Merge pull request #30 from jaredlander/fix/aes_string

Fix/aes string

Author: jaredlander

.Rprofile .Rprofile.bak.Rprofile renamed to .Rprofile.bak

@@ -26,20 +26,24 @@ jobs:
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-24.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-24.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -50,7 +54,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -78,7 +82,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/R-CMD-check.yaml

@@ -7,9 +7,8 @@ Authors@R:
            role = c("aut", "cre"),
            email = "packages@jaredlander.com",
            comment = c(ORCID = "0000-0002-7291-726X"))
-Version: 1.2.8
-Date: 2022-01-12
-Maintainer: Jared P. Lander <packages@jaredlander.com>
+Version: 1.2.9
+Date: 2025-08-23
 Description: Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models.
 License: BSD_3_clause + file LICENSE
 LazyLoad: yes
@@ -27,7 +26,7 @@ Imports:
     purrr,
     plotly
 ByteCompile: TRUE
-Packaged: 2018-01-02 Jared
+Packaged: 2025-08-23 Jared
 Suggests:
     testthat (>= 2.0.0),
     covr,
@@ -39,4 +38,4 @@ Suggests:
     knitr,
     rmarkdown
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2

DESCRIPTION

@@ -7,11 +7,20 @@ S3method(coefplot,data.frame)
 S3method(coefplot,default)
 S3method(coefplot,glm)
 S3method(coefplot,lm)
+S3method(coefplot,model_fit)
 S3method(coefplot,rxGlm)
 S3method(coefplot,rxLinMod)
 S3method(coefplot,rxLogit)
+S3method(coefplot,workflow)
 S3method(extract.coef,cv.glmnet)
+S3method(extract.coef,default)
+S3method(extract.coef,glm)
+S3method(extract.coef,glmnet)
+S3method(extract.coef,lm)
 S3method(extract.coef,maxLik)
+S3method(extract.coef,rxGlm)
+S3method(extract.coef,rxLinMod)
+S3method(extract.coef,rxLogit)
 S3method(extract.coef,xgb.Booster)
 S3method(extractPath,cv.glmnet)
 S3method(extractPath,glmnet)

NAMESPACE

@@ -82,13 +82,13 @@ buildPlotting.default <- function(
 
     ## build the layer infos
     outerCIGeom <- geom_errorbarh(
-        aes_string(xmin="LowOuter", xmax="HighOuter", color="Model", linetype="Model"), 
+        aes(xmin=.data[["LowOuter"]], xmax=.data[["HighOuter"]], color=.data[["Model"]], linetype=.data[["Model"]]), 
         lwd=lwdOuter, height=errorHeight, position=position_dodgev(height=dodgeHeight),
         na.rm=TRUE
     )
 
     innerCIGeom <- geom_errorbarh(
-        aes_string(xmin="LowInner", xmax="HighInner", color="Model", linetype="Model"),
+        aes(xmin=.data[["LowInner"]], xmax=.data[["HighInner"]], color=.data[["Model"]], linetype=.data[["Model"]]),
         lwd=lwdInner, height=errorHeight, position=position_dodgev(height=dodgeHeight),
         na.rm=TRUE
     )
@@ -97,7 +97,7 @@ buildPlotting.default <- function(
     #ribbonGeom <- list(None=NULL, geom_ribbon(aes(ymin=LowOuter, ymax=HighOuter, group=Checkers), data=modelCI, fill=fillColor, alpha=alpha, lwd=lwdOuter))
 
     # point layer
-    pointGeom <- geom_point(aes_string(x=value, color="Model", shape="Model"), size=pointSize, position=position_dodgev(height=dodgeHeight))
+    pointGeom <- geom_point(aes(x=.data[[value]], color=.data[["Model"]], shape=.data[["Model"]]), size=pointSize, position=position_dodgev(height=dodgeHeight))
 
     #colorAes <- list(None=NULL, Single=aes(color=as.factor(Model)))
     colorScaleSingle <- scale_color_manual(values=rep(color, length(unique(modelCI$Model))), guide='none')
@@ -110,8 +110,8 @@ buildPlotting.default <- function(
     faceting <- list(None=NULL, Display=facet_wrap(~Checkers, scales=scales))
 
     # for a regular coefplot or a multiplot in seperate facets
-    #p <- ggplot(data=modelCI, aes_string(x=value))
-    p <- ggplot(data=modelCI, aes_string(x=value, y=coefficient))    		# the basics of the plot
+    #p <- ggplot(data=modelCI, aes(x=.data[[value]]))
+    p <- ggplot(data=modelCI, aes(x=.data[[value]], y=.data[[coefficient]]))    		# the basics of the plot
     #p <- p + colorAes[[1 + multi]] #                                    # in case model needs to be factorized, do it here
     p <- p + geom_vline(xintercept=0, colour=zeroColor, linetype=zeroType, lwd=zeroLWD)		# the zero line
     p <- p + outerCIGeom +    				# the outer CI bars

R/buildPlot.r

@@ -1,13 +1,13 @@
+#' @keywords internal 
+"_PACKAGE"
 #' Plotting Model Coefficients
-#'
-#' Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types.
-#'
-#' Currently, methods are available for lm, glm and rxLinMod objects.
-#'
-# @import plyr ggplot2 reshape2
-#' @docType package
+#' @description
+#' A short description...
+#'  Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types.
 #' @name coefplot
-#' @aliases coefplot-package
+# @aliases coefplot-package
+
+# @import plyr ggplot2 reshape2
 NULL
 
 

R/coefplot-package.r

@@ -99,8 +99,8 @@ coefplot <- function(model, ...)
 #' @param shorten logical or character; If \code{FALSE} then coefficients for factor levels will include their variable name.  If \code{TRUE} coefficients for factor levels will be stripped of their variable names.  If a character vector of variables only coefficients for factor levels associated with those variables will the variable names stripped.  Currently not available.
 #' @param interactive If \code{TRUE} an interactive plot is generated instead of \code{ggplot2}
 #' @param \dots Arguments passed on to other functions
-#' @return If \code{plot} is \code{TRUE} then a \code{\link{ggplot}} object is returned.  Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned.
-#' @seealso \code{\link{lm}} \code{\link{glm}} \code{\link{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}}
+#' @return If \code{plot} is \code{TRUE} then a \code{\link[ggplot2]{ggplot}} object is returned.  Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned.
+#' @seealso \code{\link{lm}} \code{\link[stats]{glm}} \code{\link[ggplot2]{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}}
 #' @export coefplot.default
 #' @export
 #' @describeIn coefplot Default method
@@ -283,9 +283,9 @@ coefplot.lm <- function(...)
 
 #' coefplot.glm
 #' 
-# Dotplot for glm coefficients
+#' Dotplot for glm coefficients
 #'
-# A graphical display of the coefficients and standard errors from a fitted glm model
+#' A graphical display of the coefficients and standard errors from a fitted glm model
 #'
 # \code{\link{coefplot}} is the S3 generic method for plotting the coefficients from a fitted model.
 #' 
@@ -314,6 +314,7 @@ coefplot.glm <- function(...)
 #' @title coefplot.workflow
 #' @description Coefplot method for workflow objects
 #' @details Pulls model element out of workflow object then calls \code{coefplot}.
+#' @export
 # @author Jared P. Lander
 #' @describeIn coefplot \code{tidymodels workflows}
 #' @param model A workflow object
@@ -326,6 +327,7 @@ coefplot.workflow <- function(model, ...)
 #' @title coefplot.model_fit
 #' @description Coefplot method for parsnip objects
 #' @details Pulls model element out of parsnip object then calls \code{coefplot}.
+#' @export
 # @author Jared P. Lander
 #' @describeIn coefplot \code{parsnip}
 #' @param model A parsnip object

R/coefplot.r

@@ -7,6 +7,7 @@
 #' 
 #' @author Jared P. Lander
 #' @method extract.coef default
+#' @export
 #' @aliases extract.coef.default
 #' @param model Model object to extract information from.
 #' @param \dots Further arguments
@@ -45,6 +46,7 @@ extract.coef.default <- function(model, ...)
 #' @author Jared P. Lander
 #' @aliases extract.coef.lm
 #' @method extract.coef lm
+#' @export
 #' @inheritParams extract.coef.default
 #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
 #' error and the variable name.
@@ -73,6 +75,7 @@ extract.coef.lm <- function(model, ...)
 #' @aliases extract.coef.glm
 #' @inheritParams extract.coef.default
 #' @method extract.coef glm
+#' @export
 #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
 #' error and the variable name.
 #' @examples
@@ -136,6 +139,7 @@ extract.coef <- function(model, ...)
 #' @aliases extract.coef.rxLinMod
 #' @inheritParams extract.coef.default
 #' @method extract.coef rxLinMod
+#' @export
 #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
 #' error and the variable name.
 #' @examples
@@ -172,6 +176,7 @@ extract.coef.rxLinMod <- function(model, ...)
 #' @aliases extract.coef.rxGlm
 #' @inheritParams extract.coef.default
 #' @method extract.coef rxGlm
+#' @export
 #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
 #' error and the variable name.
 #' @examples
@@ -201,6 +206,7 @@ extract.coef.rxGlm <- function(model, ...)
 #' @aliases extract.coef.rxLogit
 #' @inheritParams extract.coef.default
 #' @method extract.coef rxLogit
+#' @export
 #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
 #' error and the variable name.
 #' @examples
@@ -216,12 +222,30 @@ extract.coef.rxLogit <- function(model, ...)
     extract.coef.default(model=model, ...)
 }
 
+# #' @title extract.coef.glmnet
+# #' @description Extract Coefficient Information from Models
+# #' @details Gets the coefficient values and variable names from a model.  Since 
+# #' glmnet does not have standard errors, those will just be NA.
+# #' @author Jared P. Lander
+# #' @method extract.coef glmnet
+# #' @aliases extract.coef.elnet
+# #' @param model Model object from which to extract information.
+# #' @param lambda Value of penalty parameter
+# #' @param \dots Further arguments
+# #' @return A \code{\link{data.frame}} containing the coefficient, the standard 
+# #' error and the variable name.
+# extract.coef.elnet <- function(model, lambda=stats::median(model$lambda), ...)
+# {
+#     extract.coef.glmnet(model, lambda, ...)
+# }
+
 #' @title extract.coef.glmnet
 #' @description Extract Coefficient Information from Models
 #' @details Gets the coefficient values and variable names from a model.  Since 
 #' glmnet does not have standard errors, those will just be NA.
 #' @author Jared P. Lander
 #' @method extract.coef glmnet
+#' @export
 #' @aliases extract.coef.glmnet
 #' @param model Model object from which to extract information.
 #' @param lambda Value of penalty parameter
@@ -233,12 +257,12 @@ extract.coef.rxLogit <- function(model, ...)
 #' library(glmnet)
 #' library(ggplot2)
 #' library(useful)
+#' library(coefplot)
 #' data(diamonds)
 #' diaX <- build.x(price ~ carat + cut + x - 1, data=diamonds, contrasts = TRUE)
 #' diaY <- build.y(price ~ carat + cut + x - 1, data=diamonds)
 #' modG1 <- glmnet(x=diaX, y=diaY)
 #' extract.coef(modG1)
-#' }
 #' \dontshow{\}}
 #' 
 extract.coef.glmnet <- function(model, lambda=stats::median(model$lambda), ...)
@@ -317,7 +341,6 @@ extract.coef.cv.glmnet <- function(model, lambda="lambda.min", ...)
 #' N <- length(x)
 #' res <- maxLik(loglik, start=c(0,1)) # use 'wrong' start values
 #' extract.coef(res)
-#' }
 #' \dontshow{
 #' \}
 #' }

R/extractCoef.r

@@ -112,7 +112,6 @@ pos_dodgev <- function(df, height) {
 
 #' Adjust position by dodging overlaps to the side.
 #'
-#' @inheritParams ggplot2::position_identity
 #' @param height Dodging height, when different to the height of the individual
 #'   elements. This is useful when you want to align narrow geoms with wider
 #'   geoms. See the examples for a use case.

R/position.r

@@ -1,6 +1,6 @@
 ## Version Number
 
-1.2.8
+1.2.9
 
 ## Test environments
 
@@ -9,20 +9,15 @@
     - macOS-latest (release)
     - ubuntu-20.04 (release)
     - ubuntu-20.04 (devel)
-- Windows 10, R 4.1.0
-- Ubuntu 18.04, R 4.1.2
-- Win-Builder
-- R-Hub
+    - ubuntu-22.04 (release)
+    - ubuntu-22.04 (devel)
+    - ubuntu-24.04 (release)
+    - ubuntu-24.04 (devel)
+- Ubuntu 12.04, R 4.5.1
 
 ## R CMD check results
 
-There were no ERRORs, WARNINGs, NOTEs when checked locally on Windows and Ubuntu or the GitHub Actions for Windows or Ubuntu-release.
-
-GitHub Actions for Mac and Ubuntu-devel had a notes of an example taking more than 5 seconds, though I imagine that has more to do with the machine doing the testing.
-
-WinBuild had a note of an example taking more than 10 seconds, though I imagine that has more to do with the machine doing the testing.
-
-R-Hub had a note of an example taking more than 5 seconds, though I imagine that has more to do with the machine doing the testing.
+There were no ERRORs, WARNINGs, NOTEs when checked locally on Ubuntu or the GitHub Actions for Windows or Mac. For Github Actions with Ubuntu-release there were no ERRORs or WARNINGs, just a NOTE, but that was related to the executiobn time of examples, likely due to using slow runners.
 
 ## Tests