Merge pull request #16 from mbranca/main

Pending changes
CTU-Bern · Dec 20, 2024 · 94581c7 · 94581c7
2 parents b83ae81 + e5e0d86
commit 94581c7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SwissASR
 Title: Automated Completion of the SwissEthics Annual Safety Report
-Version: 0.5.2
+Version: 0.5.3
 Authors@R: 
     c(person(given = "Alan G.",
            family = "Haynes",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# SwissASR 0.5.3
+
+* Last updates to align with the latest template and add a warning for special characters causing a problem in producing the Word report from R. 
+
 # SwissASR 0.5.2
 
 * Correction of template inputs, dates formatting and additional note for SAEs tables. 

diff --git a/R/asr.R b/R/asr.R
@@ -58,6 +58,7 @@
 #' @param var_relation variable containing the relationship to randomized intervention
 #' @param var_expected variable saying whether the SAE was expected
 #' @param var_devdef variable containing whether the SAE is a device deficiency
+#' @param var_devdefcouldlead variable containing whether the device deficiency could have lead to an SAE
 #' @param var_devattr variable containing whether the SAE is attributable to the device
 #' @param var_devint variable containing whether the SAE is attributable to an intervention in the trial
 #' @param var_safetymeasure variable containing whether the SAE required safety related measures
@@ -78,58 +79,6 @@
 #' file <- tempfile("asr", fileext = ".docx")
 #' asr(asr_sae, file)
 #'
-#' # # more usual use will require passing more information:
-#' # asr(asr_sae, file,
-#' #     # trial info
-#' #     trial_title = "Example Trial Name",
-#' #     protocol_number = "20221002130",
-#' #     basec_number = "",
-#' #     snctp_number = "202200458",
-#' #     swissmedic_number = "....",
-#' #     ec_name = "Kantonale Ethikskommision Bern",
-#' #     tr_number = "",
-#' #     product_name = "Drug name",
-#' #     international = FALSE,
-#' #     trial_type = "imp",
-#' #     # Sponsor info
-#' #     sponsor_contact = "Sponsor name, Sponsor phone number, Sponsor email",
-#' #     inst_name_address = "Institute name, Institute address",
-#' #     # site info
-#' #     n_centers_t = 20,        # total number
-#' #     n_centers_p = "default", # planned
-#' #     n_centers_c = "default", # closed
-#' #     n_centers_o = "default", # open
-#' #     # participant info
-#' #     n_pat_t = 1000,          # target
-#' #     n_pat_e = 300,           # enrolled
-#' #     n_pat_c = 0,             # complete
-#' #     n_pat_p = 0,             # prematurely terminated
-#' #     # report info
-#' #     report_date = format(Sys.Date(), format = "%d/%m/%Y"),
-#' #     period_from = as.Date("2020-11-02"),
-#' #     period_to = as.Date("2020-11-17"),
-#' #     # variable mapping
-#' #     var_class = "class",
-#' #     var_sae_n = "sae_n", #sae ID
-#' #     var_part_id = "record_id", #participant ID
-#' #     var_age = "age",
-#' #     var_sex ="sex",
-#' #     var_country = "country",
-#' #     var_site = "site",
-#' #     var_sae = "sae",
-#' #     var_date_onset = "sae_date",
-#' #     var_trt = "trt",
-#' #     var_date_trt_start = "sae_trtstart",
-#' #     var_date_trt_stop = "sae_trtstop",
-#' #     var_outcome = "outcome",
-#' #     var_comment = "comment",
-#' #     var_relation = "related",
-#' #     var_expected = "expected",
-#' #     var_safetymeasure = "safetymeasure"
-#' #     )
-#'
-#'
-#'
 
 asr <- function(data,
                 target = "tmp.docx",
@@ -184,6 +133,7 @@ asr <- function(data,
                 , var_relation = "related"
                 , var_expected = "expected"
                 , var_devdef = "devdef"
+                , var_devdefcouldlead = "devdefcouldlead"
                 , var_devattr = "devattr"
                 , var_devint = "devint"
                 , var_safetymeasure = "safetymeasure"
@@ -236,11 +186,12 @@ asr <- function(data,
   # if(trial_type == "medical device"){
   #   names(data)[names(data) == var_expected] <- "expected"
   #   names(data)[names(data) == var_devdef] <- "devdef"
+  #   names(data)[names(data) == var_devdefcouldlead] <- "devdefcouldlead"
   #   names(data)[names(data) == var_devattr] <- "devattr"
   #   names(data)[names(data) == var_devint] <- "devint"
   #   names(data)[names(data) == var_safetymeasure] <- "safetymeasure"
   #
-  #   vars <- c("expected", "devdef", "devattr", "devint", "safetymeasure")
+  #   vars <- c("expected", "devdef", "devdefcouldlead","devattr", "devint", "safetymeasure")
   #   if(!all(vars %in% names(data))){
   #     stop(paste(vars[!vars %in% names(data)], collapse = ", "), " not found in data")
   #   }
@@ -320,6 +271,23 @@ asr <- function(data,
 #   data$trt <- as.character(data$trt)
 #
 
+# Check in the text inputs if any detected special character causing problems is present
+  for(string in c("trial_title",
+             "protocol_number",
+             "basec_number",
+             "snctp_number",
+             "swissmedic_number",
+             "ec_name",
+             "tr_number",
+             "product_name",
+             "sponsor_contact",
+             "inst_name_address")){
+    check_field_characters(get(string)) }
+
+# This check is for the arm names in case these are available and requested
+  if(!is.null(n_per_arm)){lapply(names(n_per_arm),check_field_characters)}
+
+
   dfs <- asr_dataprep(data,
                       period_from = period_from,
                       period_to = period_to
@@ -341,6 +309,7 @@ asr <- function(data,
                       , var_relation = var_relation
                       , var_expected = var_expected
                       , var_devdef = var_devdef
+                      , var_devdefcouldlead = var_devdefcouldlead
                       , var_devattr = var_devattr
                       , var_devint = var_devint
                       , var_safetymeasure = var_safetymeasure
@@ -353,63 +322,33 @@ asr <- function(data,
   # report itself ----
   doc <- read_docx(template)
 
-
-
-  # ..general info, details of trial ----
-  #
-  # for(i in c("trial_title",
-  #            "protocol_number",
-  #            "basec_number",
-  #            "snctp_number",
-  #            "swissmedic_number",
-  #            "ec_name",
-  #            "tr_number",
-  #            "product_name",
-  #            "sponsor_contact",
-  #            "inst_name_address",
-  #            "report_date",
-  #            "period",
-  #            "n_centers_t",
-  #            "n_centers_p",
-  #            "n_centers_c",
-  #            "n_centers_o",
-  #            "n_pat_t",
-  #            "n_pat_e",
-  #            "n_pat_c",
-  #            "n_pat_p")){
-  #   x <- get(i)
-  #   doc <- doc %>%
-  #     cursor_bookmark(i) %>%
-  #     body_add_par(x, pos = "after")
-  # }
-
   # format the dates for the text
   period_from_f <- format(period_from, format = "%d/%m/%Y")
   period_to_f <- format(period_to, format = "%d/%m/%Y")
 
   period <- glue("{period_from_f} to {period_to_f}")
 ## New code to insert the fields instead of bookmarks
     doc <- doc %>%
-      set_doc_properties(trial_title = get("trial_title"),
-                                  protocol_number = get("protocol_number"),
-                                  basec_number = get("basec_number"),
-                                  snctp_number = get("snctp_number"),
-                                  swissmedic_number = get("swissmedic_number"),
-                                  ec_name = get("ec_name"),
-                                  tr_number = get("tr_number"),
-                                  product_name = get("product_name"),
-                                  sponsor_contact = get("sponsor_contact"),
-                                  inst_name_address = get("inst_name_address"),
-                                  report_date = get("report_date"),
-                                  period = get("period"),
-                                  n_centers_t = as.character(get("n_centers_t")),
-                                  n_centers_p = as.character(get("n_centers_p")),
-                                  n_centers_c = as.character(get("n_centers_c")),
-                                  n_centers_o = as.character(get("n_centers_o")),
-                                  n_centers_t_ch = as.character(get("n_centers_t_ch")),
-                                  n_centers_p_ch = as.character(get("n_centers_p_ch")),
-                                  n_centers_c_ch = as.character(get("n_centers_c_ch")),
-                                  n_centers_o_ch = as.character(get("n_centers_o_ch")),
+      set_doc_properties(trial_title = "trial_title",
+                                  protocol_number = "protocol_number",
+                                  basec_number = "basec_number",
+                                  snctp_number = "snctp_number",
+                                  swissmedic_number = "swissmedic_number",
+                                  ec_name = "ec_name",
+                                  tr_number = "tr_number",
+                                  product_name = "product_name",
+                                  sponsor_contact = "sponsor_contact",
+                                  inst_name_address = "inst_name_address",
+                                  report_date = "report_date",
+                                  period = "period",
+                                  n_centers_t = as.character(n_centers_t),
+                                  n_centers_p = as.character(n_centers_p),
+                                  n_centers_c = as.character(n_centers_c),
+                                  n_centers_o = as.character(n_centers_o),
+                                  n_centers_t_ch = as.character(n_centers_t_ch),
+                                  n_centers_p_ch = as.character(n_centers_p_ch),
+                                  n_centers_c_ch = as.character(n_centers_c_ch),
+                                  n_centers_o_ch = as.character(n_centers_o_ch),
                                   n_pat_t = as.character(n_pat_t),
                                   n_pat_e = as.character(n_pat_e),
                                   n_pat_c = as.character(n_pat_c),
@@ -427,13 +366,6 @@ asr <- function(data,
                              n_pat_e = n_pat_e,
                              n_per_arm = n_per_arm)
 
-  # doc <- doc %>%
-  #   cursor_bookmark("partsafety_text")
-  # for(i in 1:length(summ$txt)){
-  #   txt <- summ$txt[i]
-  #   doc <- doc %>% body_add_par(txt, style = "Text")
-  # }
-
   doc <- doc %>%
     officer::set_doc_properties(partsafety_text = paste0(summ$txt, collapse = " ") )
 
@@ -498,7 +430,7 @@ asr <- function(data,
   }
   llist_ft <- flextable(llist) %>%
     #add_header_lines("Line listing of SAEs, SADRs and SUSARs, including international cases
-#(code and version of used standard (e.g. MedDRA or CTCAE) should be indicated, details on SUSARs will be attached as appendices)") %>%
+    #(code and version of used standard (e.g. MedDRA or CTCAE) should be indicated, details on SUSARs will be attached as appendices)") %>%
     border(border = fp_border(color = "#4FB4E0"), part="all") %>%
     fontsize(size = 8, part = "all") %>%
     font(fontname = "Helvetica", part = "all")
@@ -517,10 +449,3 @@ asr <- function(data,
   docx_update(input = target)
 
 }
-
-
-
-
-
-
-
diff --git a/R/asr_dataprep.R b/R/asr_dataprep.R
@@ -63,8 +63,8 @@
 #     class = msample(c("SAE", "SUSAR", "SADR")),
 #     expected = msample(c(TRUE, FALSE)),
 #     devdef = msample(c(TRUE, FALSE)),
+#     devdefcouldlead = msample(c(TRUE, FALSE)),
 #     devattr = msample(c(TRUE, FALSE)),
-#     devdef = msample(c(TRUE, FALSE)),
 #     devint = msample(c(TRUE, FALSE)),
 #     safetymeasure = msample(c(TRUE, FALSE))
 # )
@@ -129,6 +129,7 @@ asr_dataprep <- function(data
                          , var_relation = "related"
                          , var_expected = "expected"
                          , var_devdef = "devdef"
+                         , var_devdefcouldlead = "devdefcouldlead"
                          , var_devattr = "devattr"
                          , var_devint = "devint"
                          , var_safetymeasure = "safetymeasure"
@@ -182,6 +183,8 @@ asr_dataprep <- function(data
   names(data)[names(data) == var_trt] <- "trt"
   if(tx_var){
     names(data)[names(data) == var_tx] <- "intervention"
+  }else{
+    data <- data[,!names(data) %in% "intervention"]
   }
 
   ## relevant variables exist
@@ -205,11 +208,12 @@ asr_dataprep <- function(data
   if(trial_type == "medical device"){
     names(data)[names(data) == var_expected] <- "expected"
     names(data)[names(data) == var_devdef] <- "devdef"
+    names(data)[names(data) == var_devdefcouldlead] <- "devdefcouldlead"
     names(data)[names(data) == var_devattr] <- "devattr"
     names(data)[names(data) == var_devint] <- "devint"
     names(data)[names(data) == var_safetymeasure] <- "safetymeasure"
 
-    vars <- c("expected", "devdef", "devattr", "devint", "safetymeasure")
+    vars <- c("expected", "devdef", "devdefcouldlead","devattr", "devint", "safetymeasure")
     if(!all(vars %in% names(data))){
       stop(paste(vars[!vars %in% names(data)], collapse = ", "), " not found in data")
     }