Devel

.Rbuildignore

@@ -5,7 +5,6 @@
 ^CODE_OF_CONDUCT\.md$
 ^README\.Rmd$
 ^app\.R$
-^R/surv_utils\.R$
 ^R/km_plot\.R$
 ^LICENSE\.md$
 ^.github$

CONTRIBUTING.md

@@ -0,0 +1,69 @@
+# Contributing to {carver}
+
+This outlines how to propose a change to {carver}.
+
+## Making Changes
+
+If you want to make a change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+Per pfizer-opensource policies, only those listed as collaborators can raise issues.  
+If you’ve found a bug, please email the maintainer (`smriti.anand@pfizer.com`) illustrating the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+Alternatively if you have access to the COSA community Slack channel for {carver}, you can raise it there.  
+See guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. 
+
+*   If needed, install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). 
+
+*   Make your changes, commit to git, and then create a PR.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Closes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code Style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+    * To apply the appropriate style with styler please use `styler:::style_active_pkg()` or `styler::style_file()`
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+*  All helper/non-exported functions are documented with roxygen2 as indicated above. 
+   Include `#' @keywords internal` to mark the function as internal.
+   Any helper functions that appear in examples will need to use the `carver:::` 
+   prefix.
+
+### Error Handling
+
+TBD  
+
+### Package Dependencies
+
+Additional package dependencies should be considered after exhausting other possibilities. If you do need to add one,  
+email the maintainer or collaborators/start a discussion to make a decision on the necessity of it.  
+Once agreed upon, the dependency can be added to the package via the relevant files.  
+
+## Scope
+
+The {carver} package will be an open-source tool and package to enable generation of
+common analysis reports (tables and interactive plots) for clinical
+review and direct inclusion in submission for regulatory agencies
+
+## Deprecation Cycle
+
+TBD  
+
+## Code of Conduct
+
+Please note that the carver project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

DESCRIPTION

@@ -34,6 +34,7 @@ Imports:
     shinyjs (>= 2.1.0),
     shinyWidgets (>= 0.7.6),
     stringr (>= 1.5.0),
+    survival,
     tibble (>= 3.2.1),
     tidyr (>= 1.3.1)
 Suggests: 
@@ -65,4 +66,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -31,6 +31,7 @@ export(mentry)
 export(msumstat)
 export(multi_interval)
 export(occ_tier_summary)
+export(ph_plot)
 export(plot_aes_opts)
 export(plot_axis_opts)
 export(plot_display_bign)
@@ -45,12 +46,15 @@ export(round_f)
 export(run_app)
 export(save_file)
 export(scatter_plot)
+export(schoenfeld_plot)
 export(shape_to_sym)
 export(split_data_by_var)
 export(split_section_headers)
 export(str_to_vec)
 export(summary_functions)
 export(summary_row_cat)
+export(surv_pre_processor)
+export(survfit_summary)
 export(tbl_display)
 export(tbl_processor)
 export(tbl_risk_labels)
@@ -67,6 +71,7 @@ import(scales)
 import(shiny)
 import(shinyWidgets)
 import(stringr)
+import(survival)
 import(tools)
 importFrom(DT,addRow)
 importFrom(DT,colReorder)

R/adae_risk_summary.R

@@ -128,7 +128,7 @@ adae_risk_summary <- function(datain,
   if (!is.na(cutoff_where) && str_detect(cutoff_where, "PCT|FREQ")) {
     datain <- datain |>
       left_join(select(ae_lsumm, all_of(c("BYVAR1", "CUTFL")), {{ lterm }} := "DPTVAL"),
-        by = c("BYVAR1", lterm)
+        by = c("BYVAR1", lterm), relationship = "many-to-many"
       )
     a_subset <- paste(na.omit(c(a_subset, "CUTFL == 'Y'")), collapse = "&")
   }

R/ae_forestplot.R

@@ -246,7 +246,7 @@ ae_forest_plot <-
         )
       })
     # Return single level list
-    return(flatten(nested_plots))
+    flatten(nested_plots)
   }
 
 #' Highlight Significant p-value points in forest plot
@@ -281,12 +281,11 @@ ae_forest_hlt_sig <- function(plotin,
       aes(
         x = .data[["PCT"]],
         y = .data[["DPTVAL"]],
-        fill = .data[["EFFECT"]],
-        key = .data[["key"]]
+        fill = .data[["EFFECT"]]
       ),
       inherit.aes = FALSE,
       shape = 23,
-      size = pts_size,
+      linewidth = pts_size,
       stroke = 0.2
     ) +
     scale_fill_manual(name = "", values = hltfill)

R/ae_pre_processor.R

@@ -166,7 +166,7 @@ ae_pre_processor <- function(datain,
   ################### ENDax SEV/CTC##############
 
   # Return processed dataframe and filter conditions
-  return(list(data = ungroup(data_pro), a_subset = filters))
+  list(data = ungroup(data_pro), a_subset = filters)
 }
 
 #' Create filter condition for Adverse Events from keyword

R/ae_volcano_plot.R

@@ -194,7 +194,7 @@ ae_volcano_plot <- function(datain,
         )
       )
   }
-  return(gplot)
+  gplot
 }
 
 #' Volcano Plot axis Options
@@ -276,8 +276,8 @@ Favors {trt2_label} (N={N2}) --->\n{statistic}"
   }
   refval <- ifelse(grepl("Ratio", statistic), 1, 0)
   xref <- c(refval, refval - xref_offset, refval + xref_offset)
-  return(list(
+  list(
     xaxis_label = xlab, yaxis_label = ylab,
     ylinearopts = ylinearopts, yaxis_scale = ytrans, xref = xref
-  ))
+  )
 }

R/app_server.R

@@ -67,7 +67,7 @@ app_server <- function(input, output, session) {
       removeUI("#readData")
       runjs("Shiny.setInputValue('data_upload', true);")
     }
-  }) %>%
+  }) |>
     bindEvent(adam_read())
 
   rep_inputs <- mod_report_selection_server(

R/bar_plot.R

@@ -147,5 +147,5 @@ bar_plot <- function(datain,
     g_plot <- g_plot + coord_flip()
   }
   message("Bar Plot Success")
-  return(g_plot)
+  g_plot
 }

R/box_plot.R

@@ -183,5 +183,5 @@ box_plot <- function(datain,
       )
   }
   message("Box Plot Success")
-  return(g_plot)
+  g_plot
 }

R/data.R

@@ -76,3 +76,10 @@
 #'
 #' @format Data frame with 7510 rows and 21 variables
 "cm"
+
+#' survival
+#'
+#' Test Data for Schoenfeld Plot, Kaplan-Meir Plot, ph plot
+#'
+#' @format List of data frames containing `adsl` and `adtte` dataset
+"survival"

R/event_analysis.R

@@ -489,7 +489,7 @@ event_plotly <- function(p, ref_line, title_text) {
 
 #' Overwrite plotly line shape without using `shapes` argument in `plotly::layout()`
 #'
-#' This is due to an existing bug in `plotly`.[https://community.rstudio.com/t/drawing-lines-from-layouts-doesnt-work-on-ggplotly/54116] # nolint
+#' This is due to an existing bug in `plotly`.<https://community.rstudio.com/t/drawing-lines-from-layouts-doesnt-work-on-ggplotly/54116> # nolint
 #'
 #' @param p `ggplot` object
 #' @param ref_line Reference line

R/event_interval.R

@@ -55,14 +55,14 @@ interval_plot <- function(datain,
                           xaxislab = "Start and End Study Day",
                           yaxislab = "") {
   # Filter subject and get info
-  ad_plot <- datain %>%
-    filter(USUBJID == subjectid) %>%
+  ad_plot <- datain |>
+    filter(USUBJID == subjectid) |>
     mutate(Status = case_when(
       (is.na(get(startvar)) & get(endvar) >= 0) ~ "End Day",
       (is.na(get(endvar)) & get(startvar) >= 0) ~ "Start Day",
       (!is.na(get(startvar)) & !is.na(get(endvar))) ~ "Complete",
       TRUE ~ "Remove"
-    )) %>%
+    )) |>
     filter(Status != "Remove")
   # Check if no data left and return accordingly
   if (nrow(ad_plot) == 0) {
@@ -81,8 +81,8 @@ interval_plot <- function(datain,
     series_color <- g_seriescol(ad_plot, series_color, seriesvar)
   }
   # Hover Information:
-  ad_plot <- ad_plot %>%
-    select(all_of(c("USUBJID", startvar, endvar, yvar, seriesvar, "Status"))) %>%
+  ad_plot <- ad_plot |>
+    select(all_of(c("USUBJID", startvar, endvar, yvar, seriesvar, "Status"))) |>
     mutate(
       HOVER_TEXT = paste0(
         !!sym(yvar), "\n",
@@ -94,15 +94,15 @@ interval_plot <- function(datain,
       !!yvar := as.factor(!!sym(yvar))
     )
   # Use data with both dates present for segment plot
-  segmentdata <- ad_plot %>%
+  segmentdata <- ad_plot |>
     filter(Status == "Complete")
 
   # Use data with either Start or end dates only for scatter plot
-  scatterdata <- ad_plot %>%
-    filter(Status != "Complete" | !!sym(startvar) == !!sym(endvar)) %>%
-    tidyr::pivot_longer(all_of(c(startvar, endvar)), names_to = "key", values_to = "Value") %>%
-    filter(!is.na(Value)) %>%
-    select(-key) %>%
+  scatterdata <- ad_plot |>
+    filter(Status != "Complete" | !!sym(startvar) == !!sym(endvar)) |>
+    tidyr::pivot_longer(all_of(c(startvar, endvar)), names_to = "key", values_to = "Value") |>
+    filter(!is.na(Value)) |>
+    select(-key) |>
     distinct(.keep_all = TRUE)
 
   # Create ggplot object - segment plot for Complete intervals and scatter for incomplete
@@ -127,7 +127,7 @@ interval_plot <- function(datain,
           color = !!sym(seriesvar)
         ),
         position = position_dodge(width = 0.3),
-        size = 1.2
+        linewidth = 1.2
       )
     # Convert to plotly object
     splotly <- plotly::ggplotly(gplot, tooltip = "text")
@@ -168,5 +168,5 @@ interval_plot <- function(datain,
     splotly$x$data[[i]]$legendgroup <- splotly$x$data[[i]]$name
     if (!legdf$is_first[[i]]) splotly$x$data[[i]]$showlegend <- FALSE
   }
-  return(list(plot = gplot, ptly = splotly, rpt_data = ad_plot))
+  list(plot = gplot, ptly = splotly, rpt_data = ad_plot)
 }

R/forest_plot.R

@@ -104,7 +104,7 @@ forest_plot_base <- function(datain,
   ) +
     ggstance::geom_errorbarh(
       height = 0.1,
-      position = ggstance::position_dodgev(height = 0.6), linewidth = 0.5
+      position = ggstance::position_dodgev(height = 0.6), size = 0.5
     ) +
     geom_point(
       shape = 22,
@@ -135,7 +135,7 @@ forest_plot_base <- function(datain,
         alpha = 0.5
       )
   }
-  return(gplot)
+  gplot
 }
 
 #' Scatter plot to be included within forest plot
@@ -254,7 +254,7 @@ forest_plot_scatter <- function(datain,
         alpha = 0.5
       )
   }
-  return(gplot)
+  gplot
 }
 
 #' Display combined Forest Plot
@@ -399,5 +399,5 @@ forest_display <- function(plot_list,
       rel_heights = c(0.85, 0.075, 0.075)
     )
   }
-  return(combine_plot)
+  combine_plot
 }

R/global.R

@@ -107,5 +107,13 @@ globalVariables(c(
   "Value",
   "ASEV",
   "TA",
-  "REPTYPE"
+  "REPTYPE",
+  "pred.x",
+  "trt",
+  "yhat",
+  "xx",
+  "zy",
+  "ylow",
+  "yup",
+  "combn"
 ))

R/graph_utils.R

@@ -638,8 +638,8 @@ series_leg_lab <- function(datain,
                            series_var = "TRTVAR",
                            series_labelvar = "TRTTXT") {
   if (series_labelvar != series_var && is.factor(datain[[series_labelvar]])) {
-    return(sort(unique(datain[[series_labelvar]])))
+    sort(unique(datain[[series_labelvar]]))
   } else {
-    return(waiver())
+    waiver()
   }
 }

R/mcatstat.R

@@ -327,5 +327,5 @@ calc_denom <- function(counts,
     df <- df |>
       mutate(CVALUE = ifelse(FREQ == 0, "0", glue(cstat)))
   }
-  return(df |> ungroup())
+  df |> ungroup()
 }

R/mod_data_check.R

@@ -99,7 +99,7 @@ mod_data_check_server <- function(id, sourcedata, domain) {
       {
         req(input$data_varlist)
 
-        data_lkup <- sourcedata()[[domain()]] %>%
+        data_lkup <- sourcedata()[[domain()]] |>
           select(unlist(strsplit(paste(input$data_varlist, collapse = ","), ",")))
 
         datatable(

R/mod_data_read.R

@@ -45,7 +45,7 @@ mod_data_read_server <-
           ui_data_source = source(),
           ui_adam_data = adam_data
         )
-      }) %>%
+      }) |>
         bindEvent(read_btn())
     })
   }

R/mod_download_report.R

@@ -81,7 +81,7 @@ mod_download_report_server <- function(id, repType, repName, repNum, save_fmt, t
         }
       }
       print("save report object created")
-    }) %>%
+    }) |>
       bindEvent(list(repType(), toutput(), goutput(), save_fmt()))
 
     observe({