratigraphic positions of hiatuses
See Also
-
get_hiat_list()to get hiatus positions and durations -
get_hiat_no()to determine number of hiatuses -
get_hiat_duration()to determine duration of hiatuses
Examples
my_adm = tp_to_adm(t = 1:4, h = c(1,2,2,3)) # one hiatus at height 2
get_hiat_pos(my_adm)
get section names from depth-depth curve
Description
get section names from depth-depth curve
Usage
get_section_names(x, ...)
Arguments
x |
a depth-depth curve (ddc object) |
... |
other parameters (currently unused) |
Value
vector of length 2, section names of the correlated sections
Determine times based on age-depth model
Description
Takes an age-depth model and vector of stratigraphic positions to determine the corresponding time of formation
Usage
get_time(x, h, hiat_mode = "start",
bdry_pts_hiat = "destructive", out_dom_val_t = "default")
Arguments
x |
an adm or multiadm object |
h |
vector of stratigraphic positions |
hiat_mode |
"start", "end", or "destroy". If a stratigraphic position coincides with a hiatus, what should be returned? |
bdry_pts_hiat |
"consistent" or "destructive". How are hiatuses at the start/end of the adm treated? |
out_dom_val_t |
:"default", "time_limits", or a numeric value. What value is returned for heights not covered by the age-depth model? |
Details
If a stratigraphic position coincides with a hiatus, should the start time or the end time of the hiatus be returned? Using "destroy" returns NA If the adm starts/ends with a hiatus, should the time returned be consistent with hiat_mode, or should it be NA?
Value
numeric vector. Times of deposition of the provided heights in h
Total duration covered
Description
Total duration covered
Usage
get_total_duration(x, ...)
Arguments
x |
age-depth model (adm/multiadm) or sediment accumulation curve (sac) |
... |
other options, currently unused |
Value
numeric, total duration covered by the age-depth models/sediment accumulation curve
See Also
min_time() and max_time() to extract the first/last tie point in time
get total thickness
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.
Usage
get_total_thickness(x, ...)
Arguments
x |
an age-depth model (adm/multiadm) or a sediment accumulation curve (sac) |
... |
other options, currently unused |
Value
numeric, total sediment thickness accumulated
See Also
max_height() and min_height() to extract the highest/lowest stratigraphic point, get_total_thicknesses() to extract thicknesses from depth-depth curves
get thicknesses of sections from depth-depth curves
Description
get thicknesses of sections from depth-depth curves
Usage
get_total_thicknesses(x, ...)
Arguments
x |
a depth-depth curve (ddc object) |
... |
other parameters (currently unused) |
Value
a numeric vector of length 2 - the thicknesses of section 1 and 2 in the depth-depth curve
See Also
-
get_total_thickness()to determine the total thickness accumulated by age-depth models or sediment accumulation curves.
Is an adm object a valid age-depth model
Description
Constructors for adm objects such as 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
Usage
is_adm(x, quietly = TRUE)
Arguments
x |
an object |
quietly |
logical. should descriptive warnings be shown? |
Value
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
Is deposition destructive?
Description
Determines whether specified time is destructive or not
Usage
is_destructive(x, t, mode = "rcll",
bdry_pts_hiat = "destructive", out_dom_mode = "default")
Arguments
x |
an adm or multiadm object |
t |
vector of times |
mode |
string, either "rcll", "lcrl", "open", or "closed" |
bdry_pts_hiat |
string, "destructive" or "consistent". If the adm starts/ends with a hiatus, should the start/end be removed, or treated consistently with mode? |
out_dom_mode |
""default", "destructive", or "conservative" |
Value
logical vector of same length as t. Is deposition at time t destructive?
is valid multiadm object?
Description
is valid multiadm object?
Usage
is_multiadm(x, quietly = TRUE)
Arguments
x |
object to be tested |
quietly |
logical, should a descriptive warning be returned? |
Value
Logical. Is the object a valid multiadm object?
is valid sac objects
Description
checks if the object is a valid sac object
Usage
is_sac(x)
Arguments
x |
the object to check |
Value
logical. Is x a valid sac object?
plot legend
Description
plots a legend for the multiadm plot
Usage
make_legend()
Value
invisible NULL
get highest stratigraphic tie point
Description
get highest stratigraphic tie point
Usage
max_height(x)
Arguments
x |
age-depth model (adm) or sediment accumulation curve (sac) |
Value
number, stratigraphic position of the highest stratigraphic tie point
See Also
min_height(), get_total_thickness()
last time tie point
Description
last time tie point
Usage
max_time(x)
Arguments
x |
age-depth model (adm) or sediment accumulation curve (sac) |
Value
number, last time tie point of the age-depth model/sediment accumulation curve
See Also
min_time(), get_total_duration()
get mean ADM
Description
returns the mean adm of a multiadm object
Usage
mean_adm(x, h)
Arguments
x |
a multiadm object |
h |
the heights at which to evaluate the adm |
Value
an adm object
See Also
median_adm() and quantile_adm() for median and quantile adms, respectively
get median ADM
Description
returns the median adm of a multiadm object
Usage
median_adm(x, h)
Arguments
x |
a multiadm object |
h |
the heights at which to evaluate the adm |
Value
an adm object
See Also
mean_adm() for the mean age-depth model, quantile_adm() for the more general implementation
combine multiple adm ojects into multiadm object
Description
combine multiple adm ojects into multiadm object
Usage
merge_adm_to_multiadm(...)
Arguments
... |
adm objects |
Value
object of class multiadm
merge multiple multiadm objects
Description
merge multiple multiadm objects
Usage
merge_multiadm(...)
Arguments
... |
adm objects |
Value
multiadm object
get lowest stratigraphic tie point
Description
get lowest stratigraphic tie point
Usage
min_height(x)
Arguments
x |
an age-depth model (adm) or sediment accumulation curve (sac) |
Value
number, stratigraphic position of lowest tie point
See Also
get_total_thickness(), max_height()
first time tie point
Description
first time tie point
Usage
min_time(x)
Arguments
x |
age-depth model (adm) or sediment accumulation curve (sac) |
Value
number, timing of first tie point of the age-depth model/sediment accumulation curve
See Also
max_time(), get_total_duration()
plotting adm objects
Description
plotting adm objects
Usage
## S3 method for class 'adm'
plot(
x,
lwd_destr = 1,
lwd_acc = 1,
lty_destr = 3,
lty_acc = 1,
col_destr = "black",
col_acc = "black",
...
)
Arguments
x |
an adm object |
lwd_destr |
line width of hiatuses |
lwd_acc |
line width of conservative intervals |
lty_destr |
linetype of hiatuses |
lty_acc |
line type of conservative intervals |
col_destr |
color of erosive intervals |
col_acc |
color of conservative intervals |
... |
arguments passed to plot |
See Also
L_axis_lab() and T_axis_lab() for plotting time and axis labels, the vignette on plotting available via browseVignettes(package = "admtools")
plot depth-depth curve
Description
plot depth-depth curve
Usage
## S3 method for class 'ddc'
plot(x, ...)
Arguments
x |
depth-depth curve |
... |
other parameters passed to plot |
plot multiadm object
Description
plots the median age (red) and the 95 % envelope (blue) of a multiadm object
Usage
## S3 method for class 'multiadm'
plot(x, ...)
Arguments
x |
multiadm object |
... |
parameters passed to |
Value
a plot of the multiadm object
Examples
## Not run:
# see
vignette("adm_from_trace_cont")
# and
vignette("adm_from_sedrate")
# for example plots.
## End(Not run)
plot sediment accumulation curve
Description
plot sediment accumulation curve
Usage
## S3 method for class 'sac'
plot(x, ...)
Arguments
x |
object of class sac |
... |
further parameters (currently ignored) |
Value
invisible NULL
plot strat list
Description
plots a stratlist, i.e. a list of values associated with stratigraphic positions (typically returned by time_to_strat). will plot the element with matching ord_name against stratigraphic positions.
Usage
## S3 method for class 'stratlist'
plot(x, orientation = "du", ord_name = "y", ...)
Arguments
x |
stratlist object |
orientation |
character, either "du" (down-up) or "lr" (left-right). Orientation of plotting |
ord_name |
name of the ordinate. Values plotted against time |
... |
further arguments passed to plot |
plot time lists
Description
plot time lists
Usage
## S3 method for class 'timelist'
plot(x, ...)
Arguments
x |
a time list |
... |
other options passed to plot |
plot condensation in height
Description
plots condensation (time per stratigraphic increment) throughout the section
Usage
plot_condensation(x, h = "default", mode = "rcll", ...)
Arguments
x |
an adm object |
h |
"default" or a numeric vector of height where the sed rate is evaluated |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
invisible null
mark erosive time intervals
Description
mark erosive time intervals
Usage
plot_erosive_intervals(
density = NULL,
angle = 45,
col = "azure3",
border = NA,
lty = 1,
lwd = 1
)
Arguments
density |
parameter passed to rect, see ?rect for details |
angle |
parameter passed to rect, see ?rect for details |
col |
parameter passed to rect, see ?rect for details |
border |
parameter passed to rect, see ?rect for details |
lty |
parameter passed to rect, see ?rect for details |
lwd |
parameter passed to rect, see ?rect for details |
Value
invisible NULL
plot sed. rate in height
Description
plot sed. rate in height
Usage
plot_sed_rate_l(x, h = "default", mode = "rcll", ...)
Arguments
x |
an adm object |
h |
"default" or a numeric vector of height where the sed rate is evaluated |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
invisible null
plot sedimentation rate in time
Description
plot sedimentation rate in time
Usage
plot_sed_rate_t(x, mode = "rcll")
Arguments
x |
adm object |
mode |
string, "rcll" or "lcrl". Should the sedimentation rate be Right Continuous with Left Limits (rcll) or Left Continuous with Right Limits (lcrl) |
Value
invisible NULL
get quantile ADM
Description
returns the quantile adm of a multiadm object
Usage
quantile_adm(x, h, p)
Arguments
x |
a multiadm object |
h |
the heights at which to evaluate the adm |
p |
percentile, as number between 0 and 1 |
Value
an adm object
See Also
median_adm() to extract the median adm, mean_adm() for the mean adm
reverse direction of time/depth axis
Description
The FossilSim package simulates fossils, trees, and taxonomies using age
meaning 0 represents the present and larger numbers indicate older ages
To interact with admtools, the direction of time must be reversed
effectively replaces the time component t of an object by ref - t
Usage
rev_dir(x, ref)
Arguments
x |
object to transform - typically a |
ref |
reference point used for reversal |
Examples
## Not run:
# for usage example, see
vignette("FossilSim_integration")
## End(Not run)
turn sed. acc curve into adm
Description
turn sed. acc curve into adm
Usage
sac_to_adm(x)
Arguments
x |
object of class sac |
Value
object of class adm
See Also
tp_to_adm() for the generator of adm
make sed rate gen from matrix
Description
Construct a sedimentation rate generator (function factory) from a matrix, e.g. one returned from get_data_from_eTimeOpt. This generator can be passed on to sedrate_to_multiadm to estimate age-depth models from it.
If mode is "deterministic", the generator evaluates the sedimentation rates at heights specified by height, if the mode is "poisson" it is evaluated at heights that are determined based on a poisson point process. At these heights, the value of the sedimentation rate is determined based on the (pseudo) pdf that is determined by the matrix values.
Usage
sed_rate_from_matrix(
height,
sedrate,
matrix,
mode = "deterministic",
rate = 1,
expand_domain = TRUE,
transform = identity
)
Arguments
height |
vector of heights |
sedrate |
vector of sed. rates x values |
matrix |
matrix of sed rate y values. Must have as many columns as length(height) and as many rows as length(sedrate). |
mode |
character, "deterministic" or "poisson". Determines at which stratigraphic heights the sed rate is determined. If "deterministic" this will be the heights in |
rate |
numeric, rate of the Poisson point process determining frequency of sedimentation rate changes. |
expand_domain |
should sedimentation rates be defined below/above the highest/lowest height in the section? If TRUE, the sed rate values are the values at the closest interpolated point, if FALSE it will be NA |
transform |
a function, the identity function by default. How should the values of the (pseudo)pdf defined by the entries of |
Value
a function factory for usage with sedrate_to_multiadm
See Also
sedrate_to_multiadm() for estimating sedimentation rates based on the outputs, get_data_from_eTimeOpt() for extracting data from the eTimeOpt function of the astrochron package. sed_rate_gen_from_bounds() for construction sedimentation rate generators from simple bounds. See also the vignettes for details on how arbitrary sedimentation rates can be constructed.
Examples
# see vignette
# vignette("adm_from_sedrate")
# for more general examples
seg rate gen from upper/lower bounds
Description
constructs a sedimentation rate generator for usage with sedrate_to_multiadm based on the following procedure: (1) determine stratigraphic points based on a Poisson point process with rate rate (2) at these points, determine the sedimentation rate based on a uniform distribution between the bounds provided by the input parameters (3) linearly interpolate between those points with sedimentation rate determined in step 2.
This approach can be used to estimate age-depth models when only rough boundaries on sedimentation rates are available. Here, the uniform distribution is chosen to reflect that no other information other than maximum and minimum sed. rate is available.
Usage
sed_rate_gen_from_bounds(h_l, s_l, h_u, s_u, rate = 1)
Arguments
h_l |
height values for lower bounds |
s_l |
sed rate values for lower bounds |
h_u |
height values for upper bounds |
s_u |
sed rate values for upper bounds |
rate |
rate of poisson point process |
Value
a function factory for usage with sedrate_to_multiadm
See Also
-
sedrate_to_multiadm()for estimating age-depth models using the outputs -
sed_rate_from_matrix()for other means of defining sedimentation rates -
sed_rate_gen_gamma()for sed. rate generator based on a gamma distribution
sedrate_to_multiadm() for estimating age-depth models using the outputs, sed_rate_from_matrix() for other means of defining sedimentation rates, the vignette on how to construct arbitrary sedimentation rate generators.
Examples
# see vignette
# vignette("adm_from_sedrate")
# for an example
sed. rate gen based on gamma distribution
Description
generates a function factory for usage with sedrate_to_multiadm. At h[i],
the sedimentation rate is given by a gamma distribution with parameters
shapes[i] and rates[i]. Between those values, sedimentation rate is linearly interpolated
Outside of the range of h, behavior is determined by the argument rule
which is passed to approxfun. See there for details.
Usage
sed_rate_gen_gamma(h, shapes, rates, rule = 1)
Arguments
h |
heights at which sedimentation rate is determined |
shapes |
shape parameters for the gamma distribution |
rates |
rate parameter for the gamma distribution |
rule |
an integer of length 1 or 2, see description for details |
Value
a function factory for usage with sedrate_to_multiadm
See Also
-
sedrate_to_multiadm()for estimating age-depth models using the outputs -
sed_rate_from_matrix()for other means of defining sedimentation rates -
sed_rate_gen_from_bounds()for sed. rate generator based on bounds on sedimentation rates.
sedimentation rate in stratigraphic height
Description
determines instantaneous sedimentation rate at a specified stratigraphic position
Usage
sed_rate_l(x, h, mode = "rcll", ...)
Arguments
x |
adm object |
h |
numeric vector, stratigraphic positions |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
a vector of sed rates (if x is an adm object), or a list of sedimentation rates
sed rate in height function
Description
returns a function that determines sed. rates in height
Usage
sed_rate_l_fun(x, mode = "rcll", ...)
Arguments
x |
an adm object |
mode |
string, handed over to sed_rate_t, see ?sed_rate_t for details |
... |
parameters passed to get_time, see ?get_time for details |
Value
a function
sedimentation rate in time domain
Description
infers the instantaneous sedimentation rate from adm objects
Usage
sed_rate_t(x, t, mode = "rcll")
Arguments
x |
adm or multiadm object |
t |
vector of times at which sedimentation rates are determined |
mode |
string, "rcll" or "lcrl". at non-differential points, is the sed rate left or right continuous? |
Value
for adm objects, a vector giving sed. accumulation rates at time t. For multiadm objects, a list with accumulation rates
sedimentation rate function
Description
returns a function that returns sedimentation rate
Usage
sed_rate_t_fun(x, mode = "rcll")
Arguments
x |
an adm object |
mode |
string, "rcll" or "lcrl". Should the sedimentation rate be Right Continuous with Left Limits (rcll) or Left Continuous with Right Limits (lcrl) |
Value
a function
Estimate age-depth model from sedimentation rates & tie points
Description
Combines information on tie points and sedimentation rates to estimate age-depth models and their associated uncertainty. For an example, see vignette("adm_from_sedrate").
Usage
sedrate_to_multiadm(
h_tp,
t_tp,
sed_rate_gen,
h,
no_of_rep = 100L,
subdivisions = 100L,
stop.on.error = TRUE,
T_unit = NULL,
L_unit = NULL
)
Arguments
h_tp |
: function, returns stratigraphic positions of tie points |
t_tp |
: function, returns times of tie points |
sed_rate_gen |
: function, returns function describing sedimentation rate |
h |
: numeric, heights where the adm is calculated |
no_of_rep |
: integer, number of repetitions |
subdivisions |
maximum no of subintervals used in numeric integration. passed to integrate, see ?stats::integrate for details |
stop.on.error |
logical passed to integrate, see ?stats::integrate for details |
T_unit |
time unit |
L_unit |
length unit |
Value
object of class multiadm
Examples
## Not run:
# see this vignette for an example
vignette("adm_from_sedrate")
## End(Not run)
set length units
Description
set length units for sac, adm and multiadm objects
Usage
set_L_unit(x, L_unit, ...)
Arguments
x |
adm or multiadm object |
L_unit |
length unit |
... |
further parameters |
Value
an adm or multiadm object with the L unit assigned
See Also
set length units
Description
set length units for depth-depth curves
Usage
set_L_units(x, L_units, ...)
Arguments
x |
depth-depth curve (ddc object) |
L_units |
length units |
... |
further parameters |
Value
an ddc object with the L unit assigned
See Also
set time units
Description
set time units for sac, adm and multiadm objects
Usage
set_T_unit(x, T_unit, ...)
Arguments
x |
sac, adm or multiadm object |
T_unit |
time unit |
... |
further parameters |
Value
an sac, adm or multiadm object with the time unit assigned
See Also
set section names for depth-depth curves
Description
set section names for depth-depth curves
Usage
set_section_names(x, sec_names, ...)
Arguments
x |
a depth-depth curve (ddc object) |
sec_names |
vector of length 2, section names assigned to the depth-depth curve |
... |
other parameters (currently unused) |
Value
a depth-depth curve with assigned section names
split multiadm objects into adm
Description
split multiadm objects into adm
Usage
split_multiadm(x)
Arguments
x |
a multiadm object |
Value
list with objects of class adm
proxy values in strat domain
Description
Generates a function factory for usage with strat_cont_to_multiadm based on empirical tracer measurements in the section
Usage
strat_cont_gen_from_tracer(
bin_borders,
df,
distribution = "normal",
cap = TRUE,
cap_val = 0
)
Arguments
bin_borders |
borders of sampling bins |
df |
data frame with proxy records |
distribution |
character, currently only "normal" implemented. Specifies the distribution of proxies |
cap |
logical. Should values below |
cap_val |
numeric. If |
Value
a functional for usage with strat_cont_to_multiadm
See Also
flux_const(), flux_linear(), flux_quad() to define tracer fluxes
Examples
## Not run:
# see this vignette for a use case
vignette("adm_from_trace_cont")
## End(Not run)
estimate age-depth model from tracer
Description
Estimates age-depth models by comparing observed tracer values in a section with assumptions on tracer flux in time. See vignette("adm_from_trace_cont") for a full example.
Usage
strat_cont_to_multiadm(
h_tp,
t_tp,
strat_cont_gen,
time_cont_gen,
h,
no_of_rep = 100L,
subdivisions = 100L,
stop.on.error = TRUE,
T_unit = NULL,
L_unit = NULL
)
Arguments
h_tp |
function, returning tie point heights |
t_tp |
function, returning tie points times |
strat_cont_gen |
function, describing tracer data observed in the section |
time_cont_gen |
function, describing tracer changes in time |
h |
numeric vector, heights where the age depth model is described |
no_of_rep |
integer, number of age depth models generated |
subdivisions |
integer, max no. of subintervals used by integration procedure. passed to integrate, see ?stats::integrate for details |
stop.on.error |
logical passed to integrate, see ?stats::integrate for details |
T_unit |
NULL or character, time unit |
L_unit |
NULL or character, length unit |
Value
Object of class multiadm
Examples
## Not run:
# see this vignette for an example
vignette("adm_from_trace_cont")
## End(Not run)
transform objects from strat. to time domain
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", "list", and "numeric" class. Wraps around get_time.
Usage
strat_to_time(obj, x, ...)
Arguments
obj |
the object to be transformed |
x |
age-depth model |
... |
other parameters |
Value
an object of the same type as obj
See Also
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.
transform fossils object from FossilSim between time and strat domain
Description
transforms fossil objects from stratigraphic to time domain
'
Usage
## S3 method for class 'fossils'
strat_to_time(obj, x, ...)
Arguments
obj |
the |
x |
the age-depth model |
... |
further parameters passed to _get_height' |
transform list from height to time domain
Description
Lists are useful to keep data closely associated. This function transforms a list that contains observations associated with a stratigraphic position (recorded in the element with name "h") into a list where the observations are associated with time.
Usage
## S3 method for class 'list'
strat_to_time(obj, x, ...)
Arguments
obj |
a list with one element named "h", which will be interpreted as stratigraphic positions |
x |
an adm object |
... |
options passed to |
Value
a timelist (inherits from list). A list with one named element "t" instead of the element "h". This element contains the times of the stratigraphic positions in "h".
See Also
time_to_strat.list() for the transformation from time to height domain, get_time() for the underlying procedure, time_to_strat() for the higher level function
Examples
# see vignette("admtools") for an example
transform numeric vectors from height to time domain
Description
This function transforms numeric vectors from the stratigraphic to the time domain Fundamentally a wrapper around get_time for consistent syntax
Usage
## S3 method for class 'numeric'
strat_to_time(obj, x, ...)
Arguments
obj |
a numeric vector representing stratigraphic positions. |
x |
an adm object |
... |
options passed to |
Value
A numeric vector with times of deposition of the entries in obj
See Also
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.
Examples
# see vignette("admtools") for an example
transform phylo object
Description
transform phylo object from the stratigraphic domain to the time domain
Usage
## S3 method for class 'phylo'
strat_to_time(obj, x, ...)
Arguments
obj |
the phylo object to be transformed |
x |
age-depth model |
... |
parameters passed to get_time |
Value
a phylo object, representation of the tree in the time domain
See Also
get_time() for the underlying procedure, strat_to_time() for the higher level function, and time_to_strat.phylo() for the transformation of phylo objects from the time to the strat domain.
transform taxonomy object from strat to time domain
Description
transform taxonomy object from strat to time domain
Usage
## S3 method for class 'taxonomy'
strat_to_time(obj, x, ...)
Arguments
obj |
|
x |
age-depth model |
... |
further parameters passed to get_time |
summary of age-depth model
Description
Displays some summary numbers of an age-depth models
Usage
## S3 method for class 'adm'
summary(object, ...)
Arguments
object |
an adm object |
... |
other variables, are ignored |
Value
Invisible NULL, prints summary to the console
Examples
my_adm = tp_to_adm(t = 1:5, h = c(2,2,3), L_unit = "m", T_unit = "Myr" )
summary(my_adm)
summary of depth-depth curve
Description
displays some summary numbers of a depth-depth curve (ddc object)
Usage
## S3 method for class 'ddc'
summary(object, ...)
Arguments
object |
depth-depth curve ( |
... |
other variables, currently ignored |
Value
invisible NULL
summary of age-depth model
Description
Displays some summary numbers of an age-depth models
Usage
## S3 method for class 'multiadm'
summary(object, ...)
Arguments
object |
a multiadm object |
... |
other variables, are ignored |
Value
Invisible NULL, prints summary to the console
summary of sediment accumulation curve
Description
displays some summary numbers of sediment accumulation curve
Usage
## S3 method for class 'sac'
summary(object, ...)
Arguments
object |
sediment accumulation curve (sac) |
... |
other variables, are ignored |
Value
invisible NULL
transform objects from time domain to strat. domain
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", "list", and "numeric" class.
Usage
time_to_strat(obj, x, ...)
Arguments
obj |
the object to be transformed |
x |
age-depth model for the transformation |
... |
other parameters |
Value
an object of the same type as obj
See Also
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 transform phylo objects, vectors, and lists. See get_height() for the underlying procedure.
transform fossils from FossilSim from time to strat domain
Description
The fossils object of the FossilSim package describe the location of fossil occurrences along a phylogeny. This function transforms the objects from the time to the stratigraphic domain.
Usage
## S3 method for class 'fossils'
time_to_strat(obj, x, ...)
Arguments
obj |
the fossils object |
x |
the age-depth model to be used, and adm object |
... |
further parameters to be passed to |
Value
a fossils object for usage with the FossilSim package
transform list from time to height domain
Description
Lists are useful to keep data closely associated. This function transforms a list that contains observations associated with a time (recorded in the element with name "t") into a list where the observations are associated with stratigraphic position.
Usage
## S3 method for class 'list'
time_to_strat(obj, x, ...)
Arguments
obj |
a list with one element named "t", which will be interpreted as time |
x |
an adm object |
... |
options passed to get_height |
Value
a stratlist (inherits from list): A list with one named element "h" instead of the element "t", containing the stratigraphic positions corresponding to the times inf "t"
See Also
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.
Examples
# see vignette("admtools") for an example
transform vectors from time to height domain
Description
This function transforms numeric vectors from the time to the stratigraphic domain Fundamentally a wrapper around get_height for consistent syntax
Usage
## S3 method for class 'numeric'
time_to_strat(obj, x, ...)
Arguments
obj |
a numeric vector, interpreted as timing of events |
x |
an adm object |
... |
options passed to get_height |
Value
a numeric vector - stratigraphic position of the events
See Also
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.
Examples
# see vignette("admtools") for an example
transform phylo object
Description
transform phylo object from the time domain to the stratigraphic domain
Usage
## S3 method for class 'phylo'
time_to_strat(obj, x, ...)
Arguments
obj |
the phylo object to be transformed |
x |
age-depth model |
... |
other parameters, currently ignored |
Value
a phylo object, representation of the tree in the strat domain
See Also
get_height() for the underlying procedure, time_to_strat() for the higher level function, and strat_to_time.phylo() for the transformation 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
transform taxomony from time to strat domain
Description
transforms taxonomy objects from time to strat domain. Ignored the destructive argument of get_height, which is automatically set to FALSE
Usage
## S3 method for class 'taxonomy'
time_to_strat(obj, x, ...)
Arguments
obj |
a |
x |
an age-depth model object |
... |
further parameters passed to |
example time tree
Description
Time tree generated using the ape package. Code used to generate is
set.seed(1) tree_in_time = ape::rlineage(birth = 1.8, death = 0.2, Tmax = 2)
Usage
timetree
Format
An object of class phylo of length 4.
deterministic tie points height domain
Description
defines deterministic stratigraphic tie points
Usage
tp_height_det(heights)
Arguments
heights |
numeric vector. Stratigraphic positions of the tie points |
Value
a function for usage with strat_cont_to_multiadm and sedrate_to_multiamd as h_tp input
See Also
tp_time_det() for deterministic tie points in time, tp_time_norm() for tie points following a normal distribution, tp_time_floating_scale() for tie points for a floating scale,
deterministic tie points in time domain
Description
defines deterministic tie points in time.
Usage
tp_time_det(times)
Arguments
times |
numeric vector, times of the tie points |
Value
a function for usage with strat_cont_to_multiadm and sedrate_to_mulitadm as t_tp input
See Also
tp_height_det() for deterministic tie points in height, tp_time_norm() for tie points following a normal distribution
tie points for floating time scale
Description
Defines tie points for a floating (auxiliary) time scale for usage with sedrate_to_multiadm and strat_cont_to_multiadm as t_tp input. This floating time scale consists of two tie points in time, the first at time t = 0, the second at time t = 1. tp_time_floating_scale is a synonym of tp_time_det(times = c(0,1))
Usage
tp_time_floating_scale()
Value
function for usage with strat_cont_to_multiadm and sedrate_to_multiamd as t_tp input
See Also
tp_time_norm() for tie points following a normal distribution, tp_height_det() for deterministic height tie points
Examples
## Not run:
# see this vignette for an example
vignette("adm_from_trace_cont")
## End(Not run)
time tie points with normal distribution
Description
defines a function factory that returns normally distributed times. FOr usage with sedrate_to_multiadm and strat_cont_to_multiadm.
Usage
tp_time_norm(mean, sd, force_order = TRUE)
Arguments
mean |
numeric vector, mean age of tie points |
sd |
numeric vector, standard deviation of tie points |
force_order |
logical, enforce strictly increasing times |
Value
function for usage with strat_cont_to_multiadm and sedrate_to_multiamd as t_tp input
See Also
tp_time_floating_scale() for tie points for a floating scale, tp_height_det() for deterministic height tie points
Construct age-depth model from tie points
Description
Turns tie points into an adm object that represents an age-depth model
Usage
tp_to_adm(t, h, T_unit = NULL, L_unit = NULL)
Arguments
t |
Vector, tie points in time |
h |
Vector, tie points in height |
T_unit |
character, time unit |
L_unit |
character, length unit |
Details
by default, intervals with no sediment accumulation are marked as destructive.
tp_to_adm does not check whether the inputs define a valid age-depth model. For this, use
is_adm
Value
object of class adm
See Also
is_adm() to check validity of adm objects, get_T_tp() and get_L_tp() to extract time and height/length tie points
Examples
my_adm = tp_to_adm(t = 1:4, h = c(1,2,2,3), T_unit = "kyr", L_unit = "m")
plot(my_adm)
# see vignette("admtools") for other examples
construct depth-depth curve from coeval heights
Description
constructs a depth-depth curve (ddc object) from a vector of coeval heights specified by h1 and h2
Usage
tp_to_ddc(
h1,
h2,
L_unit_1 = NULL,
L_unit_2 = NULL,
sec_1 = "unnamed section 1",
sec_2 = "unnamed section 2"
)
Arguments
h1 |
height tie points in section 1 |
h2 |
height tie points in section 2 |
L_unit_1 |
Length unit in section 1 |
L_unit_2 |
Length unit in section 2 |
sec_1 |
name of section 1 |
sec_2 |
name of section 2 |
define sed. acc. curve
Description
defines sac (sediment accumulation curve) object from tie points
Usage
tp_to_sac(t, h, T_unit = NULL, L_unit = NULL)
Arguments
t |
numeric vector, time coordinates of tie points |
h |
numeric vector, height coordinates of tie points |
T_unit |
time unit |
L_unit |
length unit |
Value
a sac object reflecting a sediment accumulation curve
See Also
sac_to_adm() to transform sediment accumulation curves into age-depth models, get_T_tp() and get_L_tp() to extract time and height/length tie points