NEWS

goldfish 1.7.0

Rename functions to follow tidyverse style guide.
Rename define functions to make_: make_nodes(), make_network(), make_dependent_events().
Introduce set_ functions to set options: set_estimation_opt() for algorithm options, and set_preprocess_opt() for preprocessing options.
Introduce make_data() function to create a single data object with all the data needed for estimation.
Introduce history = c("pooling", "sequential", "consecutive") argument to trans() and cycle() effect functions that define how the previous history of events is used to compute the effect.
Add a function for each model implemented in the package: estimate_dynam(), estimate_dynami() and estimate_rem().

goldfish 1.6.13

Fixes problem when parallelizing code and using preprocess objects.
Fixes incorrect computation of number of right-censored events during preprocessing when startTime is specified.
Add lifecycle and cli to imports.
Rename functions names to snake_case to comply with the tidyverse style guide and stocnet interface.
Add defunct documentation with functions that changed names.

goldfish 1.6.12 (2025-04-13)

Fixes invalid URL link in the goldfish-package.Rd.

goldfish 1.6.11

Registers S3 methods for internal functions.
Updates R version dependency to 4.1.0 to use the anonymous function syntax.
Deletes configure files; OpenMP support is now managed directly through the Makevars files.

goldfish 1.6.10 (2024-09-03)

Solves invalid URL link for the MIT Social Evolution dataset.

goldfish 1.6.9

Solving missing package anchors in the documentation.
Update deprecated functions in the vignettes from manynet.
Solve issue on Makevars.in file that produced a note when check as CRAN.

goldfish 1.6.8 (2024-04-11)

checkEvents() method addresses S3 generic/method consistency.
Solves invalid URL link in the bibliography.

goldfish 1.6.7

Debug and update yaml workflow files for GitHub Actions.
Solve note mismatches generic/method consistency

goldfish 1.6.6

Debugging and extend documentation for GatherPreprocessing().
Fix note from CRAN checks.
Debug issue when using a preprocess init object in estimate().
Debug issue with opportunity list in estimate() for DyNAM models.
Fix error in printing output from estimate() when using a parameter is fixed to a value.

goldfish 1.6.5

Solves startTime and endTime bug on DyNAM and REM models preprocessing.
Export GatherPreprocessing(). Experimental functionality.
Clean unnecessary functions imports.
Solves aes_string() deprecation.
Solves issue on C++ engine on DyNAM-rate.
Enforcing an 80-character line length on C++ code.
Comply with code style.
Changes that reduce execution time in the R estimation engine.

goldfish 1.6.4 (2022-08-24)

Change mentioning of .GlobalEnv and drop goldfishObjects().

goldfish 1.6.3

New features

Add DyNAM-i vignette.
Implement method vcov(), now is possible to use stats::confint() to obtain confidence interval for parameters estimates under asymptotic normality, and also get them from a tidy() call.

Breaking changes

silent parameter replace by progress. progress and verbose can be set with global options with the same name.

Minor improvements and fixes

Reimplement method logLik(), now is possible to use AIC() and BIC() from stats package and make likelihood ratio test of nested models using lmtest::lrtest().
Improve documentation of define functions, linkEvents() and print methods. The reserved names and expected variables are explained.
Drop fig.retina from figures in vignettes and keeps default size.
Update vignette("goldfishEffects") documentation for closure effects.
Window effects doesn't create new object on the global environment.
Add references in description.
Fix bug composition change on estimation routines.
Includes environment argument on estimation routines.

goldfish 1.6.2

Fix additional URL on Vignette "How to start".

goldfish 1.6.1

Fix URLs.
Estimate examples now use the C engine.

goldfish 1.6.0

Cleaning submission to CRAN.

goldfish 1.5.3

Effects documentation migrated to a vignette.
Precompile vignettes with long-run time for compilation.

goldfish 1.5.2

Fix minor bugs on opportunityList
New effect ego alter interaction egoAlterInt(list(egoAttr, alterAttr))
Cleaning vignettes and changing networks visualization to use migraph package

Breaking changes

Closure effects renaming.

clSender(net) -> commonSender(net)
clReceiver(net) -> commonReceiver(net)
mixedClSender(list(net1, net2)) -> mixedCommonSender(list(net1, net2))
mixedClReceiver(list(net1, net2)) -> mixedCommonReceiver(list(net1, net2))

Updated examine.outliers() and examine.changepoints() to plot more informative plots (with {ggplot2})
- These functions no longer print to the console
Added vignette teaching2.Rmd that also indicates these extensions
Added vignette teaching1.Rmd with the "How to start"

goldfish 1.5.1

Re #3 added {broom}-related functions tidy() and glance()
Updated examine.outliers() and examine.changepoints() to plot more informative plots (with {ggplot2})
- These functions no longer print to the console
Added vignette teaching2.Rmd that also indicates these extensions
Added vignette teaching1.Rmd with the "How to start"

goldfish 1.5.0

New features

New DyNAM-i model available to model face-to-face interaction data, collected through video or RFID badges.

Functions to transform interaction data into DyNAM-compatible objects

defineGroups_interaction(interactions_data, actors, seed.randomization)

Estimation functions for the joining and leaving rates of a DyNAM-i model

estimate(
  dependent.events_interactions ~  1 + intercept(network_interactions, joining = 1) +
                                ego(actors$age,joining = 1, subType = "centered") +
                               ego(actors$age,joining = -1, subType = "centered"),
  model = "DyNAMi", subModel = "rate")

Estimation functions for the choice part of a DyNAM-i model

estimate(
  dependent.events_interactions ~ diff(actors$age,subType="averaged_sum") ,
  model = "DyNAMi", subModel = "choice", 
  estimationInit = list(opportunitiesList = opportunities))

New closure effects for model = "DyNAM" with subModel = "choice" and model = "REM". Documentation is updated accordingly.

cycle(bilatnet)
clSender(bilatnet)
clReceiver(bilatnet)
mixedCycle(list(bilatnet, contignet))
mixedClSender(list(bilatnet, contignet))
mixedClReceiver(list(bilatnet, contignet))

Minor improvements and fixes

Minor bugs in parsing and printing solved.
Solves some warnings regarding S3 generic/method consistency.
Solves no visible binding for global variables.
Documentation improvements creating new documentation pages aggregating similar functions on print-method and update-method.

Breaking changes

tertius_diff() and node_trans() are changed to tertiusDiff() and nodeTrans() complaining with naming convention.

goldfish 1.4.3

New features

mixedTrans() effect is created. It requires the definition of two networks to compute the number of two paths between nodes.
```
mixedTrans(list(bilatnet, contignet))
```

Minor improvements and fixes

estimate() no longer give warnings in R 4.0.0.
Classes and types checkings are revisited and extended.
linkEvents() is refactored as a S3 method.
New print or summary methods for goldfish objects are developed.
head() and tail() methods for nodes.goldfish, network.goldfish and dependent.goldfish are available.

goldfish 1.3.2

New features

tertius() and tertius_diff() effects are created. It requires the definition of a network and an attribute.
```
tertius_diff(bilatnet, states$gdp)
tertius(bilatnet, states$gdp)
```

goldfish 1.3.1

New features

estimate() now estimation routine in C for model = "DyNAM" and subModel = "choice_coordination".

goldfish 1.3.0

New features

estimate() parameter engine through estimationInit argument control the estimation routine used.

mod01 <- estimate(callsDependent ~ inertia + recip + trans,
                  model = "DyNAM", subModel = "choice",
                  estimationInit = list(engine = "gather_compute"))

estimate() now estimation routine in C except for model = "DyNAM" and subModel = "choice_coordination".
New effects definition for model = "DyNAM" and subModel = "rate".

Minor improvements and fixes

inertia fixed bug when weighted = TRUE.

Breaking changes

modelType argument in estimate() have been deprecated in favor of model and submodel.

Internal changes

New implementation of effects to improve preprocessing time in the initialization of the statistical matrices and the reintroduction of a cache object for complex structural network effects.

Minor improvements and fixes

Added more examples for estimate().
Extend documentation of defineDependentEvents(), defineGlobalAttribute(), defineNetwork(), defineNodes() and linkEvents().

goldfish 1.2.1

Introduce a new efficient estimation routine.