Package: hmde 0.1.0

Tess OBrien

hmde: Hierarchical Methods for Differential Equations

Wrapper for Stan that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available.

Authors:Daniel Falster [aut, ctb], Tess O'Brien [aut, cre, cph], Fonti Kar [ctb], David Warton [aut, ctb]

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hmde.pdf |hmde.html✨
hmde/json (API)

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

Peer review:

Bug tracker:https://github.com/traitecoevo/hmde/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrstanstancpp

5.23 score 2 stars 8 scripts 13 exports 56 dependencies

Last updated 17 days agofrom:fed62c65a6. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-win-x86_64NOTEDec 10 2024
R-4.5-linux-x86_64NOTEDec 10 2024
R-4.4-win-x86_64NOTEDec 10 2024
R-4.4-mac-x86_64NOTEDec 10 2024
R-4.4-mac-aarch64NOTEDec 10 2024
R-4.3-win-x86_64NOTEDec 10 2024
R-4.3-mac-x86_64NOTEDec 10 2024
R-4.3-mac-aarch64NOTEDec 10 2024

Exports:hmde_assign_datahmde_canham_dehmde_const_dehmde_extract_estimateshmde_linear_dehmde_modelhmde_model_deshmde_model_nameshmde_model_parshmde_plot_de_pieceshmde_plot_obs_est_indshmde_runhmde_vb_de

Dependencies:abindbackportsBHcallrcheckmateclicolorspacedescdistributionaldplyrfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbletidyselectutf8vctrsviridisLitewithr

Case study 3: Canham function growth with tree data from Barro Colorado Island

Rendered fromcanham.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-10
Started: 2024-11-28

Case study 1: Constant growth with SUSTAIN Trout data

Rendered fromconstant-growth.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-10
Started: 2024-11-28

Here be dragons

Rendered fromhere_be_dragons.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-10
Started: 2024-12-03

hmde

Rendered fromhmde.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-03
Started: 2024-11-18

hmde for Mathematicians

Rendered fromhmde_for_mathematicians.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-02
Started: 2024-12-02

Case study 2: von Bertalanffy growth with lizard size data

Rendered fromvon-bertalanffy.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2024-12-10
Started: 2024-11-28

Readme and manuals

Help Manual

Help pageTopics
The 'hmde' package.hmde-package hmde
Assign data to template for chosen modelhmde_assign_data
Differential equation for Canham growth single and multi- individual modelshmde_canham_de
Differential equation for constant growth single and multi- individual modelshmde_const_de
Extract samples and return measurement, individual, and population-level estimateshmde_extract_estimates
Differential equation for linear growth single individual modelhmde_linear_de
Select data configuration template for hmde supported modelhmde_model
Function to select DE given model namehmde_model_des
Returns names of available models.hmde_model_names
Show parameter list for hmde supported modelhmde_model_pars
Plot pieces of chosen differential equation model for each individual. Structured to take the individual data tibble that is built by the hmde_extract_estimates function using the ind_par_name_mean estimates. Function piece will go from the first fitted size to the last. Accepted ggplot arguments will change the axis labels, title, line colour, alphahmde_plot_de_pieces
Plot estimated and observed values over time for a chosen number of individuals based on posterior estimates. Structured to take in the measurement_data tibble constructed by the hmde_extract_estimates function.hmde_plot_obs_est_inds
Run chosen pre-built model in Stanhmde_run
Differential equation for von Bertalanffy growth single and multi- individual modelshmde_vb_de
Skink size data - Lampropholis delicataLizard_Size_Data
Garcinia recondita - Barro Colorado Island dataTree_Size_Data
Garcinia recondita model estimates - Barro Colorado Island dataTree_Size_Ests
SUSTAIN Salmo trutta dataTrout_Size_Data