Update to mice 3.17.0

amices · Nov 22, 2024 · 537148e · 537148e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mice
 Type: Package
-Version: 3.16.17
+Version: 3.17.0
 Title: Multivariate Imputation by Chained Equations
 Date: 2024-11-22
 Authors@R: c(person("Stef", "van Buuren", role = c("aut","cre"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,75 +1,4 @@
-# mice 3.16.17
-
-* Create version to perform reverse dependency checks
-
-# mice 3.16.16
-
-* Prevent `as.mids()` from filling the `imp` object for complete variables
-
-# mice 3.16.15
-
-* Initialize single-variables blocks in `make.method()` in a more efficient way (resolves #672)
-
-# mice 3.16.14
-
-* Fixes a bug during initialization of factor values
-
-# mice 3.16.13
-
-* Adds support for the `literanger` package for `rf` imputation that is about twice as fast as `ranger` (#648). Thanks @stephematician for the contribution.
-
-# mice 3.16.12
-
-* Fixes an installation problem when `Rprofile` prints to `stdout` on Fedora, R version 4.1.3 (#646, #647). Thanks @brookslogan for the fix.
-
-# mice 3.16.11
-
-* Repairs lost braces in the documentation
-
-# mice 3.16.10
-
-* Adds support for non-syntactic variables names with backticks (#631)
-
-# mice 3.16.9
-
-* Fixes a problem with the `minpuc` argument in `quickpred()` (#634)
-* Fixes `coef() not available on S4 object` when using with `lavaan` (#615, #616)
-* Adds `.github/dependabot.yml` configuration to automate daily check (#598)
-* Update documentation tags to `roxygen2 7.3.1` requirements
-
-# mice 3.16.8
-
-* Fixes problems with zero predictors (#588)
-
-# mice 3.16.7
-
-### Minor changes
-
-* Solves problem with the package documentation link
-* Simplifies `NEWS.md` formatting to get correct version sequence on CRAN and in-package NEWS
-
-# mice 3.16.6
-
-### Minor changes
-
-* Prepares for the deprecation of the `blocks` argument at various places
-* Removes the need for `blocks` in `initialize_chain()`
-* In `rbind()`, when formulas are concatenated and duplicate names are found, also rename the duplicated variables in formulas by their new name
-
-### Bug fixes
-
-* Fixes a bug in `filter.mids()` that incorrectly removed empty components in the `imp` object
-* Fixes a bug in `ibind()` that incorrectly used `length(blocks)` as the first dimension of the `chainMean` and `chainVar` objects
-* Corrects the description `visitSequence`, `chainMean` and `chainVar` components of the `mids` object
-
-# mice 3.16.5
-
-### Bug fixes
-
-* Patches a bug in `complete()` that auto-repeated imputed values into cells that should NOT be imputed (occurred as a special case of `rbind()`, where the first set of rows was imputed and the second was not).
-* Replaces the internal variable `type` by the more informative `pred` (currently active row of `predictorMatrix`)
-
-# mice 3.16.4
+# mice 3.17.0
 
 ### Major changes
 
@@ -85,27 +14,42 @@
 
 * Note that we still lack solid evidence for these claims. (#576). Contributed @stefvanbuuren
 
-# mice 3.16.3
-
-### Major changes
-
 * **New system-independent method for pooling**: This version introduces a new function `pool.table()` that takes a tidy table of parameter estimates stemming from `m` repeated analyses. The input data must consist of three columns (parameter name, estimate, standard error) and a specification of the degrees of freedom of the model fitted to the complete data. The `pool.table()` function outputs 14 pooled statistics in a tidy form. The primary use of `pool.table()` is to support parameter pooling for techiques that have no `tidy()` or `glance()` methods, either within `R` or outside `R`. The `pool.table()` function also allows for a novel workflows that 1) break apart the traditional `pool()` function into a data-wrangling part and a parameters-reducing part, and 2) does not necessarily depend on classed R objects. (#574). Contributed @stefvanbuuren
 
-### Bug fixes
+* **literanger**: Adds support for the `literanger` package for `rf` imputation that is about twice as fast as `ranger` (#648). Thanks @stephematician for the contribution.
 
-* Fixes the "large logo" problem. (#574). Contributed @hanneoberman
+### Breaking changes
 
-# mice 3.16.2
+* The `complete(..., action = "long", ...)` command puts the columns named `".imp"` and `".id"` in the last two positions of the long data (instead of first two positions).  In this way, the columns of the imputed data will have the same positions as in the original data, which is more user-friendly and easier to work with. Note that any existing code that assumes that variables `".imp"` and `".id"` are in columns 1 and 2 will need to be modified. The advice is to modify the code using the variable names `".imp"` and `".id"`. If you want the old behaviour, specify the argument `order = "first"`. (#569). Contributed @stefvanbuuren
 
-### Major changes
+### Minor changes
 
-* **Breaking change:** The `complete(..., action = "long", ...)` command puts the columns named `".imp"` and `".id"` in the last two positions of the long data (instead of first two positions).  In this way, the columns of the imputed data will have the same positions as in the original data, which is more user-friendly and easier to work with. Note that any existing code that assumes that variables `".imp"` and `".id"` are in columns 1 and 2 will need to be modified. The advice is to modify the code using the variable names `".imp"` and `".id"`. If you want the old behaviour, specify the argument `order = "first"`. (#569). Contributed @stefvanbuuren
+* Adds support for the `dots` argument to `ranger::ranger(...)` in `mice.impute.rf()` (#563). Contributed @edbonneville
+* Prepares for the deprecation of the `blocks` argument at various places
+* Removes the need for `blocks` in `initialize_chain()`
+* In `rbind()`, when formulas are concatenated and duplicate names are found, also rename the duplicated variables in formulas by their new name
+* Solves problem with the package documentation link
+* Simplifies `NEWS.md` formatting to get correct version sequence on CRAN and in-package NEWS
+* Initialize single-variables blocks in `make.method()` in a more efficient way (resolves #672)
+* Prevent `as.mids()` from filling the `imp` object for complete variables
 
-# mice 3.16.1
+### Bug fixes
 
-### Minor changes
+* Fixes the "large logo" problem. (#574). Contributed @hanneoberman
+* Patches a bug in `complete()` that auto-repeated imputed values into cells that should NOT be imputed (occurred as a special case of `rbind()`, where the first set of rows was imputed and the second was not).
+* Replaces the internal variable `type` by the more informative `pred` (currently active row of `predictorMatrix`)
+* Fixes a bug in `filter.mids()` that incorrectly removed empty components in the `imp` object
+* Fixes a bug in `ibind()` that incorrectly used `length(blocks)` as the first dimension of the `chainMean` and `chainVar` objects
+* Corrects the description `visitSequence`, `chainMean` and `chainVar` components of the `mids` object
+* Fixes problems with zero predictors (#588)
+* Fixes a problem with the `minpuc` argument in `quickpred()` (#634)
+* Fixes `coef() not available on S4 object` when using with `lavaan` (#615, #616)
+* Adds `.github/dependabot.yml` configuration to automate daily check (#598)
+* Update documentation tags to `roxygen2 7.3.1` requirements
+* Repairs lost braces in the documentation
+* Fixes an installation problem when `Rprofile` prints to `stdout` on Fedora, R version 4.1.3 (#646, #647). Thanks @brookslogan for the fix.
+* Fixes a bug during initialization of factor values
 
-* Adds support for the `dots` argument to `ranger::ranger(...)` in `mice.impute.rf()` (#563). Contributed @edbonneville
 
 # mice 3.16.0
 
@@ -123,6 +67,8 @@
 * Updates GitHub actions for package checking and site building
 * Preserves user settings in `predictorMatrix` for case F by adding a `predictorMatrix` argument to `make.predictorMatrix()`
 * Polishes `mice.impute.mpmm()` example code
+* Adds support for non-syntactic variables names with backticks (#631)
+
 
 ### Bug fixes
 

diff --git a/cran-comments.Rmd b/cran-comments.Rmd
@@ -7,23 +7,19 @@ output: github_document
 knitr::opts_chunk$set(echo = TRUE)
 ```
 
-## mice 3.16.0
+## mice 3.17.0
 
 ## Overview
 
-This submission 
+This submission of `mice` adds new features, bug fixes, and documentation improvements. 
+See <https://github.com/amices/mice/blob/master/NEWS.md>
 
-- is a third resubmission, using `devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))` to mimmick CRAN incoming checks
-- is a second resubmission, with `\donttest` changed in `\dontrun` to evade `_R_CHECK_DEPENDS_ONLY_=true` errors;
-- is a resubmission of `mice 3.16.0` after the orphaned `ucminf` CRAN package got a new maintainer;
-- is tested with the `_R_CHECK_DEPENDS_ONLY_=true` flag, as requested;
-- solves the problems at `https://cran.r-project.org/web/checks/check_results_mice.html`;
-- contains new features and bug fixes, as described in the `NEWS.md`.
+The package has been tested on the CRAN incoming checks and on the `win-builder` and `rhub` platforms. The package has 132 downstream dependencies. I found one issue for which I contacted the maintainer of the `autoreg` package.
 
 ## Test environments
 
 ```{r}
-R.Version()
+R.Version()$version.string
 ```
 
 ## Checks
@@ -40,81 +36,12 @@ Status: OK
 ### Rhub
 
 ```{r eval=FALSE}
-devtools::check_rhub()
+rhub::rhub_doctor()
+rhub::rhub_check()
 ```
 
-#### Windows
+Status: OK <https://github.com/amices/mice/actions/runs/11974214695>
 
-```
-── mice 3.16.0: NOTE
-
-  Build ID:   mice_3.16.0.tar.gz-018f40fa4cdc492d8c9f43b7e5f5e0e7
-  Platform:   Windows Server 2022, R-devel, 64 bit
-  Submitted:  11m 27s ago
-  Build time: 11m 25s
-
-❯ checking HTML version of manual ... [27s] NOTE
-  Skipping checking math rendering: package 'V8' unavailable
-
-❯ checking for non-standard things in the check directory ... NOTE
-  Found the following files/directories:
-    ''NULL''
-
-❯ checking for detritus in the temp directory ... NOTE
-  Found the following files/directories:
-    'lastMiKTeXException'
-
-0 errors ✔ | 0 warnings ✔ | 3 notes ✖
-```
-
-I believe these NOTES are benign.
-
-#### Fedora Linux
-
-```
-Status: succes
-```
-
-#### Ubuntu 20.04
-
-```
-Status: succes
-```
-
-#### Debian
-
-```
-FAILURE 
-
-Running `R CMD build`...
-* checking for file ‘/tmp/Rtmp5Lhzhn/remotes13171d81356/mice/DESCRIPTION’ ... OK
-* preparing ‘mice’:
-* checking DESCRIPTION meta-information ... OK
-* cleaning src
-* checking for LF line-endings in source and make files and shell scripts
-* checking for empty or unneeded directories
-* building ‘mice_3.16.0.tar.gz’
-Installing package into ‘/home/docker/R’
-(as ‘lib’ is unspecified)
-Error : Bioconductor does not yet build and check packages for R version 4.4; see
-  https://bioconductor.org/install
-ERROR: dependency ‘mitml’ is not available for package ‘mice’
-* removing ‘/home/docker/R/mice’
-> There were 20 warnings (use warnings() to see them)
-
-> 
-Error : Bioconductor does not yet build and check packages for R version 4.4; see
-  https://bioconductor.org/install
-> library(mice)
-Error in library(mice) : there is no package called ‘mice’
-Execution halted
-Build step 'Execute shell' marked build as failure
-Pinging https://builder.r-hub.io/build/FAILURE/mice_3.16.0.tar.gz-82dc7cda08814b25ac48be4b5c9c940b/2023-06-01T11:37:52Z
-{"status":"ok"}
-Finished: FAILURE
-```
-
-I believe I cannot do something to make this problem disappear.
 
 ### Local checks
 
@@ -126,7 +53,7 @@ build()
 ```
 
 ```{bash eval=FALSE}
-R CMD CHECK mice_3.16.0.tar.gz
+R CMD CHECK mice_3.17.0.tar.gz
 
 Status: OK
 ```
@@ -137,7 +64,7 @@ Status: OK
 NOTE: Run in OSX terminal, not in Rstudio terminal.
 
 ```{bash eval=FALSE}
-env _R_CHECK_DEPENDS_ONLY_=true R CMD check mice_3.16.0.tar.gz
+env _R_CHECK_DEPENDS_ONLY_=true R CMD check mice_3.17.0.tar.gz
 
 Status: OK
 ```
@@ -147,20 +74,23 @@ Status: OK
 devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))
 
 ...
-   Status: OK
-   
-── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mice 3.16.0 ────
-Duration: 1m 13s
+Status: 1 NOTE
+
+── R CMD check results ─────────────────────────────────────────────────────────────────────── mice 3.17.0 ────
+Duration: 1m 10.9s
+
+❯ checking for future file timestamps ... NOTE
+  unable to verify current time
 
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
+0 errors ✔ | 0 warnings ✔ | 1 note ✖
 ```
 
 
 ## Downstream dependencies
 
 ### Overview
 
-`mice` has 114 downstream dependencies
+`mice` has 132 downstream dependencies
 
 ```{r eval=FALSE}
 # NOTE: Temporarily remove credentials line from .Rprofile
@@ -173,38 +103,25 @@ revdep_check(pkg = ".", num_workers = 10, quiet = FALSE)
 revdepcheck::revdep_summary()
 ```
 
-### New issues
-
-#### `MatchThem`
-
-There is one new warning, for the `MatchThem` package:
-
-```{r}
-revdepcheck::revdep_details(revdep = "MatchThem")
-```
-
-- I alerted the maintainer of the `MatchThem` package that the
-  documentation for `cbind.mids()` was removed from the `mice` package
-  to conform to CRAN guidelines. The maintainer responded this will be fixed
-  in the next release.
-
-#### `bipd`
+# Revdeps
 
-```{r}
-revdepcheck::revdep_details(revdep = "bipd")
-```
+## Failed to check (5)
 
-- The novel NOTE for `bipd` is equivalent to the old one. I contacted the maintainer previously. Did not repeat it now.
+|package     |version    |error |warning |note |                    |
+|:-----------|:----------|:-----|:-------|:----| ------------------ | 
+|brms        |2.22.0     |1     |        |2    | Unrelated to mice  |
+|dynr        |0.1.16-105 |1     |        |     | Unrelated to mice  |
+|pguIMP      |0.0.0.3    |1     |        |     | Unrelated to mice  |
+|Replication |0.1.2      |1     |        |     | Unrelated to mice  |
+|rmsb        |1.1-1      |1     |        |1    | Unrelated to mice  |
 
-#### `pre`
-
-- There is a new error generated by `test_pre_misc.R` of the `pre` package (`mice` is on `pre` Suggests):
-
-```{r}
-revdepcheck::revdep_details(revdep = "pre")
-```
+## New problems (4)
 
-- I tried reproducing the error but stopped my attempt due to the complex structure 
-  of the testing script. I contacted the `pre` maintainer by means of 
-  issue <https://github.com/marjoleinF/pre/issues/30>.
+|package  |version |error  |warning |note      |                   |
+|:--------|:-------|:------|:-------|:---------|:------------------|
+|[autoReg](problems.md#autoreg)|0.3.3   |__+2__ |        |          |  Informed the maintainer, asked for repair |
+|[bipd](problems.md#bipd)|0.3     |1      |        |-1 __+1__ |  Does not run because of different CPU's |
+|[finalfit](problems.md#finalfit)|1.0.8   |__+2__ |        |1         | Same error as autoreg, possibly related |
+|[pre](problems.md#pre)|1.0.7   |__+1__ |        |          | Unrelated to mice |
 
+See <https://github.com/amices/mice/tree/master/revdep> for details.