Package: lame 1.3.5

Shahryar Minhas

lame: Longitudinal Additive and Multiplicative Effects Models for Networks

Additive and multiplicative effects models for both cross-sectional and longitudinal network analysis. The package provides two main functions: ame() for cross-sectional networks and lame() for longitudinal networks. It supports square and rectangular network structures. Key features include: (1) Cross-sectional network analysis via ame() with support for binary, continuous, ordinal, and count data; (2) Longitudinal network analysis via lame() with additive sender/receiver and multiplicative latent-factor effects that can evolve over time through AR(1) processes (Sewell and Chen (2015) <doi:10.1080/01621459.2014.988214>; Durante and Dunson (2014) <doi:10.1093/biomet/asu040>); (3) Handling of changing actor compositions across time periods in longitudinal models; (4) Performance improvements through C++ implementations via 'Rcpp' and 'RcppArmadillo'.

Authors:Cassy Dorff [aut], Shahryar Minhas [aut, cre], Tosin Salau [aut]

lame_1.3.5.tar.gz
lame_1.3.5.zip(r-4.7-x86_64)lame_1.3.5.zip(r-4.7-arm64)lame_1.3.5.zip(r-4.6-x86_64)lame_1.3.5.zip(r-4.6-arm64)lame_1.3.5.zip(r-4.5-x86_64)
lame_1.3.5.tgz(r-4.6-x86_64)lame_1.3.5.tgz(r-4.6-arm64)lame_1.3.5.tgz(r-4.5-x86_64)lame_1.3.5.tgz(r-4.5-arm64)
lame_1.3.5.tar.gz(r-4.7-arm64)lame_1.3.5.tar.gz(r-4.7-x86_64)lame_1.3.5.tar.gz(r-4.6-arm64)lame_1.3.5.tar.gz(r-4.6-x86_64)
lame_1.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lame/json (API)

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

Bug tracker:https://github.com/netify-dev/lame/issues

Pkgdown/docs site:https://netify-dev.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • addhealthc3 - AddHealth community 3 data
  • addhealthc9 - AddHealth community 9 data
  • coldwar - Cold War data
  • comtrade - Comtrade data
  • dutchcollege - Dutch college data
  • IR90s - International relations in the 90s
  • lazegalaw - Lazega's law firm data
  • sampsonmonks - Sampson's monastery data
  • sheep - Sheep dominance data
  • Xcol - Column covariates
  • Xdyad - Dyadic covariates
  • Xrow - Row covariates
  • Y - Relational matrix
  • YX_bin - Binary relational data and covariates
  • YX_bin_list - Synthetic longitudinal binary relational data, list-form
  • YX_bin_long - Synthetic longitudinal binary relational data
  • YX_cbin - Censored binary nomination data and covariates
  • YX_frn - Fixed rank nomination data and covariates
  • YX_nrm - Normal relational data and covariates
  • YX_ord - Ordinal relational data and covariates

On CRAN:

Conda:

openblascppopenmp

6.46 score 1 stars 34 scripts 404 downloads 105 exports 42 dependencies

Last updated from:ef609b20b7. Checks:15 OK. Indexed: yes.

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Exports:ab_plotab_plot.ame_alsabsdiffals_dynamic_betaals_start_valsameame_alsame_als_bootstrapame_als_refitame_memory_settingsame_memory_usageame_optionsame_parallelarray_to_listas_drawsas_lame_yautoplotboot_amecheck_formatcombine_ame_chainscompact_amecompute_mcmc_diagnosticsdesign_arraydesign_array_listwisedeldetect_change_pointdynamic_beta_prior_summaryel2smevaluate_heldoutforecast_pitget_design_repget_fit_objectget_start_valsglancegofgof_plotgof_plot.ame_alsgof_statsgof_stats_bipartitegof_stats_unipartitegof_temporallamelame_alslame_multilame_parallellame_resumelame_snap_alslatent_positionslfolist_to_arrayloomhalfnodefactornodematchper_actor_slopesposterior_optionsposterior_quantilesprecomputeXprediction_draws_longprior_summaryprocrustes_alignraSab_bin_fcraSab_cbin_fcraSab_frn_fcrbeta_ab_fcrbeta_ab_rep_fcread_log_likreconstruct_EZreconstruct_UVPMrhat_dynamic_betarmvnormrrho_mhrs2_fcrs2_rep_fcrSab_fcrSuv_fcrUV_dynamic_fcrUV_dynamic_snap_fcrUV_dynamic_t_fcrUV_fcrUV_rep_fcrUV_sym_fcrwishrZ_bin_fcrZ_frn_fcrZ_nrm_fcrZ_pois_fcsampler_describesimulate_posteriorsimY_binsimY_frnsimY_nrmsimY_ordsimY_poissimZsm2elsnap_category_summarysnap_index_drawssnap_index_summarysnap_rank_summarytidytrace_plotuv_plotwaicXbetazscores

Dependencies:abindbackportsbase64enccheckmateclicodacpp11farverggforceggnewscaleggplot2ggrepelgluegridExtragtableigraphisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixnetifypatchworkpkgconfigpolyclipR6RColorBrewerRcppRcppArmadilloRcppEigenrlangS7scalessystemfontstidyselecttweenrvctrsviridisLitewithr

lame Overview
Package Overview | Migrating from amen | Application: Dutch College Friendships | Fitting the Model | Interpreting the Results | Checking Convergence | Bayesian-ecosystem diagnostics: posterior::as_draws() | Goodness of Fit | Posterior-predictive temporal-trend test: gof_temporal() | Latent Space | Extracting Latent Positions | Tidy-data round-trip via netify | Entry: tidy edgelist → lame() | Exit: tidy(), autoplot(), prediction_draws_long() | Coefficient tables: glance() + tidy() -> modelsummary / gt / kableExtra | Model comparison: loo::loo_compare() as a one-liner | Reproducibility: sessionInfo() and renv.lock | What's Next?

Last update: 2026-07-21
Started: 2025-06-10

Your First AME Model
Why Network Models? | The Data | Building Covariates | Fitting the Model | A note for ERGM users: what AME assumes | What Did We Find? | Did the Sampler Converge? | Numerical convergence diagnostics: posterior::as_draws() | Between-chain $\hat R$: ame_parallel(n_chains = 4) | Other quick checks | Model comparison: loo() and loo_compare() | Does the Model Fit the Data? | Visualizing the Latent Space | Who Are the Most Social / Popular Students? | Making Predictions | Held-out link prediction | Simulating from the Model | Practical Tips | What's Next? | References

Last update: 2026-07-21
Started: 2025-08-27

Bipartite Network Analysis
Introduction | The Bipartite AME Model | Supported families in bipartite mode | Cross-Sectional Analysis with ame() | Coming from long-format data? | Simulating Data | Fitting the Model | Visualizing the Latent Space | Longitudinal Analysis with lame() | Simulating Longitudinal Data | Static Model | Dynamic Model | Time-varying Interaction Matrix (dynamic_G) | Visualizing Temporal Evolution | Convergence Diagnostics | Comparing Static and Dynamic Models | Choosing Latent Dimensions | Practical Guidance | Extracting Positions for Custom Analysis

Last update: 2026-07-20
Started: 2025-08-12

Dynamic Effects in Longitudinal AME Models
Introduction | What Are Dynamic Effects? | The Static Baseline | Dynamic Latent Positions (dynamic_uv = TRUE) | Dynamic Additive Effects (dynamic_ab = TRUE) | Dynamic Regression Coefficients (dynamic_beta) | A worked dynamic_beta example | Choosing a prior family: dynamic_beta_kind | Hierarchical pooling: dynamic_beta_pool | Per-actor time-varying slopes: dynamic_beta_per_actor | Diagnosing your dynamic fit | Temporal-trend posterior-predictive check: gof_temporal() | Inspecting the priors actually in effect: prior_summary() | Multi-chain $\hat R$ via lame_parallel() and rhat_dynamic_beta() | Forecasting | Visualising the coefficient path: autoplot.lame | LOO / WAIC via save_log_lik = TRUE | Prior Specifications | Genuine Dynamics: What They Look Like | What Happens Without Temporal Structure? | Visualizing the Null Case | Comparing Model Specifications | When to Use Dynamic Effects | Dealing with Rotational Indeterminacy | References

Last update: 2026-07-20
Started: 2025-08-11

Fast (MCMC-free) AME Estimation
When to use the fast estimator | Wall-clock benchmark | What ALS can do vs. what only MCMC does | A first fit | Choosing the rank R | Non-normal families | Uncertainty | ALS bootstrap vs MCMC posterior on the same data | Longitudinal data | Summary

Last update: 2026-07-20
Started: 2026-05-28

Forecasting Longitudinal Networks with lame
What this vignette covers | Step 1: Fit | Step 2: Forecast h periods ahead | Visualising the forecast | Poisson exposure offsets via period_exposure | Step 3: Counterfactual forecasts | Step 4: Visualise the coefficient path | Step 5: Forecast diagnostics | Watching it fail: a sparse, short, drifting panel | Probability-integral-transform (PIT) calibration | Comparing two fits with loo_compare() | Memory-conscious long runs | See also

Last update: 2026-07-20
Started: 2026-05-28

Getting Started with lame
What Is lame? | Coming from a tidy edgelist? Use netify | A 5-Minute Example | What Can You Do with a Fitted Model? | Checking Your Model | Visualizing Network Structure | Cross-Sectional Models | Dynamic Effects | Bipartite Networks | Supported Data Types | Power-User Features | Where to Go Next | References

Last update: 2026-07-20
Started: 2025-08-12

Readme and manuals

Help Manual

Help pageTopics
Visualize sender and receiver random effectsab_plot
Additive-effects plot for an ame_als fitab_plot.ame_als
AddHealth community 3 dataaddhealthc3
AddHealth community 9 dataaddhealthc9
Penalised ALS time-varying coefficient estimateals_dynamic_beta
Convert an ALS fit to MCMC starting valuesals_start_vals
AME model fitting routineame
Fast (MCMC-free) AME estimation for a cross-sectional networkame_als
Bootstrap uncertainty for the fast AME estimatorame_als_bootstrap boot_ame
Refit a fast AME model with a warm startame_als_refit
Display memory usage information for AME modelsame_memory_settings
Calculate memory usage of AME model componentsame_memory_usage
AME model fitting optionsame_options
Run AME model with multiple parallel chainsame_parallel
Convert array to list.array_to_list
Generic dispatcher for posterior::as_draws on lame fitsas_draws
Convert an AME / LAME fit to a posterior draws objectas_draws.ame as_draws.ame_als as_draws.lame
Convert a graph object to a lame-ready adjacency matrixas_lame_y
autoplot method for ALS fitsautoplot.ame_als autoplot.lame_als
Ribbon plot of time-varying coefficients (or coefplot for static fits)autoplot.ame autoplot.lame
fitted/residuals are not defined for a bootstrap objectboot_ame-no-fitted fitted.boot_ame residuals.boot_ame
Validate input data format for lame functioncheck_format
Extract beta path from a penalised-ALS objectcoef.als_dynamic_beta
Extract model coefficients from AME modelcoef.ame coef.lame
Extract coefficients from a fast AME fitcoef.ame_als
Point estimates from a fast AME bootstrapcoef.boot_ame
Cold War datacoldwar
Combine multiple AME chainscombine_ame_chains
Optimize AME model output for memory efficiencycompact_ame
Compute MCMC convergence diagnostics for multiple chainscompute_mcmc_diagnostics
Compute X'X and X'y for bipartite covariate regressioncompute_XtX_Xty_bip_cpp
Comtrade datacomtrade
Bayesian credible intervals for AME model parametersconfint.ame confint.lame
Confidence intervals for a fast AME fitconfint.ame_als
Confidence intervals from a fast AME bootstrapconfint.boot_ame
Computes the design socioarray of covariate valuesdesign_array_listwisedel
Detect potential change points in a dynamic_beta posterior pathdetect_change_point
Dutch college datadutchcollege
Summarise the implied prior on a time-varying coefficient pathdynamic_beta_prior_summary
Edgelist to sociomatrixel2sm
Held-out predictive evaluation for an ame / lame fitevaluate_heldout
Extract fitted values from AME modelfitted.ame
Extract fitted values from a fast AME fitfitted.ame_als
Extract fitted values from LAME modelfitted.lame
Probability-integral-transform calibration check for h-step forecastsforecast_pit
formula() is not defined for an ame() / lame() fitformula.ame formula.lame
Create design array for replicate dataget_design_rep
Compute EZ when beta is time-varyingget_EZ_dynamic_beta_cpp
Get fitted object from MCMC resultsget_fit_object
Get fitted object from MCMC resultsget_start_vals
S3 generic for 'glance'glance
Glance method for fitted 'ame' / 'lame' objectsglance.ame glance.lame
Glance method for fitted 'ame_als' / 'lame_als' objectsglance.ame_als glance.lame_als
Compute GOF statistics from saved posterior samplesgof
Visualize goodness-of-fit statistics for AME and LAME modelsgof_plot
Goodness-of-fit check for an ame_als fitgof_plot.ame_als
Goodness of fit statisticsgof_stats
Goodness of fit statistics for bipartite networksgof_stats_bipartite
Goodness of fit statistics for unipartite networksgof_stats_unipartite
Posterior-predictive temporal-trend testgof_temporal
Initialize dynamic additive effects with AR(1) structureinit_dynamic_ab_cpp
Initialize dynamic latent positions with AR(1) structureinit_dynamic_positions
International relations in the 90sIR90s
AME model fitting routine for longitudinal relational datalame
Fast (MCMC-free) AME estimation for a longitudinal networklame_als
Multi-panel lame() with shared coefficientslame_multi
Run LAME (longitudinal AME) with multiple parallel chainslame_parallel
Resume a 'lame()' MCMC run from a checkpointlame_resume
Fast approximate dynamic snap-shift AME estimatorlame_snap_als
Extract latent positions as a tidy data framelatent_positions latent_positions.ame latent_positions.ame_als latent_positions.lame
Lazega's law firm datalazegalaw
Exact rolling-origin leave-future-out cross-validationlfo
Convert list to arraylist_to_array
Log-likelihood is not directly exposed for ame() / lame() fitslogLik.ame logLik.lame
Log-likelihood is not defined for a fast AME fitlogLik.ame_als
Generic dispatcher for loo / waic on ame / lame fitsloo waic
Approximate leave-one-out cross-validation for AME / LAME fitsloo.ame loo.ame_als loo.lame
Symmetric square root of a matrixmhalf
Number of observed dyads in an AME / LAME fitnobs.ame nobs.lame
Number of observed dyads in an ame_als fitnobs.ame_als
ERGM-style covariate helpers for ame() / lame()absdiff nodefactor nodematch
Post-MCMC per-actor time-varying slopesper_actor_slopes
Simple diagnostic plot for AME model fitplot.ame
Plot the convergence of a fast AME fitplot.ame_als
Plot diagnostics for a LAME model fitplot.lame
Options for saving posterior samples during MCMCposterior_options
Extract posterior quantiles for model componentsposterior_quantiles
Predict method for AME modelspredict.ame
Predictions from a fast AME fitpredict.ame_als
Predict method for LAME modelspredict.lame
Long-format draws of the linear predictor for marginaleffects-style useprediction_draws_long
Print method for penalised ALS time-varying betaprint.als_dynamic_beta
Print method for AME model objectsprint.ame
Print an ame_als objectprint.ame_als
Print methods for AME and LAME simulation objectsprint.ame.sim print.lame.sim
Print bootstrap results for a fast AME fitprint.boot_ame
Print method for gof_temporal outputprint.gof_temporal
Print method for LAME objectsprint.lame
Print method for lame_multiprint.lame_multi
Print method for lfo() resultsprint.lfo_lame
Print method for per_actor_slopesprint.per_actor_slopes
Print method for summary.ame objectsprint.summary.ame
Print a fast AME summaryprint.summary.ame_als
Print method for summary.lame objectsprint.summary.lame
Print the priors used by an AME / LAME / ame_als fitprior_summary prior_summary.ame prior_summary.ame_als prior_summary.default prior_summary.lame
Procrustes alignment of latent positions across timeprocrustes_align
Full bipartite Gibbs update for beta, a, brbeta_ab_bip_gibbs_cpp
Read the per-iteration log-lik matrix back from on-disk chunksread_log_lik
Reconstruct EZ and UVPM matrices from AME model outputreconstruct_EZ reconstruct_UVPM
Extract residuals from AME modelresiduals.ame
Residuals from a fast AME fitresiduals.ame_als
Extract residuals from LAME modelresiduals.lame
Multivariate split-R-hat for dynamic_beta coefficient pathsrhat_dynamic_beta
Simulation from a multivariate normal distributionrmvnorm
Gibbs update for additive effects covariancerSab_fc
Bipartite dynamic UV Gibbs updaterUV_dynamic_bip_fc_cpp
Gibbs sampling of dynamic U and V with AR(1) evolutionrUV_dynamic_fc
Update dynamic latent positions using AR(1) processrUV_dynamic_fc_cpp
Gibbs sampling of dynamic U and V with snap-shift dynamicsrUV_dynamic_snap_fc
Update dynamic latent positions with snap-shift model selectionrUV_dynamic_snap_fc_cpp
Gibbs sampling of dynamic U and V with heavy-tailed (Student-t) innovationsrUV_dynamic_t_fc
Update dynamic latent positions with heavy-tailed (Student-t) AR(1) innovationsrUV_dynamic_t_fc_cpp
Gibbs sampling of U and VrUV_sym_fc
Batch binary Z sampling across all time periods (bipartite, rho=0)rZ_bin_bip_batch_cpp
Batch normal Z sampling across all time periodsrZ_nrm_batch_cpp
Simulate missing values in a normal AME modelrZ_nrm_fc
Gibbs update for latent variable in a Poisson AME modelrZ_pois_fc
Sample the dynamic-block beta path via FFBSsample_beta_dynamic_cpp
Sample the static-block beta conditional on the dynamic pathsample_beta_static_cpp
Sample dynamic additive effects with AR(1) evolutionsample_dynamic_ab_cpp
Sample AR(1) parameter for dynamic additive effectssample_rho_ab_cpp
Sample the AR(1) rho for each dynamic blocksample_rho_beta_cpp
Sample AR(1) parameter for dynamic latent factorssample_rho_uv
Sample innovation variance for dynamic additive effectssample_sigma_ab_cpp
Sample the AR(1) innovation sigma for each dynamic blocksample_sigma_beta_cpp
Sample innovation variance for dynamic latent factorssample_sigma_uv
Describe the estimator behind a fitted objectsampler_describe sampler_describe.ame sampler_describe.ame_als sampler_describe.boot_ame sampler_describe.lame
Sampson's monastery datasampsonmonks
Sheep dominance datasheep
Simulate posterior distributions from fitted AME modelsimulate_posterior
Simulate networks from a fitted AME modelsimulate.ame
Simulate networks from a fitted ame_als modelsimulate.ame_als
Simulate longitudinal networks from a fitted LAME modelsimulate.lame
Simulate a Poisson relational matrixsimY_pois
Summarize snap indices by actor categorysnap_category_summary
Extract posterior draws of snap indicessnap_index_draws
Summarize posterior snap indicessnap_index_summary
Summarize posterior rank uncertainty for snap yearssnap_rank_summary
Summary of an AME objectsummary.ame
Summarize an ame_als objectsummary.ame_als
Summary method for AME simulationssummary.ame.sim
Summarize bootstrap results for a fast AME fitprint.summary.boot_ame summary.boot_ame
Summary of a LAME objectsummary.lame
Summary method for LAME simulationssummary.lame.sim
S3 generic for 'tidy'tidy
Tidy method for fitted 'ame' / 'lame' objectstidy.ame tidy.lame
Tidy method for fitted 'ame_als' / 'lame_als' objectstidy.ame_als tidy.lame_als
Tidy method for a standalone bootstrap object ('boot_ame')tidy.boot_ame
MCMC trace plots and density plots for AME/LAME model parameterstrace_plot
Update an AME / LAME fitupdate.ame update.lame
Update an 'ame_als' / 'lame_als' fitupdate.ame_als update.lame_als
Visualize multiplicative effects (latent factors) from AME modelsuv_plot
Posterior covariance of AME model coefficientsvcov.ame vcov.lame
Sandwich covariance for the regression coefficients of a fast AME fitvcov.ame_als
Bootstrap covariance of the regression coefficientsvcov.boot_ame
TIES sanctions data for vignettesvignette_data
WAIC for AME / LAME fitswaic.ame waic.ame_als waic.lame
Linear combinations of submatrices of an arrayXbeta
Compute Xbeta product for bipartite networksXbeta_bip_cpp
Column covariatesXcol
Dyadic covariatesXdyad
Row covariatesXrow
Relational matrixY
binary relational data and covariatesYX_bin
Synthetic longitudinal binary relational data, list-form (latent-scale)YX_bin_list
synthetic longitudinal binary relational data (latent-scale)YX_bin_long
Censored binary nomination data and covariatesYX_cbin
Fixed rank nomination data and covariatesYX_frn
normal relational data and covariatesYX_nrm
ordinal relational data and covariatesYX_ord