version 1.0.4

DESCRIPTION

@@ -1,33 +1,37 @@
 Package: coveffectsplot
 Title: Produce Forest Plots to Visualize Covariate Effects
-Version: 1.0.2
+Version: 1.0.4
 Authors@R: c(
     person("Samer", "Mouksassi", email = "samermouksassi@gmail.com",
       role = c("aut", "cre"),comment = c(ORCID = "https://orcid.org/0000-0002-7152-6654")),
+    person("Benjamin", "Rich", email = "mail@benjaminrich.net",
+      role = c("aut")),
     person("Dean", "Attali", email = "daattali@gmail.com",
       role = c("ctb"))
     )
 Description: Produce forest plots to visualize covariate effects using either
     the command line or an interactive 'Shiny' application.
-URL: https://github.com/smouksassi/coveffectsplot
+URL: https://smouksassi.github.io/coveffectsplot/,
+        https://github.com/smouksassi/coveffectsplot
 BugReports: https://github.com/smouksassi/coveffectsplot/issues
-Depends: R (>= 3.6.0), data.table (>= 1.9.8)
+Depends: R (>= 4.0.0), data.table (>= 1.9.8)
 Imports: colourpicker, egg, grid, ggplot2 (>= 3.3.2), shiny, stats,
         utils
 Suggests: markdown, dplyr, tidyr, shinyjs, shinymeta, table1, clipr,
         formatR, MASS, knitr, rmarkdown, mrgsolve, GGally, ggridges,
         ggrepel, ggstance, patchwork, plotly, scales, shinyAce, Rcpp,
-        gamlss.dist, ggh4x, ggpmisc, quantreg
+        gamlss.dist, ggdist, ggh4x, ggpmisc, quantreg
 License: MIT + file LICENSE
 SystemRequirements: pandoc with https support
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2022-05-30 10:23:30 UTC; smouksas
+Packaged: 2023-09-18 08:51:27 UTC; smouksas
 Author: Samer Mouksassi [aut, cre] (<https://orcid.org/0000-0002-7152-6654>),
+  Benjamin Rich [aut],
   Dean Attali [ctb]
 Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
 Repository: CRAN
-Date/Publication: 2022-05-30 10:50:02 UTC
+Date/Publication: 2023-09-18 12:40:16 UTC

MD5

@@ -1,57 +1,67 @@
-12181eb36caff057fb03c81460669b5c *DESCRIPTION
+964f22d587133060a80d50f1bee010cb *DESCRIPTION
 3cca4895befbf1b8025c378d28af69db *LICENSE
-59d87eb46bf8044f0cf52e201bc576e1 *NAMESPACE
-322f40645ccdb233d1427a5aee5f6ae6 *NEWS.md
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 10a4f6850c84b254472a1c620044d60b *R/data.R
-db7ecc5ca429688d5da5e453992f72e2 *R/forest_plot.R
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 7afa8b1fdc9b17a122f6a0f9a350864e *R/get_sample_data.R
-2ef4b8aa1dff6b313176be430c7b513c *R/run_interactiveforestplot.R
-012eb26de2356f28c13959e6340465d2 *README.md
-1ea459c2867a19ad27cd4eb10e65bb57 *build/vignette.rds
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 3ab983cabf81913cd1c731815bfc9ede *data/covdatasim.rda
 89a97e7e049d8c4814671a7dfad10da8 *data/prezista.rda
 0e72a516c4dc70cde61114e5e7ab50f7 *data/wtage.rda
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 114f202c6c21e15069e08aab97368712 *inst/sample_data/dataforest.csv
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 60ba0e3a14475a7e0e787427a6f62d1f *inst/sample_data/forestplotdatacpidata.csv
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 70db5fc25a073be70c890b91d5ad608f *vignettes/covdatasim.csv
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NAMESPACE

@@ -2,7 +2,9 @@
 
 export(draw_key_hpath)
 export(draw_key_pointrangeh)
+export(expand_modelframe)
 export(forest_plot)
 export(get_sample_data)
 export(run_interactiveforestplot)
 import(data.table, except = c(last,between,first))
+importFrom(colourpicker,colourInput)

NEWS.md

@@ -1,7 +1,25 @@
+# coveffectsplot 1.0.4
+* updated vignettes and examples
+* added citation and start up message
+* added `major_x_labels` argument for custom x labels
+* added `interval_linewidth` argument to control interval linewidth
+* added and exported `expand_modelframe` function
+* added the possibility to select the shapes manually via `interval_shape` and `bsv_shape`
+* added capability for user to reverse color legend separately via `legend_color_reverse`
+* added capability for user to specify text for legend titles via `interval_legend_title` and `shape_legend_title` as well as to control legend title text size via `legend_title_size`
+* added capability for user to specify facet text color via `x_facet_text_col` and `y_facet_text_col` for improved theming support
+* added possibility to add different ref line(s)/area(s) by parameter via
+ `ref_value_by_panel` and `ref_value_by_panel_data` function arguments (not in the shiny, app)
+
+# coveffectsplot 1.0.3
+* fixed a bug when ref_value when not equal 1 affecting y axis limits
+* fixed a bug when the guides for color and shape were not merged
+* updated the UI to be able to specify user-defined color for parameters
+
 # coveffectsplot 1.0.2
 * vignettes updated to reflect latest addition for the tutorial CPT:PSP paper
-* Added a function arguments `paramname_color` and `combine_interval_shape_legend` to enable color by paramname
-* Added a function arguments `combine_interval_shape_legend` to enable merging of color and pointinterval legends
+* Added function arguments `paramname_color` and `combine_interval_shape_legend` to enable color by paramname
+* Added function arguments `combine_interval_shape_legend` to enable merging of color and pointinterval legends
 * Added `covdatasim` as a dataset
 
 # coveffectsplot 1.0.1

R/expand_modelframe.R

@@ -0,0 +1,29 @@
+#' Expand covariate values choices and reference values varying one at a time
+#' 
+#' @param rv  a data.frame with columns names of covariate(s) and values equal reference
+#' @param covcol column name for the covariate being varied
+#' @param ... 	Arguments to be passed to methods
+#' @return A data.frame with combination of covariates
+#' @examples
+#' reference.values <- data.frame(WT = 85, ALB = 45, SEX = 0)   
+#' covcomb <- expand_modelframe(
+#'   WT  = c(56, 72, 98, 128), # P05, P25, P75, P95 # ref is P50
+#' ALB = c(40, 50),          # P05, P95 # ref is P50
+#'   SEX = c(1),               # Reference is for SEX=0 (female)
+#'   rv = reference.values)
+#' covcomb
+#' @export
+expand_modelframe <- function( rv, covcol="covname", ...) {
+  args <- list(...)
+  df <- lapply(args, function(x) x[[1]])
+  df[names(rv)] <- rv
+  res <- lapply(seq_along(rv), function(i) {
+    df[[covcol]] <- names(rv)[i]
+    df[[names(rv)[i]]] <- args[[names(rv)[i]]]
+    as.data.frame(df)
+  })
+  do.call(rbind, res)
+}
+
+
+