SSN2 - SSN2 v0.3.0

SSN2 0.3.0

Major Updates

• Added support for the emmeans R package for estimating marginal means of ssn_lm() and ssn_glm() models.
• Added support for applications to large data sets. The ssn_create_bigdist() function was added to create large distance matrices using the filematrix R package. Estimation for large data sets is performed by leveraging the local argument to ssn_lm() and ssn_glm(). Prediction for large data sets is performed by leveraging the local argument to predict() (and augment()). When local is used, SSN2 looks for distance matrices created using ssn_create_bigdist().
• Added support for Gaussian tail-up and tail-down covariance functions.

Minor Updates

• Updated ssn_import() so that it does not force an overwrite of the netgeom column when it already exists.
• Add a verbose argument to ssn_import(), ssn_import_predpts(), and createBinaryID() to control whether warning messages are printed to the R console.
• Added the na.action argument to predict.ssn_lm() and predict.ssn_glm() functions to clarify that missing values in newdata return an error.
• Changed the type argument in augment() for ssn_glm() models to type.predict to match broom::augment.glm().
• augment() for ssn_glm() models now returns fitted values on the link scale by default to match broom::augment.glm().
• Added a type.residuals argument for ssn_glm() models to match broom::augment.glm().
• Updated logLik() to match lm() and glm() behavior. logLik() now returns a vector with class logLik and attributes nobs and df.
• Added support for using AIC() and BIC() from stats and removed SSN2-specific AIC() methods.
• Added a warning argument to glances() that determines whether relevant warnings should be displayed or not.
• Added a warning message to glances() about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when a one model has estmethod = "ml" and another model has estmethod = "reml".
• Added a warning message to glances() about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models with estmethod = "reml" have distinct formula arguments.
• Added a warning message to glances() about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models have different sample sizes.
• Added a warning message to glances() about interpreting likelihood-based statistics (e.g., AIC, AICc, BIC) when two models have different family supports (which can happen with ssn_glm() models).
• Added a cloud argument to Torgegram() to return a cloud Torgegram.
• Added the ability to pass custom cex to plot.Torgegram().
• Added a robust semivariogram option to Torgegram(); see the robustargument to Torgegram()
• Added an AUROC() function to compute the area under the receiver operating characteristic (AUROC) curve for ssn_glm models when family is "binomial" and the response is binary (i.e., represents a single success or failure).
• Added a type argument to loocv() when cv_predict = TRUE and using ssn_glm() models so that predictions may be obtained on the link or response scale.
• Added support for "terms" prediction for ssn_lm() and ssn_glm() models.
• Added scale and df arguments to predict() for ssn_lm() models.
• Add dispersion argument to predict() for ssn_glm() models.
• Minor documentation updates.
• Minor code maintenance updates.

Bug Fixes

• Fixed a bug that caused incorrect degrees of freedom for the likelihood ratio test (anova(model1, model2)) when estmethod is "ml" for both models #25.
• Fixed a bug that caused an error in anova(object1, object2) when the name of object1 had special characters (e.g., $).

Scientific Software - Peer-reviewed - R
Published by michaeldumelle 6 months ago

SSN2 - SSN2 v0.2.1

SSN2 0.2.1

Minor Updates

• Enhanced numeric stability of deviance and pseudo R-squared for ssn_glm() models when family = "beta" (#23).
• Updated reexport.Rd to reflect changes in spmodel v0.8.0's handling of AIC() and AICc().

Scientific Software - Peer-reviewed - R
Published by michaeldumelle over 1 year ago

SSN2 - SSN2 v0.2.0

SSN2 v0.2.0

Major Updates

• Significant testing, documentation, and auxiliary (e.g., README.md) updates as part of a submission to Journal of Open Source Software. Relevant issues associated with the review are available at #11, #12, #13, #14, #15, #16, #17, #20, #21. The review is linked here.
• Added support for geopackage file formats in the .ssn folder that is accessed when importing SSN objects via ssn_import().

Minor Updates

• Added ssn_names() to return column names in the edges, obs, and preds elements of an SSN object.
• Changed Matrix::rankMatrix(X, method = "tolNorm2") to Matrix::rankMatrix(X, method = "qr") to enhance stability when determining linear independence in X, the design matrix of explanatory variables.
• Replaced an error message with a warning message when X has perfect collinearities (i.e., is not full rank).
• Removed format_additive argument from ssn_import() because of transition to geopackage support, which eliminates the need to convert additive function values to text.
• Added the create_netgeom() function to create the network geometry column for the edges, obs, and preds elements in an SSN object.
• Minor vignette updates.
• Minor documentation updates.

Scientific Software - Peer-reviewed - R
Published by michaeldumelle over 1 year ago

SSN2 - SSN2 v0.2.0(JOSS)

This is the package state of SSN2 at the time of acceptance in Journal of Open Source Software.

Scientific Software - Peer-reviewed - R
Published by michaeldumelle over 1 year ago

SSN2 - SSN2 v0.1.1

Minor Updates

• Changed network geometry name from netgeometry to netgeom to avoid exceeding the 10 character limit for column/field names while writing to shapefiles (#2).
• Added an error message when family is missing in ssn_glm() (#8).
• Added a deprecation warning for SSN_to_SSN2().
• Minor stability updates.
• Minor error message updates.
• Minor documentation updates.

Bug Fixes

• Fixed a bug in Torgegram() that prevented intended computation when cutoff was specified.
• Fixed a bug in plot.Torgegram() that occasionally prevented proper spacing of the legend.
• Fixed a bug that prevented proper printing of the dispersion parameter from ssn_glm() model objects (and their summaries) when all covariance parameters were known.
• Fixed a bug that prevented simulation when euclid_type was "none".
• Fixed a bug that could cause improper prediction behavior when taildown_type was "spherical".
• Fixed a bug that printed response residuals instead of deviance residuals for ssn_glm() objects.

Scientific Software - Peer-reviewed - R
Published by michaeldumelle about 2 years ago

SSN2 - SSN2 v0.1.0

This is the initial CRAN release of SSN2 (v0.1.0).

Scientific Software - Peer-reviewed - R
Published by michaeldumelle over 2 years ago