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hanneobermanhanneoberman
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Merge pull request #169 from amices/new_release
Prepare for `ggmice` v0.0.1
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‎.gitignore‎

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docs
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*.psd
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*.pdf
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revdep/

‎DESCRIPTION‎

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Package: ggmice
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Title: Visualizations for 'mice' with 'ggplot2'
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Version: 0.1.0.9000
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Version: 0.1.1
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Authors@R: c(
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person("Hanne", "Oberman", email = "[email protected]", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0003-3276-2141")),
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'ggmice' to inspect missing data, develop imputation models, evaluate
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algorithmic convergence, or compare observed versus imputed data.
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License: GPL (>= 3)
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URL: https://github.com/amices/ggmice, https://amices.org/,
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https://amices.org/ggmice/
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URL: https://amices.org/ggmice/
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BugReports: https://github.com/amices/ggmice/issues
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Imports:
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cli,

‎R/plot_pred.R‎

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#'
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#' @return An object of class `ggplot2::ggplot`.
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#'
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#' @details
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#' The predictor matrix in [mice::mice] determines the role an imputation model predictor takes in the imputation model.
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#' The rows correspond to incomplete target variables, and the columns to imputation model predictors.
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#'
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#' A value of `1` indicates that the column variable is a predictor to impute the target (row) variable. The value `0` means that it is not used as predictor.
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#'
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#' Imputation methods for multilevel data use other codes than `0` and `1`:
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#' - Methods `2l.bin`, `2l.lmer`, `2l.norm`, `2l.pan`, `2lonly.mean`, `2lonly.norm` and `2lonly.pmm` use code `-2` to indicate the class variable;
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#' - Methods `2l.bin`, `2l.lmer`, `2l.norm` and `2l.pan` use code `2` to indicate the random effects;
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#' - Method `2l.pan` uses codes `3` and `4` to add class means to codes `1` and `2` respectively.
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#'
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#' @references van Buuren, S. (2018). Flexible imputation of missing data. Chapman and Hall/CRC. [stefvanbuuren.name/fimd](https://stefvanbuuren.name/fimd/)
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#'
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#' @examples
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#' # generate a predictor matrix
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#' pred <- mice::quickpred(mice::nhanes)
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if (mice::is.mids(data)) {
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if (!is.null(method)) {
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cli::cli_warn(
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c("!" = "Input `method` is ignored when `data` is of class `mids`.",
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"i" = "The `method` vector from the `mids` object will be used.")
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c("!" = "Input `method` is ignored when `data` is of class `mids`.", "i" = "The `method` vector from the `mids` object will be used.")
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)
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}
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method <- data$method
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ind = matrix(data[vrb_matched, vrb_matched], nrow = p * p, byrow = TRUE)
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) %>% dplyr::mutate(clr = factor(
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.data$ind,
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levels = c(-3, -2, 0, 1, 2),
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levels = c(-3, -2, 0, 1, 2, 3, 4),
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labels = c(
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"inclusion-restriction variable",
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"cluster variable",
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"not used",
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"predictor",
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"random effect",
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"fixed effect",
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"random effect"
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),
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ordered = TRUE
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"cluster variable" = "lightyellow",
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"not used" = "grey90",
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"predictor" = "palegreen3",
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"random effect" = "deepskyblue"
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"random effect" = "deepskyblue",
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"fixed effect" = "deepskyblue"
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)
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) +
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ggplot2::labs(

‎R/plot_trace.R‎

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if (is.null(data$chainMean) && is.null(data$chainVar)) {
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cli::cli_abort("No convergence diagnostics found", call. = FALSE)
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}
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if (data$m < 2L && data$maxit < 2L) {
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cli::cli_abort("More iterations and/or imputations required", call. = FALSE)
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}
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vrb <- rlang::enexpr(vrb)
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vrbs_in_data <- names(data$imp)
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vrb_matched <- match_vrb(vrb, vrbs_in_data)

‎R/theme.R‎

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panel.grid.minor = ggplot2::element_blank(),
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panel.grid.major = ggplot2::element_blank(),
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axis.ticks = ggplot2::element_line(colour = "black"),
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axis.text = ggplot2::element_text(hjust = 0, vjust = 0),
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axis.title.y.right = ggplot2::element_text(margin = ggplot2::margin(l = 6))
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)
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}

‎cran-comments.md‎

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# ggmice 0.1.1
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## R CMD check results
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0 errors | 0 warnings | 0 notes
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## Downstream dependencies
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There are no downstream dependencies of 'ggmice' yet.
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---
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# ggmice 0.1.0
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## R CMD check results

‎man/figures/README-example-1.png‎

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‎man/figures/README-example-2.png‎

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‎man/plot_pred.Rd‎

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‎revdep/README.md‎

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# Platform
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|field |value |
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|:--------|:------------------------------------------------------------------------------------|
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|version |R version 4.3.0 (2023-04-21 ucrt) |
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|os |Windows 10 x64 (build 19045) |
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|system |x86_64, mingw32 |
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|ui |RStudio |
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|language |(EN) |
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|collate |Dutch_Netherlands.utf8 |
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|ctype |Dutch_Netherlands.utf8 |
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|tz |Europe/Amsterdam |
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|date |2023-07-24 |
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|rstudio |2023.06.1+524 Mountain Hydrangea (desktop) |
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|pandoc |3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) |
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|field |value |
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|:--------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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|version |R version 4.5.0 (2025-04-11) |
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|os |macOS Sequoia 15.5 |
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|system |aarch64, darwin20 |
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|ui |RStudio |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |Europe/Amsterdam |
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|date |2025-07-30 |
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|rstudio |2025.05.1+513 Mariposa Orchid (desktop) |
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|pandoc |NA |
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|quarto |1.6.42 @ /private/var/folders/mz/40zv3f2x0ws1bznpf0md3w7h0000gn/T/AppTranslocation/3852367F-EA29-4389-8A95-F2F66D6CA5E6/d/RStudio.app/Contents/Resources/app/quarto/bin/quarto |
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# Dependencies
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|package |old |new |Δ |
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|:------------|:----------|:----------|:--|
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|ggmice |0.0.1 |0.0.1.9000 |* |
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|backports |1.4.1 |1.4.1 | |
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|bit |4.0.5 |4.0.5 | |
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|bit64 |4.0.5 |4.0.5 | |
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|brio |1.1.3 |1.1.3 | |
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|broom |1.0.5 |1.0.5 | |
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|callr |3.7.3 |3.7.3 | |
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|cli |3.6.1 |3.6.1 | |
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|clipr |0.8.0 |0.8.0 | |
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|colorspace |2.1-0 |2.1-0 | |
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|cpp11 |0.4.5 |0.4.5 | |
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|crayon |1.5.2 |1.5.2 | |
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|desc |1.4.2 |1.4.2 | |
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|diffobj |0.3.5 |0.3.5 | |
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|digest |0.6.33 |0.6.33 | |
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|dplyr |1.1.2 |1.1.2 | |
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|ellipsis |0.3.2 |0.3.2 | |
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|evaluate |0.21 |0.21 | |
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|fansi |1.0.4 |1.0.4 | |
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|farver |2.1.1 |2.1.1 | |
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|forcats |1.0.0 |1.0.0 | |
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|foreach |1.5.2 |1.5.2 | |
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|fs |1.6.3 |1.6.3 | |
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|generics |0.1.3 |0.1.3 | |
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|ggplot2 |3.4.2 |3.4.2 | |
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|glmnet |4.1-7 |4.1-7 | |
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|glue |1.6.2 |1.6.2 | |
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|gtable |0.3.3 |0.3.3 | |
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|haven |2.5.3 |2.5.3 | |
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|hms |1.1.3 |1.1.3 | |
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|isoband |0.2.7 |0.2.7 | |
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|iterators |1.0.14 |1.0.14 | |
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|jomo |2.7-6 |2.7-6 | |
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|jsonlite |1.8.7 |1.8.7 | |
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|labeling |0.4.2 |0.4.2 | |
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|lifecycle |1.0.3 |1.0.3 | |
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|lme4 |1.1-34 |1.1-34 | |
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|magrittr |2.0.3 |2.0.3 | |
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|mice |3.16.0 |3.16.0 | |
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|minqa |1.2.5 |1.2.5 | |
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|mitml |0.4-5 |0.4-5 | |
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|munsell |0.5.0 |0.5.0 | |
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|nloptr |2.0.3 |2.0.3 | |
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|numDeriv |2016.8-1.1 |2016.8-1.1 | |
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|ordinal |2022.11-16 |2022.11-16 | |
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|pan |1.8 |1.8 | |
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|pillar |1.9.0 |1.9.0 | |
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|pkgconfig |2.0.3 |2.0.3 | |
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|pkgload |1.3.2.1 |1.3.2.1 | |
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|praise |1.0.0 |1.0.0 | |
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|prettyunits |1.1.1 |1.1.1 | |
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|processx |3.8.2 |3.8.2 | |
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|progress |1.2.2 |1.2.2 | |
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|ps |1.7.5 |1.7.5 | |
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|purrr |1.0.1 |1.0.1 | |
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|R6 |2.5.1 |2.5.1 | |
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|RColorBrewer |1.1-3 |1.1-3 | |
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|Rcpp |1.0.11 |1.0.11 | |
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|RcppEigen |0.3.3.9.3 |0.3.3.9.3 | |
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|readr |2.1.4 |2.1.4 | |
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|rematch2 |2.1.2 |2.1.2 | |
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|rlang |1.1.1 |1.1.1 | |
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|rprojroot |2.0.3 |2.0.3 | |
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|scales |1.2.1 |1.2.1 | |
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|shape |1.4.6 |1.4.6 | |
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|stringi |1.7.12 |1.7.12 | |
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|stringr |1.5.0 |1.5.0 | |
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|testthat |3.1.10 |3.1.10 | |
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|tibble |3.2.1 |3.2.1 | |
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|tidyr |1.3.0 |1.3.0 | |
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|tidyselect |1.2.0 |1.2.0 | |
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|tzdb |0.4.0 |0.4.0 | |
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|ucminf |1.2.0 |1.2.0 | |
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|utf8 |1.2.3 |1.2.3 | |
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|vctrs |0.6.3 |0.6.3 | |
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|viridisLite |0.4.2 |0.4.2 | |
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|vroom |1.6.3 |1.6.3 | |
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|waldo |0.5.1 |0.5.1 | |
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|withr |2.5.0 |2.5.0 | |
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|package |old |new |Δ |
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|:-------|:-----|:----------|:--|
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|ggmice |0.1.0 |0.1.0.9000 |* |
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|broom |NA |1.0.9 |* |
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|glmnet |NA |4.1-10 |* |
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|pillar |NA |1.11.0 |* |
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|purrr |NA |1.1.0 |* |
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|Rcpp |NA |1.1.0 |* |
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|tibble |NA |3.3.0 |* |
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|utf8 |NA |1.2.6 |* |
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# Revdeps
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