Package: admtools 0.4.0.9000

Niklas Hohmann

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, cre]

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admtools.pdf |admtools.html✨
admtools/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

age-depth-modelgeochronologysedimentologystratigraphy

7.31 score 4 stars 1 packages 34 scripts 410 downloads 62 exports 5 dependencies

Last updated 2 months agofrom:9f4faf2a90. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winOKNov 03 2024
R-4.5-linuxOKNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macOKNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:add_adm_to_multiadmanchorcondensationcondensation_funflux_constflux_linearflux_quadget_completenessget_data_from_eTimeOptget_heightget_hiat_durationget_hiat_listget_hiat_noget_hiat_posget_incompletenessget_L_tpget_L_unitget_T_tpget_T_unitget_timeget_total_durationget_total_thicknessis_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_admsac_to_admsed_rate_from_matrixsed_rate_gen_from_boundssed_rate_lsed_rate_l_funsed_rate_tsed_rate_t_funsedrate_to_multiadmset_L_unitset_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_sac

Dependencies:apedigestlatticenlmeRcpp

admtools: Getting Started

Niklas Hohmann

Rendered fromadmtools.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-10-03
Started: 2023-10-08

Estimating Age-Depth Models from Sedimentation Rates

Niklas Hohmann

Rendered fromadm_from_sedrate.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-08-30
Started: 2023-11-27

Estimating Age-Depth Models from Tracer Contents of Rocks and Sediments

Niklas Hohmann

Rendered fromadm_from_trace_cont.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

Plotting Age-Depth Models

Rendered fromadm_plotting.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

Structure and classes of the admtools package

Niklas Hohmann

Rendered fromadmtools_doc.Rmdusingknitr::rmarkdownon Nov 03 2024.

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

Readme and manuals

Help Manual

Help pageTopics
add adm object ot multiadm objectadd_adm_to_multiadm
anchor age-depth modelanchor
Example data from CarboCATLiteCarboCATLite_data
condensation with heightcondensation
condensation functioncondensation_fun
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 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
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 multiadm objectplot.multiadm
plot sediment accumulation curveplot.sac
plot strat listplot.stratlist
plot time listsplot.timelist
get quantile ADMquantile_adm
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
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 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 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
summary of age-depth modelsummary.adm
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 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
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
define sed. acc. curvetp_to_sac