knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(admtools)
This vignette provides an overview of the larger scale structure of the admtools
package and the classes used therein.
adm
The S3 class adm
represents age depth models. Structurally, they are lists with five fields:
t
: numeric vector, time points
h
: numeric vectors, heights
destr
: logical vector, is the interval destructive
T_unit
: NULL
or a string, time unit
L_unit
: NULL
or a string, length unit
h[i]
is the height at time t[i]
. h
and t
must be of same length and have at least 2 elements, t
must be strictly increasing and h
must be nondecreasing. length(destr)
must be identical to length(t) - 1
. destr[i] == TRUE
indicates that the time interval from t[i]
to t[i+1]
is destructive and no information is preserved. Whether tie points are considered destructive is determined by the function is_destructive
. Geologically, destr[i] == TRUE
should imply h[i] == h[i+1]
, as no sediment is accumulated during hiatuses.
The following functions construct adm
objects:
tp_to_adm
for construction from tie pointssac_to_adm
for construction from sediment accumulation curves sac
split_multiadm
for extraction from multiple age-depth models multiadm
The following functions examine the logic of adm
objects:
is_adm
to check for validity of an adm objectThe following functions yield a representation of adm
objects:
plot.adm
for plottingprint.adm
for printing to the consolesummary.adm
to provide a quick summary of an objectThe following functions modify adm
objects:
set_L_unit
and set_T_unit
to change unitsThe following functions extract information from adm
objects:
condensation
and condensation_fun
to extract condensationget_L_unit
and get_T_unit
to extract dataget_completeness
and get_incompleteness
get_height
get_time
get_hiat_duration
get_hiat_list
get_hiat_no
get_hiat_pos
get_total_duration
get_total_thickness
is_destructive
sed_rate_l
and sed_rate_l_fun
to extract sedimentation rate in height domainsed_rate_t
and sed_rate_t_fun
to extract sedimentation rate in time domainmax_height.adm
extracts highest stratigraphic point in admmin_height.adm
extracts lowest stratigraphic point in admmin_time.adm
extracts timing of first tie point in admmax_time.adm
extracts timing of last tie point in admget_L_tp
and get_T_tp
to extract tie points.The following functions transform adm
objects into other S3 classes:
merge_adm_to_multiadm
into multiamd
add_adm_to_multiadm
to add adm
to multiadm
anchor
to transform anchor adm
at a tie point with uncertainty, resulting in a multiadm
sac
The S3 class sac
represents sediment accumulation curves. Structurally, they are lists with four fields:
t
: numeric vector, time pointsh
: numeric vectors, heightsT_unit
: NULL
or a string, time unitL_unit
: NULL
or a string, length unith[i]
is the height at time t[i]
. h
and t
must be of same length and have at least 2 elements, t
must be increasing.
The following functions construct sac
objects:
Standard constructor is tp_to_sac
(tie point to sediment accumulation curve)
The following functions inspect the logic of sac
objects:
is_sac
to check validity of sac
objectThe following functions yield a representation of sac
objects:
plot.sac
for plottingprint.sac
for printing to the consolesummary.sac
to provide a quick summaryThe following functions modify sac
objects:
set_L_unit
and set_T_unit
to change unitsThe following functions extract information from sac
objects:
get_L_unit
and get_T_unit
to extract unitsget_T_tp
and get_L_tp
to extract tie pointsget_total_duration
to extract total duration coveredget_total_thickness
min_time
and max_time
min_height
and max_height
The following functions transform sac
objects into other S3 classes:
sac_to_adm
to transform sac
into the S3 class adm
multiadm
The S3 class multiadm
represents multiple age depth models.. Structurally, they are lists with the following elements:
no_of_entries
: Positive integer, number of age depth models containedt
list of length no_of_entries
. Each element contains a numeric vectorh
: list of length no_of_entries
. Each element contain a numeric vectordestr
: list of length no_of_entries
. Each element contain a logicT_unit
: NULL
or a string, time unitL_unit
: NULL
or a string, length unith[[i]][j]
is the height of the i-th age-depth model at time t[[i]][j]
. For each i
, the quintuple h[[i]]
, t[[i]]
, destr[[i]]
, T_unit
and L_unit
specify an adm
object with the constraints as specified in the section S3 class adm
(e.g., on monotonicity, length, etc.). T_unit
and L_unit
are shared among all age-depth models in an multiamd
object.
The following functions construct multiadm
objects:
anchor
to construct multiadm
from uncertain tie points and adm
objects.merge_adm_to_multiadm
to construct multiadm
from adm
objectssedrate_to_multiadm
construct multiadm
from info on sedimentation rates, see vignette("adm_from_sedrate")
strat_cont_to_multiadm
construct multiadm
from tracer information, see vignette("adm_from_trace_cont")
The following functions inspect the logic of multiadm
objects:
is_multiadm
to check for validity of multiadm objectThe following functions yield a representation multiadm
objects:
plot.multiadm
for plottingprint.multiadm
for printing to consolesummary.multiadm
for providing summary statisticsThe following functions modify multiadm
objects:
merge_multiadm
to combine multiple multiadm
objectsset_L_unit
and set_T_unit
to change unitsThe following functions extract information from multiadm
objects:
condensation
to extract condensationget_completeness
and get_incompleteness
get_height
get_hiat_duration
get_hiat_list
get_hiat_no
get_hiat_pos
get_L_unit
and get_T_unit
to extract dataget_time
get_total_duration
get_total_thickness
is_destructive
sed_rate_l
sed_rate_t
get_T_tp
and get_L_tp
to extract time and length/height tie pointsThe following functions transform multiadm
objects into other S3 classes:
split_multiadm
to split multiadm
into list of adm
objectsmean_adm
, median_adm
and quantile_adm
to extract mean, median, and quantile age-depth model of adm
class.mstratlist
and timelist
stratlist
and timelist
inherit from the base list
. They are list of stratigraphic positions or times, associated with other data (e.g. trait values, proxy values)
stratlist
is a list with one element named "h"timelist
is a list with one element named "t"stratlist
is returned by time_to_strat.list
timelist
is returned by strat_to_time.list
plot.stratlist
for plotting stratlist
plot.timelist
for plotting timelist
list
admtools
implements the following methods for list
:
strat_to_time.list
: Transform strat-val pairs into time domaintime_to_strat.list
: Transform time-val pairs into strat domainphylo
admtools
implements the following methods for phylo
:
strat_to_time.phylo
: Transform stratigraphic tree into time domaintime_to_strat.phylo
: Transform time tree into strat domainnumeric
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
The following functions are used for plotting:
plot.adm
plotting for S3 class adm
plot.multiadm
plotting for S3 class multiadm
plot.sac
plotting for S3 class sac
plot.timelist
for plotting timelist
plot.stratlist
for plotting stratlist
T_axis_lab
to annotate time axis
L_axis_lab
to annotate length/depth axis
plot_sed_rate_l
to plot sedimentation rate in length/depth domain
plot_sed_rate_t
to plot sedimentation rate in time domain
plot_condensation
plot_erosive_intervals
to highlight erosive intervals, called after plot.adm
The following functions are used internally and not exposed to users. They can be accessed via admtools:::function_name
.
plot_destr_parts
plot_acc_parts
make_adm_canvas
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