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emmeans R
package for estimating marginal means of ssn_lm() and
ssn_glm() models.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().ssn_import() so that it does not force an
overwrite of the netgeom column when it already
exists.verbose argument to ssn_import(),
ssn_import_predpts(), and createBinaryID() to
control whether warning messages are printed to the R
console.na.action argument to
predict.ssn_lm() and predict.ssn_glm()
functions to clarify that missing values in newdata return
an error.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().type.residuals argument for
ssn_glm() models to match
broom::augment.glm().logLik() to match lm() and
glm() behavior. logLik() now returns a vector
with class logLik and attributes nobs and
df.AIC() and BIC()
from stats and removed SSN2-specific
AIC() methods.warning argument to glances() that
determines whether relevant warnings should be displayed or not.glances() about interpreting
likelihood-based statistics (e.g., AIC, AICc, BIC) when a one model has
estmethod = "ml" and another model has
estmethod = "reml".glances() about interpreting
likelihood-based statistics (e.g., AIC, AICc, BIC) when two models with
estmethod = "reml" have distinct formula
arguments.glances() about interpreting
likelihood-based statistics (e.g., AIC, AICc, BIC) when two models have
different sample sizes.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).cloud argument to Torgegram() to
return a cloud Torgegram.cex to
plot.Torgegram().Torgegram(); see
the robustargument to Torgegram()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).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."terms" prediction for
ssn_lm() and ssn_glm() models.scale and df arguments to
predict() for ssn_lm() models.dispersion argument to predict() for
ssn_glm() models.anova(model1, model2)) when
estmethod is "ml" for both models #25.anova(object1, object2) when the name of
object1 had special characters (e.g., $).ssn_glm() models when family = "beta" (#23).reexport.Rd to reflect changes in
spmodel v0.8.0’s handling of AIC() and
AICc().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..ssn
folder that is accessed when importing SSN objects via
ssn_import().ssn_names() to return column names in the
edges, obs, and preds elements of
an SSN object.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.X
has perfect collinearities (i.e., is not full rank).format_additive argument from
ssn_import() because of transition to geopackage support,
which eliminates the need to convert additive function values to
text.create_netgeom() function to create the
network geometry column for the edges, obs,
and preds elements in an SSN object.SSN_to_SSN2() that caused an error using
ssn_write() with no prediction sites.names.SSN() with ssn_names(), as
names.SSN() prevented proper naming of elements in the SSN
object.netgeometry to
netgeom to avoid exceeding the 10 character limit for
column/field names while writing to shapefiles (#2).family is missing in
ssn_glm() (#8).SSN_to_SSN2().Torgegram() that prevented intended
computation when cutoff was specified.plot.Torgegram() that occasionally
prevented proper spacing of the legend.ssn_glm() model objects (and their
summaries) when all covariance parameters were known.euclid_type
was "none".taildown_type was "spherical".ssn_glm() objects.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.