MoNAn 2.0.0

Version 2 runs the simulations in C++, which makes estimation typically 20-50 times faster, adds Geyer-Thompson MCMC maximum likelihood estimation, and corrects several effects. Some changes are not backward compatible (see “Breaking changes”), and results of models with corrected effects differ from version 1.

Breaking changes

• Removed effects:
  • in_weights_exponent: its change and target statistics did not match (the target statistic excludes loops and divides by the number of nodes, the change statistic does neither).
  • concentration_basic_squared, concentration_norm, concentration_norm_squared, concentration_prop_orig_cov and concentration_rankGW: older concentration effects that were only used for testing.
• concentration_prop has a new definition: each resource contributes the proportion of the resources from its origin that go to the same destination. The statistic of version 1 is no longer available.
• Corrections that change results; models that use them should be re-run:
  • reciprocity_min_resource_covar: the change statistic was +/-1 even when the moving resource did not have the attribute. It now uses the resource’s value on the attribute, which also makes it correct for non-binary attributes.
  • multinomialProposal = TRUE: the statistics for the candidate destinations were calculated with the cache from before the resource was removed, which gave wrong proposal probabilities for all non-linear effects.
  • simulateMobilityNetworks: allowLoops was ignored after the burn-in (loops were never allowed).
  • Parallel estimation (parallel = TRUE): allowLoops was ignored in Phase 1. This only affected starting values and step sizes, not the final estimates.
• If neither initialParameters nor prevAns are given, estimateMobilityNetwork starts from maximum pseudo-likelihood estimates instead of zero (see below), so results for the same seed differ from version 1 (within Monte Carlo error).
• simulateMobilityNetworks stops if the number of parameters differs from the number of effects; before, parameters were silently recycled.
• The package contains compiled C++ code: installing it from source requires a C++ compiler.

New features

• Phase 2 can use Geyer-Thompson MCMC maximum likelihood estimation instead of the Robbins-Monro algorithm: createAlgorithm(..., phase2Method = "GT"), with the new arguments iterationsGT, maxIterationsGT and finalIterationsGT. Robbins-Monro remains the default, and algorithm objects created with earlier versions use it.
• Maximum pseudo-likelihood estimates (the multinomial logit model for which getMultinomialStatistics provides the data) are used as starting values if neither initialParameters nor prevAns are given, for both Robbins-Monro and Geyer-Thompson estimation. With Robbins-Monro, Phase 1 then only determines the step sizes; with Geyer-Thompson, Phase 1 is not needed. If the estimates do not exist, estimation starts from zero as before.
• Fixed effects for locations: monanDataCreate(..., fixedEffectDummies = TRUE) adds a dummy variable for each location (except the first) to the process state, and addDummyEffects() / addFixedEffects() add them to the model.
• New effects: concentration_max, concentration_basic_cube and concentration_prop_AC.
• options(MoNAn.useCpp = FALSE) switches to the sampler written in R, which gives identical results for the same seed and is also used for models with effects written only in R.

Performance

• The MCMC sampler and all effects run in C++. A sampler step is about 20-50 times faster, depending on the effects; the estimation of the example model with the default algorithm takes 17 seconds instead of 13 minutes.
• The sampler updates the edgelist and the cache in place instead of copying them in every simulation step, so the time per step no longer grows with the number of locations and resources.
• The transitivity and triad effects no longer copy the network in every call and are vectorised, and the checks that covariates are symmetric or binary run once when an effect is added and when estimation or simulation starts, instead of in every call.

Other bug fixes

• Estimation of models with only one effect.
• multinomialProposal = TRUE stopped with an error (“‘x’ must be an array of at least two dimensions”) in models with only one effect.
• avoiding_dissimilar_covar_cont and joining_similar_avoiding_dissimilar_covar_cont only worked if the dependent variable was called “transfers”.
• loops_x_loops_additional_origin stopped estimation and simulation with “missing value where TRUE/FALSE needed” when a resource whose additional origin is its origin was proposed to move into a loop.
• The example of simulateMobilityNetworks used 6 parameters for 7 effects.

Documentation

• monanDataCreate: the fixedEffectDummies argument is documented (the documentation used the misspelled name fixedEffectsDummies).
• Removed outdated help pages of effects that are no longer part of the package.
• For developers, ADDING_EFFECTS.md in the GitHub repository explains how to add an effect in R and C++.

Tests

• Tests check for every effect that the change statistic equals the difference in target statistics before and after a move, and that the C++ effects and sampler give exactly the same results as their R versions.

MoNAn 1.1.0

Added effects that improve on the old GW effects (where AC stands for alternating cliques):

• concentration_AC, concentration_AC_dyad_covar, concentration_AC_resource_covar_bin, reciprocity_AC, reciprocity_AC_dyad_covar_bin, reciprocity_AC_dyad_covar, transitivity_AC, loops_AC, in_weights_AC

MoNAn 1.0.1

MoNAn 1.0.0

!! Backward breaking change !!

The “cache” is not visible to the user anymore, it is created automatically and there is no more use for the function createWeightedCache.

The following functions are used differently:

• gofMobilityNetwork does not require the specification of simulations anymore!

New functions (aliases) for easier use

• monanDependent (createEdgelist), monanNodes (createNodeSet), monanEdges (createNodeSet), monadicCovariate (createNodeAttribute), dyadicCovariate (createNetwork), monanEstimate (estimateMobilityNetwork), monanSimulate (simulateMobilityNetwork), monanGOF (gofMobilityNetwork)

Further changes:

• createEffect and addEffects; specification of node.attribute and edge.attribute instead of attribute.index and resource.attribute.index

• The results objects are much smaller and contain less redundant information.

• The State and Effects objects have print functions for easier inspection.

• The algorithm is now stored in the outcome object for later reference.

MoNAn 0.3.0

New functions to specify the model: createEffects and addEffect New function to generate the process state: monanDataCreate

Creation of alias: monanAlgorithmCreate for createAlgorithm Creation of alias: monan07 for estimateMobilityNetwork

Implementation of new effects

MoNAn 0.2.0

Implementation of parallelization in Phase 1 of the estimation.

MoNAn 0.1.3

Various bugfixes and improvements.

Implementation of new effects.

User-friendly checks in creation of MoNAn objects.

MoNAn 0.1.2

Original Submission