1 blockr update

DESCRIPTION

@@ -1,14 +1,18 @@
 Package: blockr.clinical.timelines
 Title: Clinical Timeline Block
-Version: 0.0.0.9000
+Version: 0.0.1.9000
 Authors@R: 
     c(
         person(family = "Bristol Myers Squibb",
            role = c("cph", "fnd")),
         person(given = "John",
            family = "Coene",
            role = c("aut", "cre"),
-           email = "[email protected]")
+           email = "[email protected]"),
+           person(given = "David",
+             family = "Granjon",
+             role = c("ctb"),
+             email = "[email protected]")
     )
 Description: Create clinical timeline blocks.
 License: GPL (>= 3)

NAMESPACE

@@ -1,9 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(evaluate_block,clinical_timeline_block)
 S3method(generate_server,clinical_timeline_block)
 S3method(server_output,clinical_timeline_block)
 S3method(uiOutputBlock,clinical_timeline_block)
-export(clinical_timeline_block)
-export(clinical_timeline_data_block)
+export(new_clinical_timeline_block)
+export(new_clinical_timeline_data_block)
 import(blockr)

NEWS.md

@@ -0,0 +1,12 @@
+# blockr.pharmaversesdtm 0.0.1.9000
+
+## Documentation
+- Updated readme example with new API.
+
+## Breaking changes
+- Change blocks constructor names to `new_*_block` according to `{blockr}` 0.0.2.
+- Remove `data` parameter from constructor functions.
+
+# blockr.clinical.timelines
+
+* Initial GitHub release.

R/core.R

@@ -1,46 +1,61 @@
-new_clinical_timeline_block <- function(data, ...) {
+#' Clinical timeline block
+#'
+#' Clinical timeline block
+#'
+#' @param ... Ignored.
+#'
+#' @import blockr
+#' @export
+new_clinical_timeline_block <- function(...) {
   all_cols <- function(data) colnames(data)
   usubjid_col <- function(data) {
     cols <- colnames(data)
 
-    if("USUBJID" %in% cols)
+    if ("USUBJID" %in% cols) {
       return("USUBJID")
+    }
 
-    if("SUBJID" %in% cols) 
+    if ("SUBJID" %in% cols) {
       return("SUBJID")
+    }
 
     cols[1]
   }
-  
+
   event_col <- function(data) {
     cols <- colnames(data)
 
-    if("DOMAIN" %in% cols) 
+    if ("DOMAIN" %in% cols) {
       return("DOMAIN")
+    }
 
     cols[1]
   }
 
   stdt_col <- function(data) {
     cols <- colnames(data)
 
-    if("STDT" %in% cols) 
+    if ("STDT" %in% cols) {
       return("STDT")
+    }
 
-    if("STDTC" %in% cols) 
+    if ("STDTC" %in% cols) {
       return("STDTC")
+    }
 
     cols[1]
   }
 
   endt_col <- function(data) {
     cols <- colnames(data)
 
-    if("ENDT" %in% cols) 
+    if ("ENDT" %in% cols) {
       return("ENDT")
+    }
 
-    if("ENDTC" %in% cols) 
+    if ("ENDTC" %in% cols) {
       return("ENDTC")
+    }
 
     cols[1]
   }
@@ -95,44 +110,23 @@ new_clinical_timeline_block <- function(data, ...) {
   )
 }
 
-#' Clinical timeline block
-#' 
-#' Clinical timeline block
-#' 
-#' @param data Dataset.
-#' @param ... Ignored.
-#' 
-#' @import blockr
-#' @export
-clinical_timeline_block <- function(data, ...){
-  blockr::initialize_block(new_clinical_timeline_block(data, ...), data)
-}
-
 #' @method server_output clinical_timeline_block
 #' @export
-server_output.clinical_timeline_block <- function (x, result, output) {
+server_output.clinical_timeline_block <- function(x, result, output) {
   clinical.timelines::renderClinical_timeline(result())
 }
 
 #' @method uiOutputBlock clinical_timeline_block
 #' @export
-uiOutputBlock.clinical_timeline_block <- function (x, ns) {
+uiOutputBlock.clinical_timeline_block <- function(x, ns) {
   shiny::div(
     style = "overflow-y:auto",
     clinical.timelines::clinical_timelineOutput(ns("res"), height = "70vh")
   )
 }
 
-#' @method evaluate_block clinical_timeline_block
-#' @export
-evaluate_block.clinical_timeline_block <- function (x, data, ...) {
-  stopifnot(...length() == 0L)
-  eval(substitute(data %>% expr, list(expr = blockr::generate_code(x))), 
-      list(data = data))
-}
-
 #' @method generate_server clinical_timeline_block
 #' @export
-generate_server.clinical_timeline_block <- function (...) {
+generate_server.clinical_timeline_block <- function(...) {
   blockr:::generate_server_block(...)
 }

R/data.R

@@ -1,43 +1,41 @@
 #' Clinical Timeline Data Block
-#' 
+#'
 #' This data block is used to create a clinical timeline data frame from the ADaM data sets.
-#' 
+#'
 #' @param ... Ignored.
-#' 
+#'
 #' @export
-clinical_timeline_data_block <- function(...){
+new_clinical_timeline_data_block <- function(...) {
   blockr::new_block(
     fields = list(),
     expr = quote({
-      build <- function(
-          adex = pharmaverseadam::adex, 
-          adcm = pharmaverseadam::adcm, 
-          adae = pharmaverseadam::adae
-      ){
+      build <- function(adex = pharmaverseadam::adex,
+                        adcm = pharmaverseadam::adcm,
+                        adae = pharmaverseadam::adae) {
+        cm <- adcm |>
+          dplyr::select(SUBJID, SITEID, CMSTDY, CMENDY, CMSTDTC, CMENDTC, CMDECOD, CMSEQ) |>
+          dplyr::rename(STDY = CMSTDY, ENDY = CMENDY, STDTC = CMSTDTC, ENDTC = CMENDTC, SEQ = CMSEQ, DECOD = CMDECOD) |>
+          dplyr::mutate(DOMAIN = "Concomitant Medications")
 
-        cm <- adcm |> 
-          dplyr::select(SUBJID, SITEID, CMSTDY, CMENDY, CMSTDTC, CMENDTC, CMDECOD, CMSEQ) |>  
-          dplyr::rename(STDY = CMSTDY, ENDY = CMENDY, STDTC = CMSTDTC, ENDTC = CMENDTC, SEQ = CMSEQ, DECOD = CMDECOD) |> 
-          dplyr::mutate(DOMAIN = "Concomitant Medications") 
+        ae <- adae |>
+          dplyr::select(SUBJID, SITEID, AESTDY, AEENDY, AESTDTC, AEENDTC, AEDECOD, AESEQ) |>
+          dplyr::rename(STDY = AESTDY, ENDY = AEENDY, STDTC = AESTDTC, ENDTC = AEENDTC, SEQ = AESEQ, DECOD = AEDECOD) |>
+          dplyr::mutate(DOMAIN = "Adverse Events")
 
-        ae <- adae |> 
-          dplyr::select(SUBJID, SITEID, AESTDY, AEENDY, AESTDTC, AEENDTC, AEDECOD, AESEQ) |>  
-          dplyr::rename(STDY = AESTDY, ENDY = AEENDY, STDTC = AESTDTC, ENDTC = AEENDTC, SEQ = AESEQ, DECOD = AEDECOD) |>  
-          dplyr::mutate(DOMAIN = "Adverse Events") 
-
-        ex <- adex |> 
-          dplyr::select(SUBJID, SITEID, EXSTDY, EXENDY, EXSTDTC, EXENDTC, EXDOSE, EXDOSU, EXDOSFRQ, EXSEQ) |>  
+        ex <- adex |>
+          dplyr::select(SUBJID, SITEID, EXSTDY, EXENDY, EXSTDTC, EXENDTC, EXDOSE, EXDOSU, EXDOSFRQ, EXSEQ) |>
           dplyr::mutate(DOMAIN = "Exposure", EXDECOD = paste(EXDOSE, EXDOSU, EXDOSFRQ)) |>
           dplyr::rename(STDY = EXSTDY, ENDY = EXENDY, STDTC = EXSTDTC, ENDTC = EXENDTC, SEQ = EXSEQ, DECOD = EXDECOD)
 
-        dplyr::bind_rows(ex, ae, cm) |> 
-          dplyr::select(DOMAIN, SITEID,  SUBJID, SEQ, STDY, ENDY, STDTC, ENDTC, DECOD) |> 
-          dplyr::arrange(DOMAIN, SUBJID, SEQ, STDY) |> 
+        dplyr::bind_rows(ex, ae, cm) |>
+          dplyr::select(DOMAIN, SITEID, SUBJID, SEQ, STDY, ENDY, STDTC, ENDTC, DECOD) |>
+          dplyr::arrange(DOMAIN, SUBJID, SEQ, STDY) |>
           dplyr::filter(!is.na(STDY), !is.na(ENDY))
       }
 
       build()
     }),
+    ...,
     class = c("clinical_timeline_data_block", "data_block")
   )
 }

R/zzz.R

@@ -1,6 +1,6 @@
 .onLoad <- \(...){
   blockr::register_block(
-    clinical_timeline_block,
+    new_clinical_timeline_block,
     "Clinical timeline",
     "Visualise events over time",
     input = "data.frame",
@@ -10,7 +10,7 @@
   )
 
   blockr::register_block(
-    clinical_timeline_data_block,
+    new_clinical_timeline_data_block,
     "Clinical timeline data",
     "Prepare data for clinical timeline visualisation",
     input = NA_character_,

README.md

@@ -15,24 +15,14 @@ remotes::install_github("blockr-org/blockr.clinical.timelines")
 ## Example
 
 ``` r
-library(shiny)
 library(blockr)
 library(blockr.clinical.timelines)
 
 stack <- blockr::new_stack(
-  clinical_timeline_data_block,
-  clinical_timeline_block
+  new_clinical_timeline_data_block,
+  new_clinical_timeline_block
 )
 
-ui <- fluidPage(
-  theme = bslib::bs_theme(5L),
-  generate_ui(stack)
-)
-
-server <- function(input, output, session) {
-  generate_server(stack)
-}
-
-shinyApp(ui, server)
+serve_stack(stack)
 ```