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.
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.