Package: hmde 1.4.0

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. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.

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

hmde_1.4.0.tar.gz
hmde_1.4.0.zip(r-4.7-x86_64)hmde_1.4.0.zip(r-4.7-arm64)hmde_1.4.0.zip(r-4.6-x86_64)hmde_1.4.0.zip(r-4.6-arm64)hmde_1.4.0.zip(r-4.5-x86_64)
hmde_1.4.0.tgz(r-4.6-x86_64)hmde_1.4.0.tgz(r-4.6-arm64)hmde_1.4.0.tgz(r-4.5-x86_64)hmde_1.4.0.tgz(r-4.5-arm64)
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hmde_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hmde/json (API)

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

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

Pkgdown/docs site:https://traitecoevo.github.io

Uses libs:
  • onetbb– Parallelism library for C++
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

bayesian-inverse-problemsbayesian-methodsdifferential-equationshierarchical-modelsrstanstanonetbbcpp

6.26 score 5 stars 12 scripts 422 downloads 43 exports 57 dependencies

Last updated from:4a8f6a7981. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK518
linux-devel-x86_64OK667
source / vignettesOK833
linux-release-arm64OK492
linux-release-x86_64OK560
macos-release-arm64OK370
macos-release-x86_64OK725
macos-oldrel-arm64OK437
macos-oldrel-x86_64OK821
windows-devel-arm64OK551
windows-devel-x86_64OK843
windows-release-arm64OK552
windows-release-x86_64OK508
windows-oldrel-x86_64OK706
wasm-releaseOK248

Exports:error_estserror_ests<-fit_summaryfit_summary<-hmde_affine_dehmde_canham_dehmde_const_dehmde_data_templatehmde_estimateshmde_extract_Rhathmde_modelhmde_model_deshmde_model_nameshmde_model_parshmde_plot_de_pieceshmde_plot_obs_est_indshmde_plot_Rhat_histhmde_runhmde_vb_deindividual_estsindividual_ests<-measurement_estsmeasurement_ests<-methodmethod<-model_levelmodel_level<-model_namemodel_name<-obs_dataobs_data<-par_namespar_names<-plotpopulation_estspopulation_ests<-printprior_parsprior_pars<-runtimeruntime<-showsummary

Dependencies:abindbackportsBHcallrcheckmateclicowplotcpp11descdistributionaldplyrevaluatefarvergenericsggplot2gluegridExtragtablehighrinlineisobandknitrlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbletidyselectutf8vctrsviridisLitewithrxfunyaml

Case study 3: Canham function growth with tree data from Barro Colorado Island
References
Rendered fromcanham.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2024-11-28

Case study 1: Constant growth with SUSTAIN Trout data
Overview | Load dependencies | Priors | Simulate data | Visualise data | SUSTAIN trout data | Transform data | Visualise raw data | Fit model using | Inspect estimates | $R^2$ | Individual growth functions ($\beta$) | Population hyper-parameters | References
Rendered fromconstant-growth.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2024-11-28

Here be dragons
Load dependencies | The model | Simulating data | Implementing models and collecting posterior estimates | Step size data | Analysis | Second cluster analysis | Where to from here?
Rendered fromhere_be_dragons.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2024-12-03

hmde for Mathematicians
Getting started with | The Theory | The Maths | The Stats | Integration of time series | Demonstration: Canham Growth - Multiple Individuals
Rendered fromhmde_for_mathematicians.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2024-12-02

Case study 2: von Bertalanffy growth with lizard size data
Load dependencies | Overview | Priors | Visualise model | Lizard size data | Implementation | References
Rendered fromvon-bertalanffy.Rmdusingknitr::rmarkdown

Last update: 2026-05-04
Started: 2024-11-28

hmde
Installation | Overview | Notation | hmde supported growth functions | Workflow | References
Rendered fromhmde.Rmdusingknitr::rmarkdown

Last update: 2025-06-24
Started: 2024-11-18

Readme and manuals

Help Manual

Help pageTopics
The 'hmde' package.hmde-package hmde
generic error_ests gettererror_ests error_ests<-
generic fit_summary getterfit_summary fit_summary<-
Differential equation for affine growth single individual modelhmde_affine_de
Differential equation for Canham growth single and multi- individual modelshmde_canham_de
Differential equation for constant growth single and multi- individual modelshmde_const_de
Calculate Rhat statistics for a hmde_fit objecthmde_extract_Rhat
helper function for hmde_data_template that provides data structure for model, Also used to guide the user on the required structure for the model they want.hmde_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_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
Plot histogram of R_hat values for hmde_fit object.hmde_plot_Rhat_hist
Run chosen pre-built model in Stanhmde_run
Differential equation for von Bertalanffy growth single and multi- individual modelshmde_vb_de
generic individual_ests getterindividual_ests individual_ests<-
Skink size data - Lampropholis delicataLizard_Size_Data
generic measurement_ests gettermeasurement_ests measurement_ests<-
generic method gettermethod method<-
generic model_level settermodel_level model_level<- obs_data obs_data<-
generic model_name gettermodel_name model_name<-
generic par_names getterpar_names par_names<-
generic population_ests setterpopulation_ests population_ests<-
generic prior_pars getterprior_pars prior_pars<-
generic runtime getterruntime runtime<-
Garcinia recondita - Barro Colorado Island dataTree_Size_Data
Garcinia recondita model estimates - Barro Colorado Island dataTree_Size_Ests
SUSTAIN Salmo trutta dataTrout_Size_Data