NEWS.md

In ClemensWittenbecher/NetCoupler: Inference of Causal Links Between a Network and an External Variable

NetCoupler (development version)

NetCoupler 0.1.0

• General preparation for submitting package to CRAN.

New features

• Added to nc_estimate_* function output the full model list as an attribute, that is really only necessary for those interested in the underlying models used for classifying the effects
• Added a continuous outcome variable to simulated data that also links in with the DAG so that the linkage is more obvious (#97)
• Added function to create an edge table (#117)
• Incorporate tidyselect helpers into functions for selection of variables (#62)
• Added Getting Started vignette and an article on examples of using different models (#70)
• Added argument to nc_estimate_*_links() functions to set thresholds for classifying links (#157)
• Added weights to be included to as_edge_tbl() (#142)

Removed features

• Removed nc_classify_effects() and nc_filter_estimates(), merged them into the two main estimation functions instead
• Model summary statistics for lm and glm models were removed for improving computing speed (they slowed things down quite a bit)

Internal changes

• Output all models used for classification as an attribute for the nc_estimate_* functions output
• Use lavaan instead of dagitty to generate the simulated data
• Use standard GitHub Actions and remove AppVeyor
• Refactored some code within estimation method so it runs faster
• Tidied up the unit tests to run faster
• Removed duplicate or extra roxygen examples and instead referenced a common source with @seealso
• Removed survival dependency
• Switch to using main instead of master branch

NetCoupler 0.0.4

Added features

• For lm and glm models, model summary statistics are added (#88).
• Add a function to classify the direct effects between outcome or exposure and the network (#98).
• Add function to plot network graph: nc_plot_network() (#89, #110).
• Added helper functions nc_adjacency_graph(), nc_adjacency_matrix(), and nc_partial_corr_matrix() to help create the weights for the network plot. (Issue #80, PR #89).
• Removed soft deprecated functions. Using MuMIn over glmulti doesn't change the results too much, see #60 for details (#83).
• Removed stringr dependency (#65, #83).

Fixed bugs and other problems

• Fix bug where too many digits caused a problem for pcor() (#125, #131).
• Fix bug that didn't properly filter variables nor identify neighbour nodes in nc_filter_estimates() (#109).
• Fix problem with nc_standardize() that prevented the ability to use the .regressed_on. argument to extract residuals (#108).
• Input dataset can include missingness. Input data is treated as complete case for only the variables used in the modelling (#88).

Internal changes

• Rewrote underlying model estimation algorithm so it doesn't use MuMIn and so there is one unified function for both outcome and exposure side estimation (#101)

NetCoupler 0.0.3.9000

• Add nc_standardize() function to standardize the metabolic variables (#73).
• Export tidyselect functions like matches() or starts_with() (#73).
• Add CONTRIBUTING guidelines (#56).
• Add lifecycle badges to functions, soft deprecating net_coupler_out(), getExp.coef.permetabolite(), and getExp.coef.out() (#59)
• Add defensive checks to input arguments with assertive.types (#59).
• Add AppVeyor to repo. Started Travis to run on repo (#61).
• Added function for exposure side estimation: nc_exposure_estimates()

NetCoupler 0.0.2.9000

• Major revision of underlying code for generating the outcome-network link estimation (#55), resulting in created and streamlined nc_outcome_estimates() function. Because of this streamlining, the code is much faster and with the move to use MuMIn we can remove our dependency on rJava via glmulti.
• Tidied up nc_create_network() function so that only the graph skeleton is output (#55).
• Started cleaning up, along with leftover files.
• Updated and generated documentation of nc_create_network().
• Added unit tests for nc_create_network() and the outcome estimation functions. Travis and code coverage were added as well.
• Renamed nc_make_network() to nc_create_network() and moved into own file.
• Modularized nc_make_network() code and moved into another file.

NetCoupler 0.0.1.9000

• Added a NEWS.md file to track changes to the package.
• Added package infrastructure
• Added initial code that other projects use
• Added basic introduction vignette

ClemensWittenbecher/NetCoupler documentation built on Jan. 14, 2024, 2:41 a.m.