Package: admtools 0.6.0.9000

Emilia Jarochowska

admtools: Estimate and Manipulate Age-Depth Models

Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.

Authors:Niklas Hohmann [aut], Emilia Jarochowska [cre]

admtools_0.6.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
admtools/json (API)

# Install 'admtools' in R:
install.packages('admtools', repos = c('https://mindthegap-erc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mindthegap-erc/admtools/issues

Pkgdown/docs site:https://mindthegap-erc.github.io

Datasets:

On CRAN:

Conda:

age-depth-modelgeochronologysedimentologystratigraphy

6.96 score 4 stars 1 packages 73 scripts 596 downloads 72 exports 5 dependencies

Last updated from:55c7d4aa12. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK120
source / vignettesOK230
linux-releaseOK117
macos-releaseOK102
macos-oldrelOK107
windows-develOK86
windows-releaseOK85
windows-oldrelOK79
wasm-releaseOK105

Exports:add_adm_to_multiadmadm_to_ddcanchorcondensationcondensation_funflip_ddcflux_constflux_linearflux_quadget_completenessget_data_from_eTimeOptget_heightget_hiat_durationget_hiat_listget_hiat_noget_hiat_posget_incompletenessget_L_tpget_L_unitget_L_unitsget_section_namesget_T_tpget_T_unitget_timeget_total_durationget_total_thicknessget_total_thicknessesis_admis_destructiveis_sacL_axis_labmake_legendmax_heightmax_timemean_admmedian_admmerge_adm_to_multiadmmerge_multiadmmin_heightmin_timeplot_condensationplot_erosive_intervalsplot_sed_rate_lplot_sed_rate_tquantile_admrev_dirsac_to_admsed_rate_from_matrixsed_rate_gen_from_boundssed_rate_gen_gammased_rate_lsed_rate_l_funsed_rate_tsed_rate_t_funsedrate_to_multiadmset_L_unitset_L_unitsset_section_namesset_T_unitsplit_multiadmstrat_cont_gen_from_tracerstrat_cont_to_multiadmstrat_to_timeT_axis_labtime_to_strattp_height_dettp_time_dettp_time_floating_scaletp_time_normtp_to_admtp_to_ddctp_to_sac

Dependencies:apedigestlatticenlmeRcpp

Integration with the FossilSim and paleotree packages
Integration with the FossilSim package | Integration with paleotree | References
Rendered fromFossilSim_integration.Rmdusingknitr::rmarkdown

Last update: 2025-05-20
Started: 2025-04-01

Estimating Age-Depth Models from Sedimentation Rates
Introduction | Inputs | Example | Data | Tie points | Sedimentation rates | Estimate age depth model | Coding tie points | Background | Wrappers | Manually coding tie points | Coding sedimentation rates | Manually coding sedimentation rates | Further information
Rendered fromadm_from_sedrate.Rmdusingknitr::rmarkdown

Last update: 2025-04-01
Started: 2023-11-27

admtools: Getting Started
Introduction | Installation | From GitHub | From CRAN | Loading the package | Getting help | The adm and multiadm classes | Conventions | Example | Defining age-depth models | Representation | Extracting data from age-depth models | Transforming data between time and stratigraphic domain | Heights and times | Phylogenetic trees | Lists and time/stratigraphic series | Numeric vectors | Further information | References
Rendered fromadmtools.Rmdusingknitr::rmarkdown

Last update: 2025-04-01
Started: 2023-10-08

Depth-depth curves and correlation
Constructing depth-depth curves | Plotting and summaries | Modification
Rendered fromcorrelation.Rmdusingknitr::rmarkdown

Last update: 2025-04-01
Started: 2025-04-01

Structure and classes of the admtools package
Introduction | S3 Classes | S3 class adm | Description | Construction | Logic | Representation | Modification | Extracting information | Transformation into other S3 classes | S3 class sac | S3 class multiadm | S3 class ddc | S3 classes stratlist and timelist | Methods implemented for external S3 classes | S3 class list | S3 class phylo | S3 class pre_paleoTS | Class numeric | Plotting | Internals | Vignettes
Rendered fromadmtools_doc.Rmdusingknitr::rmarkdown

Last update: 2025-04-01
Started: 2024-03-01

Plotting Age-Depth Models
Plotting age-depth models | Simple age-depth models (class "adm") | Adding axis labels | Multiple age-depth models (class "multiadm") | Lists in time and stratigraphic domain
Rendered fromadm_plotting.Rmdusingknitr::rmarkdown

Last update: 2024-10-03
Started: 2024-01-16

Estimating Age-Depth Models from Tracer Contents of Rocks and Sediments
Introduction | Idea | Example | Data | Tie points | Tracer values | Estimate age depth model | Coding tie points | Background | Wrappers | Manually coding tie points | Coding tracer data and hypothesis | Manually coding tracer data and hypothesis | Further information | See also
Rendered fromadm_from_trace_cont.Rmdusingknitr::rmarkdown

Last update: 2024-07-14
Started: 2023-11-27

Readme and manuals

Help Manual

Help pageTopics
add adm object ot multiadm objectadd_adm_to_multiadm
construct depth-depth curve from age-depth modelsadm_to_ddc
anchor age-depth modelanchor
Example data from CarboCATLiteCarboCATLite_data
condensation with heightcondensation
condensation functioncondensation_fun
reverse direction of depth-depth curveflip_ddc
constant deterministic tracer fluxflux_const
linear deterministic tracer fluxflux_linear
quadratic deterministic tracer fluxflux_quad
Determine stratigraphic (in)completenessget_completeness get_incompleteness
extract data from eTimeOpt resultsget_data_from_eTimeOpt
determine stratigraphic height deposited at specific timeget_height
extract hiatus durationget_hiat_duration
extract hiatus infoget_hiat_list
get no. of hiatusesget_hiat_no
get hiatus positionsget_hiat_pos
get height/length tie pointget_L_tp
extract length unitget_L_unit
extract length unitsget_L_units
get section names from depth-depth curveget_section_names
extract time tie pointsget_T_tp
extract Time unitget_T_unit
Determine times based on age-depth modelget_time
Total duration coveredget_total_duration
get total thicknessget_total_thickness
get thicknesses of sections from depth-depth curvesget_total_thicknesses
Is an adm object a valid age-depth modelis_adm
Is deposition destructive?is_destructive
is valid multiadm object?is_multiadm
is valid sac objectsis_sac
plot height axis labelL_axis_lab
plot legendmake_legend
get highest stratigraphic tie pointmax_height
last time tie pointmax_time
get mean ADMmean_adm
get median ADMmedian_adm
combine multiple adm ojects into multiadm objectmerge_adm_to_multiadm
merge multiple multiadm objectsmerge_multiadm
get lowest stratigraphic tie pointmin_height
first time tie pointmin_time
plot condensation in heightplot_condensation
mark erosive time intervalsplot_erosive_intervals
plot sed. rate in heightplot_sed_rate_l
plot sedimentation rate in timeplot_sed_rate_t
plotting adm objectsplot.adm
plot depth-depth curveplot.ddc
plot multiadm objectplot.multiadm
plot sediment accumulation curveplot.sac
plot strat listplot.stratlist
plot time listsplot.timelist
get quantile ADMquantile_adm
reverse direction of time/depth axisrev_dir
turn sed. acc curve into admsac_to_adm
make sed rate gen from matrixsed_rate_from_matrix
seg rate gen from upper/lower boundssed_rate_gen_from_bounds
sed. rate gen based on gamma distributionsed_rate_gen_gamma
sedimentation rate in stratigraphic heightsed_rate_l
sed rate in height functionsed_rate_l_fun
sedimentation rate in time domainsed_rate_t
sedimentation rate functionsed_rate_t_fun
Estimate age-depth model from sedimentation rates & tie pointssedrate_to_multiadm
set length unitsset_L_unit
set length unitsset_L_units
set section names for depth-depth curvesset_section_names
set time unitsset_T_unit
split multiadm objects into admsplit_multiadm
proxy values in strat domainstrat_cont_gen_from_tracer
estimate age-depth model from tracerstrat_cont_to_multiadm
transform objects from strat. to time domainstrat_to_time
transform 'fossils' object from 'FossilSim' between time and strat domainstrat_to_time.fossils
transform list from height to time domainstrat_to_time.list
transform numeric vectors from height to time domainstrat_to_time.numeric
transform phylo objectstrat_to_time.phylo
transform taxonomy object from strat to time domainstrat_to_time.taxonomy
summary of age-depth modelsummary.adm
summary of depth-depth curvesummary.ddc
summary of age-depth modelsummary.multiadm
summary of sediment accumulation curvesummary.sac
plot time axis labelT_axis_lab
transform objects from time domain to strat. domaintime_to_strat
transform 'fossils' from FossilSim from time to strat domaintime_to_strat.fossils
transform list from time to height domaintime_to_strat.list
transform vectors from time to height domaintime_to_strat.numeric
transform phylo objecttime_to_strat.phylo
transform 'taxomony' from time to strat domaintime_to_strat.taxonomy
example time treetimetree
deterministic tie points height domaintp_height_det
deterministic tie points in time domaintp_time_det
tie points for floating time scaletp_time_floating_scale
time tie points with normal distributiontp_time_norm
Construct age-depth model from tie pointstp_to_adm
construct depth-depth curve from coeval heightstp_to_ddc
define sed. acc. curvetp_to_sac