contributing.md added

Author: smritia

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.

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/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

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({

R/mod_generic_filters.R

@@ -424,7 +424,7 @@ mod_generic_filters_server <-
           "Analysis Subset",
           text
         )
-      }) %>%
+      }) |>
         bindEvent(repName())
 
       # observer to control showing/hiding inputs based on report selection
@@ -563,7 +563,7 @@ mod_generic_filters_server <-
 
           rv$ae_pre_comp <- rv$ae_pre_comp + 1
         }
-      }) %>%
+      }) |>
         bindEvent(
           list(
             repName(), input$ae_filter, input$period, input$period_spec
@@ -714,7 +714,7 @@ mod_generic_filters_server <-
           })
           print("AE treatment pair processing end")
         }
-      }) %>%
+      }) |>
         bindEvent(list(rv$ae_pre_comp, rv$ment_out))
 
       # Tornado Plot
@@ -741,7 +741,7 @@ mod_generic_filters_server <-
             selected = c("Primary System Organ Class (AESOC)" = "AESOC")
           )
         }
-      }) %>%
+      }) |>
         bindEvent(list(
           repName()
         ))
@@ -919,7 +919,7 @@ mod_generic_filters_server <-
 
           print("AE Tornado plot pre-processing end")
         }
-      }) %>%
+      }) |>
         bindEvent(list(
           repName(), trt_var(), trt_sort(), popfilter(),
           input$ae_filter, input$ae_catvar, input$period, input$period_spec,
@@ -938,10 +938,10 @@ mod_generic_filters_server <-
         req(input$overall_subset)
         print("Edish process start")
 
-        merged_df <- sourcedata()$adsl %>%
+        merged_df <- sourcedata()$adsl |>
           adsl_merge(
             dataset_add = filter(sourcedata()$adlb, !!!rlang::parse_exprs(input$a_subset))
-          ) %>%
+          ) |>
           mentry(
             subset = input$overall_subset,
             byvar = NA_character_,
@@ -955,14 +955,14 @@ mod_generic_filters_server <-
             sgtotalyn = "N",
             add_grpmiss = ifelse(repType() == "Table", input$grpvarmiss, "N")
           )
-        rv$ae_pre <- merged_df %>%
+        rv$ae_pre <- merged_df |>
           process_edish_data(
             alt_paramcd = "ALT",
             ast_paramcd = "AST",
             bili_paramcd = "BILI"
           )
         print("Edish process ends")
-      }) %>%
+      }) |>
         bindEvent(list(
           trt_var(), trt_sort(), popfilter(), input$apply_gen_filt
         ))

R/mod_goutput.R

@@ -150,7 +150,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
       )
       print("AE risk_stat process end")
       rv$output_trigger <- rv$output_trigger + 1
-    }) %>%
+    }) |>
       bindEvent(process_btn())
 
     observe({
@@ -199,7 +199,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         "Dashed Vertical line represents risk value reference line \n",
         "The number of participants reporting at least 1 occurrence of the event specified."
       )
-    }) %>%
+    }) |>
       bindEvent(rv$output_trigger)
 
     observe({
@@ -255,7 +255,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         "are not necessarily the sum of those at the lower",
         "levels since a participant may report two or more."
       )
-    }) %>%
+    }) |>
       bindEvent(rv$output_trigger)
 
     observe({
@@ -289,7 +289,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         rv$footnote <- ""
       })
       print("AE Tornado Plot process end")
-    }) %>%
+    }) |>
       bindEvent(process_btn())
 
     observe({
@@ -333,7 +333,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
       })
       rv$title <- "eDISH Plot of Laboratory Data"
       rv$footnote <- ""
-    }) %>%
+    }) |>
       bindEvent(process_btn())
 
     observe({
@@ -506,7 +506,7 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         )
       })
       print("AE event analysis process end")
-    }) %>%
+    }) |>
       bindEvent(process_btn())
 
     plot_data <- reactive({
@@ -521,11 +521,11 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         } else {
           test <- rv$outdata$query_df
           trt_level_diff <- length(levels(test$TRTVAR)) - length(unique(test$TRTVAR))
-          test <- test %>%
+          test <- test |>
             mutate(point_n = as.numeric(as.factor(TRTVAR)) - trt_level_diff)
-          order_df <- data.frame(DPTVAL = levels(reorder(test$DPTVAL, -test$DECODh))) %>%
+          order_df <- data.frame(DPTVAL = levels(reorder(test$DPTVAL, -test$DECODh))) |>
             mutate(curve_n = row_number() + 1)
-          test <- full_join(test, order_df, by = "DPTVAL") %>%
+          test <- full_join(test, order_df, by = "DPTVAL") |>
             filter(point_n == event$x, curve_n == event$curveNumber)
         }
       }
@@ -545,20 +545,20 @@ mod_goutput_server <- function(id, sourcedata, repName, filters, process_btn) {
         relocate(c("USUBJID", "TRTVAR"))
 
       ## displaying the listing table
-      plot_table <- plot_table %>%
+      plot_table <- plot_table |>
         rename(
           !!filters()$ae_hlt := "BYVAR1",
           !!filters()$trt_var := "TRTVAR"
-        ) %>%
+        ) |>
         distinct()
-    }) %>%
+    }) |>
       bindEvent(plotly::event_data("plotly_click", source = "plot_output"))
 
     # set selected point to null every time plot updates
     observe({
       req(length(plotly::event_data("plotly_click", source = "plot_output")) > 0)
       runjs("Shiny.setInputValue('plotly_click-plot_output', null);")
-    }) %>%
+    }) |>
       bindEvent(list(repName(), rv$goutput$x$data, rv$goutput$plot$data))
 
     observe({

R/mod_plot_profile.R

@@ -85,7 +85,7 @@ mod_plot_profile_server <- function(id, sourcedata, sel_rows, datain, plot_data)
           footer = tagList(actionButton(ns("closeCM"), "Close", class = "sidebar-btn"))
         ))
       }
-    }) %>%
+    }) |>
       bindEvent(sel_rows())
 
     observe({
@@ -99,7 +99,7 @@ mod_plot_profile_server <- function(id, sourcedata, sel_rows, datain, plot_data)
         ui_adam_data = input$cm_data
       )$adam
       rv$sourcedata <- append(sourcedata(), cm_data)
-    }) %>%
+    }) |>
       bindEvent(input$closeCM)
 
     observe({