Changes in version 0.1.1.9000                      

                 Changes in version 0.1.1 (2025-05-20)                  

Fixes

  - Switched to using lifecycle::badge() in Roxygen docs because of CRAN
    Note.
  - Converted .data$ to simply "" in all functions to fix test warnings
    from dplyr.

Internals

  - Set up rhub GitHub Action workflow to check CRAN compatibility more
    fully.
  - Remove Codecov because of issues with connection to it.

                 Changes in version 0.1.0 (2022-04-08)                  

  - 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

                        Changes in version 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)

                     Changes in version 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()

                     Changes in version 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.

                     Changes in version 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