NEWS.md
-
- install.on.demand() for recommended packagesinstall.on.demand() only in interactive modemice::MCAR() and associated plot method. Contributed by @cjvanlissa (#423).Contributed by @EdoardoCostantini (#438).
-mice:::barnard.rubin() function for infinite dfcom. Thanks @huftis (#441).Adds Jamshidian && Jalal’s non-parametric MCAR test, mice::MCAR() and associated plot method. Contributed by @cjvanlissa (#423).
Adds two new functions pool.syn() and pool.scalar.syn() that specialise pooling estimates from synthetic data. The "reiter2003" pooling rule assumes that synthetic data were created from complete data. Thanks Thom Volker (#436).
Avoids changing the global .Random.seed (#426, #432) by implementing withr::local_preserve_seed() and withr::local_seed(). This change provides stabler behavior in complex scripts. The change does not appear to break reproducibility when mice() was run with a seed. Nevertheless, if you run into a reproducibility problem, install mice 3.13.12 or before.
Improves the imputation of parabolic data in mice.impute.quadratic(), adds a parameter quad.outcome containing the name of the outcome variable in the complete-data model. Contributed @Mingyang-Cai, @gerkovink (#408)
By default, mice.impute.rf() now uses the faster ranger package as back-end instead of randomForest package. If you want the old behaviour specify the rfPackage = "randomForest" argument to the mice(...) call. Contributed @prockenschaub (#431).
Generalises pool() so that it processes the parameters from all gamlss sub-models. Thanks Marcio Augusto Diniz (#406, #405)
Uses the robust standard error estimate for pooling when pool() can extract robust.se from the object returned by broom::tidy() (#310)
pool.syn() and pool.scalar.syn() that specialise pooling estimates from synthetic data. The "reiter2003" pooling rule assumes that synthetic data were created from complete data. Thanks Thom Volker (#436).install.on.demand() broke the standard CRAN workflow. mice 3.14.0 does not call install.on.demand() anymore for recommended packages. Also, install.on.demand() will not run anymore in non-interactive mode.mice:::barnard.rubin() function for infinite dfcom. Thanks @huftis (#441).Xi <- as.matrix(...) in mice.impute.2l.lmer() that occurred when a cluster contains only one observation (#384)predictorMatrix to a monotone pattern if visitSequence = "monotone" and maxit = 1 (#316)md.pattern() (#318, #323)make.formulas() (#305, #324)newdata in mice.mids() (#313, #325)where element created in rbind() (#319).Random.seed (#426, #432) by implementing withr::local_preserve_seed() and withr::local_seed(). This change provides stabler behavior in complex scripts, but may break exact reproducibility in some cases. If you run into a problem, I fear the only way to solve is to install mice 3.13.12 or before.mice.impute.quadratic(), adds a parameter quad.outcome containing the name of the outcome variable in the complete-data model. Contributed @Mingyang-Cai, @gerkovink (#408)mice.impute.rf() now uses the faster ranger package as back-end instead of randomForest package. If you want the old behaviour specify the rfPackage = "randomForest" argument to the mice(...) call. Contributed @prockenschaub (#431).mice.impute.2l.lmer() to indicate a problem in fitting the imputation model (#385)Xi <- as.matrix(...) in mice.impute.2l.lmer() that occurred when a cluster contains only one observation (#384)md.pattern() (#318, #323)make.formulas() (#305, #324)newdata in mice.mids() (#313, #325)pool() can extract robust.se from the object returned by broom::tidy() (#310)mids2spss() replaces the foreign by haven package. Contributed Gerko Vink (#291)tests\testhat\test-D1.R that failed on mitml 0.4-0
matcher algorithm in pmm has changed to matchindex for speed improvements. If you want the old behavior, specify mice(..., use.matcher = TRUE).
cpp11 package (#286)with.mids() by calling eval_tidy() on a quosure. Does not yet solve #265.df.residual, which caused problematic behavior in the D1(), D2(), D3(), anova() and pool(). mice now extracts the relevant information from other parts of the objects returned by survival::coxph(), which solves long-standing issues with the integration of the Cox model (#246).Rccp dependency to work with tidyr 1.1.1 (#248).Non-file package-anchored link(s) in documentation object.ampute documentation (#251).tidy.mipo() and glance.mipo() return standardized output that conforms to broom specifications. Kindly contributed by Vincent Arel Bundock (#240).D3 testing script that produced an error on CRAN (#244).D3() function in mice gave incorrect results. This version solves a problem in the calculation of the D3-statistic. See #226 and #228 for more details. The documentation explains why results from mice::D3() and mitml::testModels() may differ.pool() function is now more forgiving when there is no glance() function (#233)remove.lindep() by setting eps = 0 (#225)plot.mids() documentationmice.impute.mnar.norm() and mice.impute.mnar.logreg(). These functions aid in performing sensitivity analysis to investigate the impact of different MNAR assumptions on the conclusion of the study. An alternative for MNAR is the older mice.impute.ri() function.mice is faster. External packages needed for imputation and analyses are now installed on demand. The number of dependencies as estimated by rsconnect::appDepencies() decreased from 132 to 83.pool() function that integrates better with the broom and broom.mixed packages.pool.compare(). Use D1() instead (#220)utils::globalVariables()
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 6b0683b6e..216b9ce2a 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
articles:
oldfriends: oldfriends.html
overview: overview.html
-last_built: 2021-11-23T10:03Z
+last_built: 2021-11-23T13:41Z
urls:
reference: https://amices.org/mice/reference
article: https://amices.org/mice/articles
diff --git a/docs/reference/D1.html b/docs/reference/D1.html
index 28c011799..be2eae2e3 100644
--- a/docs/reference/D1.html
+++ b/docs/reference/D1.html
@@ -78,7 +78,7 @@
model0 <- lm(Volume ~ Girth + Height, data = trees) formula(model0) #> Volume ~ Girth + Height -#> <environment: 0x7fd177b41700> +#> <environment: 0x7fdeb03e9e38> coef(model0) #> (Intercept) Girth Height #> -57.9876589 4.7081605 0.3392512 @@ -195,7 +195,7 @@diff --git a/docs/reference/make.method.html b/docs/reference/make.method.html index d1779fe41..15f6eeef6 100644 --- a/docs/reference/make.method.html +++ b/docs/reference/make.method.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/make.post.html b/docs/reference/make.post.html index 6eec707ec..b29c9e5a8 100644 --- a/docs/reference/make.post.html +++ b/docs/reference/make.post.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/make.predictorMatrix.html b/docs/reference/make.predictorMatrix.html index ca583bc70..058bc7966 100644 --- a/docs/reference/make.predictorMatrix.html +++ b/docs/reference/make.predictorMatrix.html @@ -83,7 +83,7 @@ diff --git a/docs/reference/make.visitSequence.html b/docs/reference/make.visitSequence.html index 791aa2386..03102bdc3 100644 --- a/docs/reference/make.visitSequence.html +++ b/docs/reference/make.visitSequence.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/make.where.html b/docs/reference/make.where.html index 6353f5598..2dccef706 100644 --- a/docs/reference/make.where.html +++ b/docs/reference/make.where.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mammalsleep.html b/docs/reference/mammalsleep.html index 831d1c662..23873daf6 100644 --- a/docs/reference/mammalsleep.html +++ b/docs/reference/mammalsleep.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/matchindex.html b/docs/reference/matchindex.html index 6935d45f2..494852c2e 100644 --- a/docs/reference/matchindex.html +++ b/docs/reference/matchindex.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mcar.html b/docs/reference/mcar.html index 21eb94f96..5320935d2 100644 --- a/docs/reference/mcar.html +++ b/docs/reference/mcar.html @@ -80,7 +80,7 @@ @@ -265,14 +265,14 @@Examp model1 <- fix.coef(model0) formula(model1) #> Volume ~ 1 -#> <environment: 0x7fd177b41700> +#> <environment: 0x7fdeb03e9e38> coef(model1) #> (Intercept) #> 3.988039e-14 diff --git a/docs/reference/flux.html b/docs/reference/flux.html index 8db74077c..e020b4e56 100644 --- a/docs/reference/flux.html +++ b/docs/reference/flux.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/fluxplot.html b/docs/reference/fluxplot.html index a63ae9322..cb3df5e72 100644 --- a/docs/reference/fluxplot.html +++ b/docs/reference/fluxplot.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/getfit.html b/docs/reference/getfit.html index 960a9110b..06676bfd3 100644 --- a/docs/reference/getfit.html +++ b/docs/reference/getfit.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/getqbar.html b/docs/reference/getqbar.html index 86fcb9453..f500bd3c7 100644 --- a/docs/reference/getqbar.html +++ b/docs/reference/getqbar.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/glance.mipo.html b/docs/reference/glance.mipo.html index c353c4f51..824f9df2d 100644 --- a/docs/reference/glance.mipo.html +++ b/docs/reference/glance.mipo.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/glm.mids.html b/docs/reference/glm.mids.html index 58e07ce66..a2aa183f9 100644 --- a/docs/reference/glm.mids.html +++ b/docs/reference/glm.mids.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/ibind.html b/docs/reference/ibind.html index deba4670b..d2a3a5a8b 100644 --- a/docs/reference/ibind.html +++ b/docs/reference/ibind.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/ic.html b/docs/reference/ic.html index 053371b2f..5bfdeb04f 100644 --- a/docs/reference/ic.html +++ b/docs/reference/ic.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/ici.html b/docs/reference/ici.html index 1f501a1c7..99387ff37 100644 --- a/docs/reference/ici.html +++ b/docs/reference/ici.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/ifdo.html b/docs/reference/ifdo.html index 69efe2250..36892e275 100644 --- a/docs/reference/ifdo.html +++ b/docs/reference/ifdo.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/index.html b/docs/reference/index.html index 09238a67b..0d781b788 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -77,7 +77,7 @@ diff --git a/docs/reference/is.mads.html b/docs/reference/is.mads.html index bb5fa237c..b4ee04b87 100644 --- a/docs/reference/is.mads.html +++ b/docs/reference/is.mads.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/is.mids.html b/docs/reference/is.mids.html index abf383c9f..0b99b4724 100644 --- a/docs/reference/is.mids.html +++ b/docs/reference/is.mids.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/is.mipo.html b/docs/reference/is.mipo.html index ad7e64d22..64fd44858 100644 --- a/docs/reference/is.mipo.html +++ b/docs/reference/is.mipo.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/is.mira.html b/docs/reference/is.mira.html index 3aa4297a1..aaaca781e 100644 --- a/docs/reference/is.mira.html +++ b/docs/reference/is.mira.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/is.mitml.result.html b/docs/reference/is.mitml.result.html index fc4a4f85e..7bc1239da 100644 --- a/docs/reference/is.mitml.result.html +++ b/docs/reference/is.mitml.result.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/leiden85.html b/docs/reference/leiden85.html index f062a5b7e..9a1839518 100644 --- a/docs/reference/leiden85.html +++ b/docs/reference/leiden85.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/lm.mids.html b/docs/reference/lm.mids.html index 26a97552b..25c6c1c76 100644 --- a/docs/reference/lm.mids.html +++ b/docs/reference/lm.mids.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mads-class.html b/docs/reference/mads-class.html index dfef8add3..87a1cf155 100644 --- a/docs/reference/mads-class.html +++ b/docs/reference/mads-class.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/make.blocks.html b/docs/reference/make.blocks.html index c0b2762b1..3dd08ffb8 100644 --- a/docs/reference/make.blocks.html +++ b/docs/reference/make.blocks.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/make.blots.html b/docs/reference/make.blots.html index 0a4299164..956437f9c 100644 --- a/docs/reference/make.blots.html +++ b/docs/reference/make.blots.html @@ -83,7 +83,7 @@ diff --git a/docs/reference/make.formulas.html b/docs/reference/make.formulas.html index 5ccd9e866..95e122671 100644 --- a/docs/reference/make.formulas.html +++ b/docs/reference/make.formulas.html @@ -81,7 +81,7 @@ @@ -185,25 +185,25 @@
Examp f1 #> $age #> age ~ bmi + hyp + chl -#> <environment: 0x7fd174daff18> +#> <environment: 0x7fdeb72dbc98> #> #> $bmi #> bmi ~ age + hyp + chl -#> <environment: 0x7fd174daff18> +#> <environment: 0x7fdeb72dbc98> #> #> $hyp #> hyp ~ age + bmi + chl -#> <environment: 0x7fd174daff18> +#> <environment: 0x7fdeb72dbc98> #> #> $chl #> chl ~ age + bmi + hyp -#> <environment: 0x7fd174daff18> +#> <environment: 0x7fdeb72dbc98> #> f2 <- make.formulas(nhanes, blocks = make.blocks(nhanes, "collect")) f2 #> $collect #> age + bmi + hyp + chl ~ 0 -#> <environment: 0x7fd174ce42d0> +#> <environment: 0x7fde945753f8> #> # for editing, it may be easier to work with the character vector @@ -217,19 +217,19 @@
Examp f3 #> $age #> age ~ bmi + hyp + chl -#> <environment: 0x7fd174bad990> +#> <environment: 0x7fde719ed6b0> #> #> $bmi #> bmi ~ age + hyp + chl -#> <environment: 0x7fd174bad990> +#> <environment: 0x7fde719ed6b0> #> #> $hyp #> hyp ~ age + bmi + chl -#> <environment: 0x7fd174bad990> +#> <environment: 0x7fde719ed6b0> #> #> $chl #> chl ~ age + bmi + hyp -#> <environment: 0x7fd174bad990> +#> <environment: 0x7fde719ed6b0> #>
Rubin, D. B. (1976). Inference and Missing Data. Biometrika, Vol. 63, No. 3, -pp. 581-592. doi:10.2307/2335739
+pp. 581-592. doi: 10.2307/2335739Eekhout, I., M. A. Wiel, & M. W. Heymans (2017). Methods for Significance Testing of Categorical Covariates in Logistic Regression Models After Multiple Imputation: Power and Applicability Analysis. BMC Medical Research Methodology 17 (1): 129.
Jamshidian, M., & Jalal, S. (2010). Tests of homoscedasticity, normality, and missing completely at random for incomplete multivariate data. Psychometrika, -75(4), 649–674. doi:10.1007/s11336-010-9175-3
+75(4), 649–674. doi: 10.1007/s11336-010-9175-3Caspar J. Van Lissa
diff --git a/docs/reference/md.pairs.html b/docs/reference/md.pairs.html index 00d09ec29..4964503a0 100644 --- a/docs/reference/md.pairs.html +++ b/docs/reference/md.pairs.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/md.pattern.html b/docs/reference/md.pattern.html index 3fad52e9f..5b2d81264 100644 --- a/docs/reference/md.pattern.html +++ b/docs/reference/md.pattern.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mdc.html b/docs/reference/mdc.html index d12ce141b..69407b6e7 100644 --- a/docs/reference/mdc.html +++ b/docs/reference/mdc.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mice.html b/docs/reference/mice.html index a59bc6282..41843e24a 100644 --- a/docs/reference/mice.html +++ b/docs/reference/mice.html @@ -87,7 +87,7 @@ diff --git a/docs/reference/mice.impute.2l.bin.html b/docs/reference/mice.impute.2l.bin.html index d1abf4df4..13795acdc 100644 --- a/docs/reference/mice.impute.2l.bin.html +++ b/docs/reference/mice.impute.2l.bin.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.2l.lmer.html b/docs/reference/mice.impute.2l.lmer.html index 0098aa5ed..844c89dbf 100644 --- a/docs/reference/mice.impute.2l.lmer.html +++ b/docs/reference/mice.impute.2l.lmer.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.2l.norm.html b/docs/reference/mice.impute.2l.norm.html index a1fb59aa6..04d50b1be 100644 --- a/docs/reference/mice.impute.2l.norm.html +++ b/docs/reference/mice.impute.2l.norm.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.2l.pan.html b/docs/reference/mice.impute.2l.pan.html index 354ad2452..166151131 100644 --- a/docs/reference/mice.impute.2l.pan.html +++ b/docs/reference/mice.impute.2l.pan.html @@ -82,7 +82,7 @@ diff --git a/docs/reference/mice.impute.2lonly.mean.html b/docs/reference/mice.impute.2lonly.mean.html index 68fb7e8ff..2526abbe8 100644 --- a/docs/reference/mice.impute.2lonly.mean.html +++ b/docs/reference/mice.impute.2lonly.mean.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mice.impute.2lonly.norm.html b/docs/reference/mice.impute.2lonly.norm.html index 7fbf82c35..faa8cc848 100644 --- a/docs/reference/mice.impute.2lonly.norm.html +++ b/docs/reference/mice.impute.2lonly.norm.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mice.impute.2lonly.pmm.html b/docs/reference/mice.impute.2lonly.pmm.html index 8dfe2d35f..94d306a30 100644 --- a/docs/reference/mice.impute.2lonly.pmm.html +++ b/docs/reference/mice.impute.2lonly.pmm.html @@ -80,7 +80,7 @@ diff --git a/docs/reference/mice.impute.cart.html b/docs/reference/mice.impute.cart.html index e74aed55b..8356b92dc 100644 --- a/docs/reference/mice.impute.cart.html +++ b/docs/reference/mice.impute.cart.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.jomoImpute.html b/docs/reference/mice.impute.jomoImpute.html index 40923a820..a43b5519e 100644 --- a/docs/reference/mice.impute.jomoImpute.html +++ b/docs/reference/mice.impute.jomoImpute.html @@ -85,7 +85,7 @@ diff --git a/docs/reference/mice.impute.lasso.logreg.html b/docs/reference/mice.impute.lasso.logreg.html index e6466b7ed..63400f6c3 100644 --- a/docs/reference/mice.impute.lasso.logreg.html +++ b/docs/reference/mice.impute.lasso.logreg.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.lasso.norm.html b/docs/reference/mice.impute.lasso.norm.html index e1dc45580..7a8d123ba 100644 --- a/docs/reference/mice.impute.lasso.norm.html +++ b/docs/reference/mice.impute.lasso.norm.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.lasso.select.logreg.html b/docs/reference/mice.impute.lasso.select.logreg.html index 4ebffa989..1f92cc21d 100644 --- a/docs/reference/mice.impute.lasso.select.logreg.html +++ b/docs/reference/mice.impute.lasso.select.logreg.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.lasso.select.norm.html b/docs/reference/mice.impute.lasso.select.norm.html index c26de076e..e1b993b52 100644 --- a/docs/reference/mice.impute.lasso.select.norm.html +++ b/docs/reference/mice.impute.lasso.select.norm.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.lda.html b/docs/reference/mice.impute.lda.html index a627c5925..09887bf68 100644 --- a/docs/reference/mice.impute.lda.html +++ b/docs/reference/mice.impute.lda.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.logreg.boot.html b/docs/reference/mice.impute.logreg.boot.html index 424cab08f..bd6ed2a49 100644 --- a/docs/reference/mice.impute.logreg.boot.html +++ b/docs/reference/mice.impute.logreg.boot.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mice.impute.logreg.html b/docs/reference/mice.impute.logreg.html index cfa1fb421..e76a6fa33 100644 --- a/docs/reference/mice.impute.logreg.html +++ b/docs/reference/mice.impute.logreg.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.mean.html b/docs/reference/mice.impute.mean.html index d88d1bd4f..67bd6f2f8 100644 --- a/docs/reference/mice.impute.mean.html +++ b/docs/reference/mice.impute.mean.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.midastouch.html b/docs/reference/mice.impute.midastouch.html index 8da6d8559..9f7b62cc0 100644 --- a/docs/reference/mice.impute.midastouch.html +++ b/docs/reference/mice.impute.midastouch.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.mnar.html b/docs/reference/mice.impute.mnar.html index e9d6b5248..4a64acf31 100644 --- a/docs/reference/mice.impute.mnar.html +++ b/docs/reference/mice.impute.mnar.html @@ -81,7 +81,7 @@ diff --git a/docs/reference/mice.impute.norm.boot.html b/docs/reference/mice.impute.norm.boot.html index a551711d7..c501cc963 100644 --- a/docs/reference/mice.impute.norm.boot.html +++ b/docs/reference/mice.impute.norm.boot.html @@ -78,7 +78,7 @@ diff --git a/docs/reference/mice.impute.norm.html b/docs/reference/mice.impute.norm.html index 8f13a2514..fa36b5725 100644 --- a/docs/reference/mice.impute.norm.html +++ b/docs/reference/mice.impute.norm.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.norm.nob.html b/docs/reference/mice.impute.norm.nob.html index 82a5baac2..7c5cc9557 100644 --- a/docs/reference/mice.impute.norm.nob.html +++ b/docs/reference/mice.impute.norm.nob.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.norm.predict.html b/docs/reference/mice.impute.norm.predict.html index 3f51fced1..cb0713561 100644 --- a/docs/reference/mice.impute.norm.predict.html +++ b/docs/reference/mice.impute.norm.predict.html @@ -79,7 +79,7 @@ diff --git a/docs/reference/mice.impute.panImpute.html b/docs/reference/mice.impute.panImpute.html index 6f8b4b351..0dc3134fd 100644 --- a/docs/reference/mice.impute.panImpute.html +++ b/docs/reference/mice.impute.panImpute.html @@ -84,7 +84,7 @@ diff --git a/docs/reference/mice.impute.passive.html b/docs/reference/mice.impute.passive.html index 25947df7a..6774d12a6 100644 --- a/docs/reference/mice.impute.passive.html +++ b/docs/reference/mice.impute.passive.html @@ -78,7 +78,7 @@ diff --git 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