Rh survival

.Rbuildignore

@@ -30,3 +30,5 @@ vignettes/x0*
 ^CRAN-SUBMISSION$
 ^scripts$
 \.sass$
+manifest.json
+^\.posit$

.github/workflows/pkgdown.yaml

@@ -29,20 +29,17 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
 
-      - name: Install specific pkgdown version
-        run: install.packages("remotes") ; remotes::install_version("pkgdown", version = "2.0.3", repos = "cran.rstudio.com", dependencies = FALSE)
+      - name: Install dev dependencies
+        run: install.packages(c("pkgdown", "devtools", "covr"))
         shell: Rscript {0}
 
       - name: Install tidyCDISC
         shell: bash
         run: R CMD INSTALL --preclean .
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

.github/workflows/test-coverage.yaml

@@ -24,8 +24,10 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
-        with:
-          extra-packages: covr
+
+      - name: Install dev dependencies
+        run: install.packages(c("devtools", "covr"))
+        shell: Rscript {0}
 
       - name: Install tidyCDISC
         shell: bash

.gitignore

@@ -8,3 +8,4 @@ docs/
 revdep/
 /doc/
 /Meta/
+/.posit

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tidyCDISC
 Title: Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets
-Version: 0.2.1
+Version: 0.2.1.9000
 Authors@R: c(
     person("Aaron", "Clark", , "clark.aaronchris@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0123-0970")),
@@ -10,6 +10,8 @@ Authors@R: c(
     person("Maya", "Gans", , "maya.gans@biogen.com", role = "aut"),
     person("Robert", "Krajcik", , "robert.krajcik@biogen.com", role = "ctb"),
     person("Marly", "Gotti", , "marly.cormar@biogen.com", role = "ctb"),
+    person("Ryan", "Harrison", , "harrison.ryan.w@gmail.com", role = "aut", 
+           comment = c(ORCID = "0000-0003-4575-006X")),
     person("Biogen", "Inc", role = "cph")
   )
 Description: Provides users a quick exploratory dive into common
@@ -36,40 +38,56 @@ License: AGPL (>= 3)
 URL: https://github.com/Biogen-Inc/tidyCDISC/, https://Biogen-Inc.github.io/tidyCDISC/
 BugReports: https://github.com/Biogen-Inc/tidyCDISC/issues
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1)
 Imports: 
+    arrow,
+    broom.helpers,
     cicerone,
+    cli,
     config,
     dplyr,
     DT,
+    fs,
     GGally,
     ggcorrplot,
     ggplot2,
+    ggsurvfit,
     glue,
     golem,
     gt,
+    gtsummary,
     haven,
     IDEAFilter,
+    pkgload,
     plotly,
     purrr,
+    readxl,
     rlang,
     rmarkdown,
     shiny,
     shinyjs,
     shinyWidgets,
     sjlabelled,
+    stringdist,
     stringr,
     survival,
+    tibble,
     tidyr,
+    tidyselect,
     timevis,
-    tippy (== 0.1.0)
+    tippy (== 0.1.0),
+    vroom
 Suggests: 
+    devtools,
     knitr,
+    shinyalert,
     spelling,
     testthat
 VignetteBuilder: 
     knitr
+Config/Needs/website: pkgdown
+Config/Needs/coverage: covr
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(error_handler,default)
+S3method(error_handler,purrr_error_indexed)
+S3method(error_handler,rlang_error)
 export(app_methods)
 export(col_for_list_expr)
 export(common_rownames)
@@ -36,6 +39,11 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggsurvfit,add_censor_mark)
+importFrom(ggsurvfit,add_confidence_interval)
+importFrom(ggsurvfit,add_risktable)
+importFrom(ggsurvfit,ggsurvfit)
+importFrom(ggsurvfit,survfit2)
 importFrom(glue,glue)
 importFrom(golem,activate_js)
 importFrom(golem,add_resource_path)
@@ -111,6 +119,7 @@ importFrom(shinyjs,useShinyjs)
 importFrom(sjlabelled,get_label)
 importFrom(sjlabelled,set_label)
 importFrom(stats,as.formula)
+importFrom(stats,reformulate)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_locate_all)
 importFrom(stringr,str_remove)

NEWS.md

@@ -1,3 +1,17 @@
+# tidyCDISC (development version)
+
+* Update wordlist
+* Add Ryan Harrison as author
+
+### Population Explorer
+* Refactor KM plots from plotly to ggsurvfit
+* Add estimated median table to KM plot
+* Add estimate survival probabilities table to KM plot
+* Add time-axis ticks configuration to KM plot
+* Enable multiple groups to KM plot
+* Add Cox PH Hazard Ratios table to KM plot
+* Add ADaM validation functions
+* Allow more input file types: csv, parquet, txt, xls, xlsx
 
 # tidyCDISC 0.2.1 (CRAN Release)
 

R/global.R

@@ -1,6 +1,6 @@
 utils::globalVariables(c(
   "AEDECOD",
-  "AESER", 
+  "AESER",
   "AESEV",
   "AESTDT",
   "..prop..",
@@ -29,17 +29,17 @@ utils::globalVariables(c(
   "value",
   "ymax",
   "ymin",
-  "stats", 
-  "as.dist", 
-  "cor", 
+  "stats",
+  "as.dist",
+  "cor",
   "hclust",
   "PopuExplor",
-  "AVAL", 
-  "AVISIT", 
-  "AVISITN", 
-  "CMDECOD", 
-  "CMSTDT", 
-  "DECODE", 
+  "AVAL",
+  "AVISIT",
+  "AVISITN",
+  "CMDECOD",
+  "CMSTDT",
+  "DECODE",
   "DOMAIN",
   "END",
   "EVENTTYP",
@@ -48,7 +48,7 @@ utils::globalVariables(c(
   "LBDY",
   "LBSTNRHI",
   "LBSTNRLO",
-  "MHCAT", 
+  "MHCAT",
   "MHDECOD",
   "MHENDTC",
   "MHSTDTC",
@@ -57,8 +57,8 @@ utils::globalVariables(c(
   "PARAMCD",
   "START",
   "USUBJID",
-  "VISIT", 
-  "Visit", 
+  "VISIT",
+  "Visit",
   "all_of",
   "className",
   "col_exist",
@@ -74,7 +74,7 @@ utils::globalVariables(c(
   "hcl",
   "min_lbdt",
   "missing_disp",
-  "not_exist", 
+  "not_exist",
   "not_exist_disp",
   "ord",
   "setNames",
@@ -113,20 +113,73 @@ utils::globalVariables(c(
   "adtte",
   "warn",
   "dy_min",
-  "AEACN", "AEACNOTH", "AREL", "CNSR", "FASFL", "ITTFL", "LOWER", "Lower", 
-  "MEAN", "Mean (SD)",
-  "Median", "Min | Max", "N", "PANEL", "Q1 | Q3", "SAFFL", "SEM", "STD",
-  "TRTEMFL", "UPPER", "Upper",
-  "Variable", "ae_data", "avals_by", "bds_data", "colour", "colour2",
-  "corr", "corr_lab",
-  "corr_lab_hover", "descr", "grp", "id_block", "id_desc", "id_rn",
-  "id_stat", "inner_sort",
-  "lab", "n_subgroups", "n_tot", "orig_id_rn", "orig_var_rn", "param_x",
-  "param_y", "pt", "pval",
-  "pval_hover", "sort_n", "v", "var", "var_rn", "where", "y",
-  "type", "title"
-  ,":=",
-  "DATE", "EVENT_TIME", "DATE_ST", "DECODE_ST", "DATE_EN", "DECODE_EN"
+  "AEACN",
+  "AEACNOTH",
+  "AREL",
+  "CNSR",
+  "FASFL",
+  "ITTFL",
+  "LOWER",
+  "Lower",
+  "MEAN",
+  "Mean (SD)",
+  "Median",
+  "Min | Max",
+  "N",
+  "PANEL",
+  "Q1 | Q3",
+  "SAFFL",
+  "SEM",
+  "STD",
+  "TRTEMFL",
+  "UPPER",
+  "Upper",
+  "Variable",
+  "ae_data",
+  "avals_by",
+  "bds_data",
+  "colour",
+  "colour2",
+  "corr",
+  "corr_lab",
+  "corr_lab_hover",
+  "descr",
+  "grp",
+  "id_block",
+  "id_desc",
+  "id_rn",
+  "id_stat",
+  "inner_sort",
+  "lab",
+  "n_subgroups",
+  "n_tot",
+  "orig_id_rn",
+  "orig_var_rn",
+  "param_x",
+  "param_y",
+  "pt",
+  "pval",
+  "pval_hover",
+  "sort_n",
+  "v",
+  "var",
+  "var_rn",
+  "where",
+  "y",
+  "type",
+  "title",
+  ":=",
+  "DATE",
+  "EVENT_TIME",
+  "DATE_ST",
+  "DECODE_ST",
+  "DATE_EN",
+  "DECODE_EN",
+  "time",
+  "est_ci",
+  "Strata",
+  "0.95LCL",
+  "0.95UCL",
+  "label",
+  "id"
 ))
-
-

R/mod_dataUpload.R

@@ -41,7 +41,8 @@ mod_dataUpload_ui <- function(id){
                div(style="display: inline-block; ",h3("Data upload")),
                div(style="display: inline-block; float:right;",mod_dataComplyRules_ui("dataComplyRules_ui_1")),
                HTML("<br>ADSL file is mandatory & BDS/ OCCDS files are optional"),
-               fileInput(ns("file"), "Upload sas7bdat files",accept = c(".sas7bdat"), multiple = TRUE),
+              #  fileInput(ns("file"), "Upload sas7bdat files",accept = c(".sas7bdat"), multiple = TRUE),
+              fileInput(ns("file"), "Upload datasets", accept = c(".txt", ".csv", ".xls", ".xlsx", ".sas7bdat"), multiple = TRUE),
                uiOutput(ns("radio_test"))
              )
       ),
@@ -91,18 +92,25 @@ mod_dataUpload_server <- function(input, output, session){
     data_list <- list()
 
     ## data list
-    for (i in 1:nrow(input$file)){
-      if(length(grep(".sas7bdat", input$file$name[i], ignore.case = TRUE)) > 0){
-        data_list[[i]] <- haven::zap_formats(haven::read_sas(input$file$datapath[i])) %>%
-          dplyr::mutate(dplyr::across(.cols = where(is.character),
-                               .fns = na_if, y = ""))
-      }else{
-        data_list[[i]] <- NULL
-      }
-    }
+    # for (i in 1:nrow(input$file)){
+    #   if(length(grep(".sas7bdat", input$file$name[i], ignore.case = TRUE)) > 0){
+    #     data_list[[i]] <- haven::zap_formats(haven::read_sas(input$file$datapath[i])) %>%
+    #       dplyr::mutate(dplyr::across(.cols = where(is.character),
+    #                            .fns = na_if, y = ""))
+    #   }else{
+    #     data_list[[i]] <- NULL
+    #   }
+    # }
+
+    data_list <- input$file$datapath |> 
+      purrr::map(\(x) {
+        read_data(x)
+      }) |> 
+      purrr::set_names(toupper(tools::file_path_sans_ext(input$file$name)))
+
 
     # names
-    names(data_list) <- toupper(stringr::str_remove(input$file$name, ".sas7bdat"))
+    # names(data_list) <- toupper(stringr::str_remove(input$file$name, ".sas7bdat"))
 
 
 
@@ -111,11 +119,19 @@ mod_dataUpload_server <- function(input, output, session){
                              id = NULL, #"dataComply_ui_1", 
                              datalist = reactive(data_list))
 
+    # if(length(names(dl_comply)) > 0){
+    #   # append to existing reactiveValues list
+    #   dd$data <-  c(dd$data, dl_comply) # dl_comply #
+
+    # }
     if(length(names(dl_comply)) > 0){
-      # append to existing reactiveValues list
-      dd$data <-  c(dd$data, dl_comply) # dl_comply #
+      # Normalize ADaM dataset names based on domain validation
+      dl_normalized <- normalize_adam_datasets(dl_comply)
 
+      # append to existing reactiveValues list
+      dd$data <-  c(dd$data, dl_normalized)
     }
+
 
     # set dd$current to FALSE for previous & TRUE for current uploads
     dd$current <- c(rep(FALSE, length(dd$current)), rep(TRUE, length(data_list)))