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Changelog

Source: NEWS.md

silentema 1.0.0

First CRAN release. The statistical code is unchanged from version 0.2.1, so every estimate produced with 0.2.0 or 0.2.1 is reproduced exactly; the release prepares the package for CRAN, completes its documentation and fixes one display issue.

  • Renamed argument: the number of prompts per person is set by n_prompts in simulate_ema() and simulate_from_fit() (it was called T in 0.2.x, which masks TRUE); the corresponding elements of the returned objects are settings$n_prompts (simulations) and n_prompts (FIML fits). Code written for 0.2.x must replace T = by n_prompts =; the generated data are unchanged.
  • New vignettes: dm-graphs (the motif taxonomy, d-separation and recoverability), testing-informativeness (the silence test, the sensor-gap test and the fatigue check), sensitivity-analysis (tilting, break-even values, the three calibration designs and the missingness declaration) and simulation-and-design (the simulator, every motif’s parameters, design planning). The workflow vignette is revised.
  • Every exported function documents its return value in full and has runnable examples; the documentation cites the methods (Mohan & Pearl, 2021; Dhaene & Jochmans, 2015; Shumway & Stoffer, 1982; Cameron & Miller, 2015; Manski, 2003) instead of the numbered propositions of the accompanying manuscript.
  • Package overview (?silentema) describing the workflow, the data format and the simulator.
  • DESCRIPTION: method references with DOIs, URL and BugReports fields pointing to the GitHub repository and the documentation site; the title is shortened.
  • citation("silentema") now points to the CRAN page of the package.
  • American spelling throughout the documentation.
  • Subsetting a recoverability, silence_test or sensor_gap_test object with [ now returns a plain data frame; previously the class was kept and the print method showed an incomplete report. No estimate is affected.
  • Input validation with clear messages: a response-indicator column must be 0/1 without NA; state columns must be complete at answered prompts (item-level missingness is reported instead of producing NA results); a response column named other than the default "R" must exist; the prompt index must be an integer index without NA, also in fatigue_check(); the “too few pairs/triples” messages report the counts and hint at the prompt index. bounds_support() checks its columns and returns the whole scale for a person without any answered prompt (previously NaN).
  • fit_pairs() (and the tilted fits) warn when no person reaches min_pairs complete pairs, instead of silently returning NaN between-person summaries; fit_fiml() starts from a diagonal between-person covariance when fewer than three persons have enough pairs (previously it failed for one to three persons), stops when the prompt index spans a single prompt, and warns when prompt indices are missing for some persons; fatigue_check() no longer fails when the prompt index has fewer than four distinct values.
  • tilt_profile(which = ) accepts a variable name; plot.tilt_profile() reports unknown coefficient names; plot.dm_graph() honors a user main; print.delta_calibration() reports failed bootstrap resamples; the EM loop of fit_fiml() checks for user interrupts.

silentema 0.2.1

Metadata release; no change to any R or C++ code, so every result produced with 0.2.0 is reproduced exactly (checked bit-for-bit on six simulation cells).

  • URL points to the OSF project; the placeholder BugReports field is removed (contact the maintainer by email).
  • citation("silentema") uses the revised title of the accompanying manuscript, “What skipped prompts hide: Detecting, diagnosing, and correcting informative nonresponse in ecological momentary assessment”.

silentema 0.2.0

Revision after peer review of the accompanying manuscript.

  • calibrate_delta(method = "postskip") gains burden = "fit": the simulated model includes a burden term (motif M3) calibrated to the observed response persistence, so that the post-skip calibration is valid under a declared M2 + M3 graph. The number of simulated data sets is now n_sim (default 20; formerly B = 10). The result reports the number of crossings, and no crossing is reported as such.
  • simulate_from_fit() gains days and kappa_R, and stops with a clear message when the fitted dynamics are not stable.
  • recoverability() distinguishes, under reactivity (M6), the recoverable assessment-conditioned kernel (Phi and Psi) from the dynamics-recovered person mean, which is biased; the observed person mean is judged by d-separation as for the other motifs.
  • fit_tilt() returns every quantity from one undamped weighted fit at the converged iterate, reports max_weight, passes min_pairs through, and returns class tilt_fit also at delta = 0.
  • silence_test() gains poly (polynomial degree in the lagged states) and seed; fatigue_check() gains day and a print method; summary.pairs_fit() uses a t(G - 1) reference; coef(), vcov(), confint(), nobs() methods for fits; plot() method for calibrations; plot.dm_graph() redrawn.
  • missingness_declaration() fills its sections from the test, profile and calibration objects when they are supplied.
  • Input validation with informative messages (motif codes, column names, integer prompt index, delta length, weights); functions that simulate or bootstrap restore the caller’s random-number state.
  • Examples for every exported function; American spelling throughout.

silentema 0.1.0

  • First release accompanying the manuscript “When silence is informative: Dynamic missingness graphs, recoverability, and sensitivity analysis for ecological momentary assessment” (Yu, 2026).