lame

Longitudinal Additive and Multiplicative Effects Models for Networks

Network ties – trade flows, friendships, alliances, sanctions – are not independent observations. Some actors send a lot of ties, some receive a lot, ties tend to be reciprocated, and similar actors behave similarly. Run a plain regression on every (sender, receiver) pair and both your coefficients and your standard errors come out wrong.

lame fits models that account for that structure. Every actor gets a sender effect (how active they are), a receiver effect (how popular they are), and a position in a low-dimensional latent space that soaks up patterns covariates miss – homophily, clustering, transitivity. Covariates enter additively, just like in a regression, and the “longitudinal” part lets each piece drift across time.

The package implements the additive and multiplicative effects (AME) framework developed by Peter Hoff (and popularised by his amen package), and extends it in a few directions: lame() fits panel networks with time-varying effects; both ame() and lame() handle bipartite (rectangular) networks alongside the usual square case; the sampler is written in C++ (Rcpp / RcppArmadillo) to scale; and a fit exposes the usual coef(), vcov(), confint(), predict(), fitted(), residuals(), and simulate() methods, so it slots into the R modelling ecosystem like lm() or glm().

There is also a fast, MCMC-free point estimator – ame_als() / lame_als(), adapted from the Social Influence Regression estimator of Minhas & Hoff (2025). Reach for it when exploring, screening models, generating starting values, or fitting large networks; use the MCMC path when you need a full posterior or the rank/censored families.

New to probit, latent space, or AR(1)? vignette("lame") introduces each in context before the first fit.

Installation

Needs C++ build tools (Xcode CLI on macOS, Rtools on Windows, build-essential on Linux). The first install takes a few minutes while the C++ compiles.

# install.packages("devtools")
devtools::install_github("netify-dev/lame", dependencies = TRUE, build_vignettes = TRUE)

Quick Start

library(lame)

# YX_bin: a bundled 100-actor binary network (Y) with dyadic covariates (X). ?YX_bin
data("YX_bin")
Y     <- YX_bin$Y          # 100 x 100 0/1 sociomatrix, diagonal NA
Xdyad <- YX_bin$X[, , -1]  # drop the explicit intercept slice; ame() adds its own

fit <- ame(
  Y, Xdyad = Xdyad,
  family  = "binary",
  R       = 2,             # latent-space dimension (see below)
  burn    = 500,
  nscan   = 4000,          # ~400 stored draws with odens = 10
  odens   = 10,
  verbose = FALSE
)

summary(fit)               # coefficients, variance components, gof
trace_plot(fit)            # check mixing; gof_plot(fit) for posterior-predictive fit

What is R? The dimension of the latent space that captures who-ties-to-whom beyond the covariates and sender/receiver effects. R = 0 is the additive part only; R = 2 adds structure like homophily and transitivity. lame warns above R > floor(n/3), where high-rank factors start stealing signal from the additive effects. Start at R = 2, then compare gof_plot() across R = 0, 1, 2, 3.

Naming gotcha. Actors are aligned across Y, Xdyad, Xrow, Xcol by sorted dimnames, so paste0("N", 1:25) misaligns everything ("N1","N10","N11",... sorts before "N2"). Zero-pad (sprintf("N%02d", 1:25)) or use real names, and set matching dimnames on every input.

Longitudinal

Pass a list of Y matrices (and lists of covariates) to lame():

data("vignette_data")      # Y: list of 4 binary 35 x 35 matrices (sanctions, 35 countries x 4 yrs)

fit_long <- lame(
  Y, Xdyad = Xdyad, Xrow = Xrow, Xcol = Xcol,
  family = "binary", R = 2,
  burn = 500, nscan = 4000, odens = 10, verbose = FALSE
)
summary(fit_long)

Dynamic effects

The headline extension is letting effects vary over time:

fit_dynamic <- lame(
  Y, Xdyad = Xdyad, Xrow = Xrow, Xcol = Xcol,
  family = "binary", R = 2,
  dynamic_ab   = TRUE,       # time-varying sender/receiver effects
  dynamic_uv   = TRUE,       # time-varying latent positions
  dynamic_beta = "dyad",     # time-varying dyadic coefficients
  dynamic_beta_kind = "ar1", # "ar1" / "rw1" / "rw2" / "matern32"
  burn = 500, nscan = 4000, odens = 10,
  prior = list(rho_uv_mean = 0.9, rho_ab_mean = 0.8),
  verbose = FALSE
)

predict(fit_dynamic, h = 3, type = "response") forecasts three periods ahead; add interval = "credible" for per-period $lower / $median / $upper. See vignette("forecasting") and, for the dynamic_beta_kind decision tree, vignette("dynamic_effects").

Families

Pick the family that matches your tie type. All are supported unipartite, bipartite, and (where the tie type allows) symmetric – pass symmetric = TRUE for undirected networks and mode = "bipartite" for two-mode data.

family	tie type	unipartite	bipartite	symmetric
normal	continuous	yes	yes	yes
binary	0/1	yes	yes	yes
ordinal	ordered categories	yes	yes	yes
poisson	counts	yes	yes	yes
cbin	censored binary	yes	yes	no (directed row-cone)
frn	fixed rank nominations	yes	yes	no (directed row-cone)

Coming from another package

Tidy edgelists, panels, bipartite data: build the object with netify and hand it straight to ame() / lame():

net <- netify::netify(edges, actor1 = "sender", actor2 = "receiver", time = "year",
                      weight = "tie", dyad_vars = c("distance", "shared_border"),
                      nodal_vars = c("gdp", "population"), symmetric = FALSE)
fit <- lame(net, family = "binary", R = 2, burn = 500, nscan = 4000, odens = 10, verbose = FALSE)

For a lone igraph / network / adjacency matrix, as_lame_y(g) returns a plain Y.

From ERGM: lame is not an ergm substitute – ERGM specifies a joint distribution over the whole graph via change statistics (gwesp, triangle), while AME assumes dyads are conditionally independent given the actor effects, latent positions, and covariates, and captures higher-order structure through those random effects. So AME sidesteps ERGM’s degeneracy failure modes but does not give change-statistic interpretations, and it tends to under-predict transitivity. If gwesp is your target, stay in ERGM; if you want actor heterogeneity, dynamics, or forecasts, AME is the better fit. vignette("cross_sec_ame") scores ERGM-style triangle / two-path / clustering statistics through gof(fit, custom_gof = ...). The ERGM-style helpers nodematch(), absdiff(), and nodefactor() build dyadic covariates that drop straight into Xdyad.

Visualization

ab_plot(fit, effect = "sender")                 # additive effects; plot_type = "trajectory" over time
uv_plot(fit)                                     # latent positions;  plot_type = "trajectory" over time
trace_plot(fit); gof_plot(fit)                   # mcmc mixing; goodness of fit

Features

• Modes: cross-sectional (ame()), longitudinal (lame()), unipartite and bipartite, six families.
• Dynamics: time-varying latent positions (dynamic_uv), sender/receiver effects (dynamic_ab), and regression coefficients (dynamic_beta, per-block AR(1) / RW1 / RW2 / Matern 3/2), with forecasting via predict(fit, h = K).
• S3 methods on both MCMC and ALS fits: coef(), vcov(), confint(), predict(), fitted(), residuals(), summary(), update(), simulate(), plus autoplot().
• Ecosystem: broom::tidy() / glance(), modelsummary, as_draws() for posterior / tidybayes, and loo::loo() when save_log_lik = TRUE.
• Fit assessment: simulate() and gof() posterior-predictive checks; gof_temporal() for panels.
• Scale and robustness: ame_parallel() / lame_parallel() multi-chain runs with R-hat / ESS via compute_mcmc_diagnostics(); lame_multi() for several panels sharing coefficients; checkpoint/resume via checkpoint_path= and lame_resume().

Fast (MCMC-free) estimation

ame_als() / lame_als() fit the same model by iterative block coordinate descent (alternating least squares / IRLS) – a port of the Social Influence Regression estimator of Minhas & Hoff (2025), implemented in the sir package. They return point estimates rather than a posterior, so they are much faster.

• Scope: normal, binary, poisson; use the MCMC path for ordinal, cbin, frn.
• Dynamic ALS: lame(..., method = "als") fits dynamic additive effects, selected dynamic coefficients, AR(1) and Student-t latent factors (directed, symmetric, bipartite), and bipartite dynamic G, as penalized point estimates. Tune with als_max_iter, als_tol, als_stability.
• Snap-shift: lame_snap_als() (or method = "als", dynamic_uv_kind = "snap") estimates dynamic positions for normal unipartite/bipartite panels. snap_prob is an ALS score, not a posterior probability – read it through rankings and the stability diagnostics.
• Uncertainty: ame_als_bootstrap(), or ame_als(..., bootstrap = N), for block/parametric bootstrap intervals; confint() uses them when present, the sandwich vcov() otherwise.

Documentation

Vignette	Topic
vignette("lame")	5-minute getting-started on a small simulated panel
vignette("lame-overview")	Full tour on the bundled Dutch college friendship data
vignette("cross_sec_ame")	Cross-sectional AME on the Add Health friendship network
vignette("bipartite")	Two-mode networks, cross-sectional and longitudinal
vignette("dynamic_effects")	dynamic_uv / dynamic_ab / dynamic_beta and the transition-kind decision tree
vignette("forecasting")	predict(fit, h = K) forecasts and counterfactuals
vignette("fast_estimation")	the ame_als() / lame_als() point estimator

Reproducibility

MCMC results depend on the RNG seed and package versions. Set a seed, and record the environment:

set.seed(6886)
fit <- lame(...)
sessionInfo()          # or pin the toolchain with an renv.lock / a @<commit-sha> install

Citation

@Manual{lame2026,
  title  = {lame: Longitudinal Additive and Multiplicative Effects Models for Networks},
  author = {Cassy Dorff and Shahryar Minhas and Tosin Salau},
  year   = {2026},
  note   = {R package version 1.3.5},
  url    = {https://github.com/netify-dev/lame},
}

The dynamic effects draw on Sewell & Chen (2015, doi:10.1080/01621459.2014.988214) and Durante & Dunson (2014, doi:10.1093/biomet/asu040); the fast estimator adapts Minhas & Hoff (2025, Political Analysis).

Contributors

Cassy Dorff (Vanderbilt), Shahryar Minhas (Michigan State), Tosin Salau (Michigan State).

License

MIT. See the LICENSE file.

Support

Issues · Discussions · minhassh@msu.edu