From 873d2b6f4159e5ecc17253f851c8019136b9b5b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 19 Sep 2023 16:14:11 +0200
Subject: [PATCH] Patient Profile Modules only show relevant datanames (#828)

# Pull Request

- Fixes #821

### How to test

Use
[`patient-profile`](https://github.com/insightsengineering/teal.gallery/blob/main/patient-profile/app.R)
app from `teal.gallery`, or the code below.

Note: the code below that adds 2 `tm_t_summary` modules to
patient-profile _(the 2nd doesn't use `dataname = "ADSL"` to show that
`ADSL` is added as `parentname`)_

<details>

<summary>See to code</summary>

```R
pkgload::load_all()
library(teal.modules.clinical)
library(teal.modules.general)
library(scda)
library(scda.2022)
library(nestcolor)

options(shiny.useragg = FALSE)

nest_logo <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png"

ADSL <- synthetic_cdisc_data("latest")$adsl
ADMH <- synthetic_cdisc_data("latest")$admh
ADAE <- synthetic_cdisc_data("latest")$adae
ADCM <- synthetic_cdisc_data("latest")$adcm
ADVS <- synthetic_cdisc_data("latest")$advs
ADLB <- synthetic_cdisc_data("latest")$adlb

## Modify ADCM
ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
ADCM$CMDOSE <- 1
ADCM$CMTRT <- ADCM$CMCAT
ADCM$CMDOSU <- "U"
ADCM$CMROUTE <- "CMROUTE"
ADCM$CMDOSFRQ <- "CMDOSFRQ"
ADCM$CMASTDTM <- ADCM$ASTDTM
ADCM$CMAENDTM <- ADCM$AENDTM

teal.data::col_labels(
  ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]
) <- c(
  "Indication",
  "Reported Name of Drug, Med, or Therapy",
  "Study Day of Start of Medication",
  "Study Day of End of Medication"
)

## Modify ADHM
ADMH[["MHDISTAT"]] <- "ONGOING"
teal.data::col_labels(ADMH[c("MHDISTAT")]) <- c("Status of Disease")

## Define variable inputs
aeterm_input <- data_extract_spec(
  dataname = "ADAE",
  select = select_spec(
    choices = variable_choices(ADAE, "AETERM"),
    selected = c("AETERM"),
    multiple = FALSE,
    fixed = FALSE
  )
)

cmtrt_input <- data_extract_spec(
  dataname = "ADCM",
  select = select_spec(
    choices = variable_choices(ADCM, "CMTRT"),
    selected = c("CMTRT"),
    multiple = FALSE,
    fixed = FALSE
  )
)

cmindc_input <- data_extract_spec(
  dataname = "ADCM",
  select = select_spec(
    choices = variable_choices(ADCM, "CMINDC"),
    selected = c("CMINDC"),
    multiple = FALSE,
    fixed = FALSE
  )
)

atirel_input <- data_extract_spec(
  dataname = "ADCM",
  select = select_spec(
    choices = variable_choices(ADCM, "ATIREL"),
    selected = c("ATIREL"),
    multiple = FALSE,
    fixed = FALSE
  )
)

cmdecod_input <- data_extract_spec(
  dataname = "ADCM",
  select = select_spec(
    choices = variable_choices(ADCM, "CMDECOD"),
    selected = c("CMDECOD"),
    multiple = FALSE,
    fixed = FALSE
  )
)

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
    cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae"),
    cdisc_dataset("ADMH", ADMH, code = "ADMH <- synthetic_cdisc_data(\"latest\")$admh
      ADMH[['MHDISTAT']] <- 'ONGOING'
      teal.data::col_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')"),
    cdisc_dataset("ADCM", ADCM, code = 'ADCM <- synthetic_cdisc_data(\"latest\")$adcm
      ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
      ADCM$CMDOSE <- 1
      ADCM$CMTRT <- ADCM$CMCAT
      ADCM$CMDOSU <- "U"
      ADCM$CMROUTE <- "CMROUTE"
      ADCM$CMDOSFRQ <- "CMDOSFRQ"
      ADCM$CMASTDTM <- ADCM$ASTDTM
      ADCM$CMAENDTM <- ADCM$AENDTM
      teal.data::col_labels(
        ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c(
          "Indication",
          "Reported Name of Drug, Med, or Therapy",
          "Study Day of Start of Medication",
          "Study Day of End of Medication")'),
    cdisc_dataset("ADVS", ADVS, code = "ADVS <- synthetic_cdisc_data(\"latest\")$advs"),
    cdisc_dataset("ADLB", ADLB, code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb"),
    check = TRUE
  ),
  filter = teal_slices(
    count_type = "all",
    teal_slice(dataname = "ADSL", varname = "SEX"),
    teal_slice(dataname = "ADSL", varname = "AGE")
  ),
  modules = modules(
    tm_front_page(
      label = "App Info",
      header_text = c("Info about input data source" = "This app uses CDISC ADaM datasets randomly generated by `scda` & `scda.2022` R packages"),
      tables = list(`NEST packages used in this demo app` = data.frame(Packages = c("teal.modules.general", "teal.modules.clinical", "scda", "scda.2022")))
    ),
    tm_t_summary(
      label = "Demographic Table",
      dataname = "ADSL",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      add_total = TRUE,
      summarize_vars = choices_selected(
        c("SEX", "RACE", "BMRKR2", "EOSDY", "DCSREAS", "AGE"),
        c("SEX", "RACE")
      ),
      useNA = "ifany"
    ),
    tm_t_summary(
      label = "Demographic Table (2)",
      dataname = "ADMH",
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
      add_total = TRUE,
      summarize_vars = choices_selected(
        c("SEX", "RACE", "BMRKR2", "EOSDY", "DCSREAS", "AGE"),
        c("SEX", "RACE")
      ),
      useNA = "ifany"
    ),
    tm_t_pp_basic_info(
      label = "Basic info",
      dataname = "ADSL",
      patient_col = "USUBJID",
      vars = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(ADSL),
          selected = c("ARM", "AGE", "SEX", "COUNTRY", "RACE", "EOSSTT"),
          multiple = TRUE,
          fixed = FALSE
        )
      )
    ),
    tm_t_pp_medical_history(
      label = "Medical history",
      parentname = "ADSL",
      patient_col = "USUBJID",
      mhterm = data_extract_spec(
        dataname = "ADMH",
        select = select_spec(
          choices = variable_choices(ADMH, c("MHTERM")),
          selected = c("MHTERM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      mhbodsys = data_extract_spec(
        dataname = "ADMH",
        select = select_spec(
          choices = variable_choices(ADMH, "MHBODSYS"),
          selected = c("MHBODSYS"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      mhdistat = data_extract_spec(
        dataname = "ADMH",
        select = select_spec(
          choices = variable_choices(ADMH, "MHDISTAT"),
          selected = c("MHDISTAT"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_t_pp_prior_medication(
      label = "Prior medication",
      parentname = "ADSL",
      patient_col = "USUBJID",
      atirel = atirel_input,
      cmdecod = cmdecod_input,
      cmindc = cmindc_input,
      cmstdy = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "ASTDY"),
          selected = c("ASTDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_g_pp_vitals(
      label = "Vitals",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      paramcd = data_extract_spec(
        dataname = "ADVS",
        select = select_spec(
          choices = variable_choices(ADVS, "PARAMCD"),
          selected = c("PARAMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      xaxis = data_extract_spec(
        dataname = "ADVS",
        select = select_spec(
          choices = variable_choices(ADVS, "ADY"),
          selected = c("ADY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      aval = data_extract_spec(
        dataname = "ADVS",
        select = select_spec(
          choices = variable_choices(ADVS, "AVAL"),
          selected = c("AVAL"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_g_pp_therapy(
      label = "Therapy",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = atirel_input,
      cmdecod = cmdecod_input,
      cmindc = cmindc_input,
      cmdose = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMDOSE"),
          selected = c("CMDOSE"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      cmtrt = cmtrt_input,
      cmdosu = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMDOSU"),
          selected = c("CMDOSU"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      cmroute = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMROUTE"),
          selected = c("CMROUTE"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      cmdosfrq = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMDOSFRQ"),
          selected = c("CMDOSFRQ"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      cmstdy = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "ASTDY"),
          selected = c("ASTDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      cmendy = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "AENDY"),
          selected = c("AENDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_g_pp_adverse_events(
      label = "Adverse events",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      aeterm = aeterm_input,
      tox_grade = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AETOXGR"),
          selected = c("AETOXGR"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      causality = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AEREL"),
          selected = c("AEREL"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      outcome = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AEOUT"),
          selected = c("AEOUT"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      action = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AEACN"),
          selected = c("AEACN"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      time = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "ASTDY"),
          selected = c("ASTDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      decod = NULL
    ),
    tm_t_pp_laboratory(
      label = "Lab values",
      parentname = "ADSL",
      patient_col = "USUBJID",
      paramcd = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "PARAMCD"),
          selected = c("PARAMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      param = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "PARAM"),
          selected = c("PARAM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      timepoints = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "ADY"),
          selected = c("ADY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      anrind = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "ANRIND"),
          selected = c("ANRIND"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      aval = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "AVAL"),
          selected = c("AVAL"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      avalu = data_extract_spec(
        dataname = "ADLB",
        select = select_spec(
          choices = variable_choices(ADLB, "AVALU"),
          selected = c("AVALU"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    ),
    tm_g_pp_patient_timeline(
      label = "Patient timeline",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      font_size = c(15L, 8L, 25L),
      cmdecod = cmdecod_input,
      aeterm = aeterm_input,
      aetime_start = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "ASTDTM"),
          selected = c("ASTDTM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      aetime_end = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AENDTM"),
          selected = c("AENDTM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      dstime_start = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMASTDTM"),
          selected = c("CMASTDTM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      dstime_end = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "CMAENDTM"),
          selected = c("CMAENDTM"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      aerelday_start = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "ASTDY"),
          selected = c("ASTDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      aerelday_end = data_extract_spec(
        dataname = "ADAE",
        select = select_spec(
          choices = variable_choices(ADAE, "AENDY"),
          selected = c("AENDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      dsrelday_start = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "ASTDY"),
          selected = c("ASTDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      dsrelday_end = data_extract_spec(
        dataname = "ADCM",
        select = select_spec(
          choices = variable_choices(ADCM, "AENDY"),
          selected = c("AENDY"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  ),
  header = tags$span(
    style = "display: flex; align-items: center; justify-content: space-between; margin: 10px 0 10px 0;",
    tags$head(tags$link(rel = "shortcut icon", href = nest_logo), tags$title("Patient Profile Analysis Teal Demo App")),
    tags$span(
      style = "font-size: 30px;",
      "Example teal app focusing on patient-level analysis of clinical trial data with teal.modules.clinical"
    ),
    tags$span(
      style = "display: flex; align-items: center;",
      tags$img(src = nest_logo, alt = "NEST logo", height = "45px", style = "margin-right:10px;"),
      tags$span(style = "font-size: 24px;", "NEST @ Roche")
    )
  ),
  footer = tags$p(
    actionLink("showAboutModal", "About,"),
    tags$a(
      href = "https://github.com/insightsengineering/teal.gallery/tree/main/patient-profile",
      target = "_blank",
      "Source Code,"
    ),
    tags$a(
      href = "https://github.com/insightsengineering/teal.gallery/issues",
      target = "_blank",
      "Report Issues"
    )
  )
)

body(app$server)[[length(body(app$server)) + 1]] <- quote(
  observeEvent(input$showAboutModal, {
    showModal(modalDialog(
      tags$p("This teal app is brought to you by the NEST Team at Roche/Genentech. For more information, please visit:"),
      tags$ul(
        tags$li(tags$a(
          href = "https://github.com/insightsengineering", "Insights Engineering",
          target = "blank"
        )),
        tags$li(tags$a(
          href = "https://pharmaverse.org", "Pharmaverse",
          target = "blank"
        ))
      ),
      easyClose = TRUE
    ))
  })
)

shinyApp(app$ui, app$server)
```

</details>

### Changes description

With the exception of `tm_t_summary`, only patient_profile modules were
modified.

- Change to `datanames = c(dataname)`
  - `tm_t_pp_basic_info`

- Change to `datanames = c(dataname_adcm, dataname_adae, parentname)`
  - `tm_g_pp_patient_timeline`

* Change to `datanames = c(dataname, parentname)`
  * `tm_g_pp_adverse_events`
  * `tm_g_pp_therapy`
  * `tm_g_pp_vitals`
  * `tm_t_pp_laboratory`
  * `tm_t_pp_medical_history`
  * `tm_t_pp_prior_medication`
  * `tm_t_summary`
* Special case, as `parentname` server parameter is used on
`data_extract_list`, but was not used in `module()` call
---
 NEWS.md                      | 1 +
 R/tm_g_pp_adverse_events.R   | 2 +-
 R/tm_g_pp_patient_timeline.R | 2 +-
 R/tm_g_pp_therapy.R          | 2 +-
 R/tm_g_pp_vitals.R           | 2 +-
 R/tm_t_pp_basic_info.R       | 2 +-
 R/tm_t_pp_laboratory.R       | 2 +-
 R/tm_t_pp_medical_history.R  | 2 +-
 R/tm_t_pp_prior_medication.R | 2 +-
 R/tm_t_summary.R             | 2 +-
 10 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 0d79db3369..1fe479c543 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -10,6 +10,7 @@
 
 ### Miscellaneous
 * Updated `control_incidence_rate` parameter names in `tm_t_events_patyear` from `time_unit_input` and `time_unit_output` to `input_time_unit` and `num_pt_year`, respectively, after parameter names were changed in `tern`.
+* Hid the datasets that were not being used by the _patient profile_ modules in the filter panel. Replaced the `datanames = "all"` parameter with the datasets used internally by the module.
 
 # teal.modules.clinical 0.8.15
 
diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
index eaba9e7e9d..59d3cd1b43 100644
--- a/R/tm_g_pp_adverse_events.R
+++ b/R/tm_g_pp_adverse_events.R
@@ -292,7 +292,7 @@ tm_g_pp_adverse_events <- function(label,
         ggplot2_args = ggplot2_args
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
index 35d1926b30..19c558204a 100644
--- a/R/tm_g_pp_patient_timeline.R
+++ b/R/tm_g_pp_patient_timeline.R
@@ -511,7 +511,7 @@ tm_g_pp_patient_timeline <- function(label,
         ggplot2_args = ggplot2_args
       )
     ),
-    datanames = "all"
+    datanames = c(dataname_adcm, dataname_adae, parentname)
   )
 }
 
diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
index 72a1197954..c5356c8be4 100644
--- a/R/tm_g_pp_therapy.R
+++ b/R/tm_g_pp_therapy.R
@@ -389,7 +389,7 @@ tm_g_pp_therapy <- function(label,
         ggplot2_args = ggplot2_args
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
index cdf538ba10..1b91b4b3b8 100644
--- a/R/tm_g_pp_vitals.R
+++ b/R/tm_g_pp_vitals.R
@@ -283,7 +283,7 @@ tm_g_pp_vitals <- function(label,
         ggplot2_args = ggplot2_args
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_t_pp_basic_info.R b/R/tm_t_pp_basic_info.R
index 8ef6386c7d..f535393aea 100644
--- a/R/tm_t_pp_basic_info.R
+++ b/R/tm_t_pp_basic_info.R
@@ -108,7 +108,7 @@ tm_t_pp_basic_info <- function(label,
         patient_col = patient_col
       )
     ),
-    datanames = "all"
+    datanames = dataname
   )
 }
 
diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R
index 919c80c275..84b961e776 100644
--- a/R/tm_t_pp_laboratory.R
+++ b/R/tm_t_pp_laboratory.R
@@ -196,7 +196,7 @@ tm_t_pp_laboratory <- function(label,
         patient_col = patient_col
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R
index 6d95738ba6..f77bd6f17e 100644
--- a/R/tm_t_pp_medical_history.R
+++ b/R/tm_t_pp_medical_history.R
@@ -155,7 +155,7 @@ tm_t_pp_medical_history <- function(label,
         patient_col = patient_col
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R
index ccd4e5dd15..4d3c2ab862 100644
--- a/R/tm_t_pp_prior_medication.R
+++ b/R/tm_t_pp_prior_medication.R
@@ -152,7 +152,7 @@ tm_t_pp_prior_medication <- function(label,
         patient_col = patient_col
       )
     ),
-    datanames = "all"
+    datanames = c(dataname, parentname)
   )
 }
 
diff --git a/R/tm_t_summary.R b/R/tm_t_summary.R
index 8971dbc126..191a9a57aa 100644
--- a/R/tm_t_summary.R
+++ b/R/tm_t_summary.R
@@ -317,7 +317,7 @@ tm_t_summary <- function(label,
         basic_table_args = basic_table_args
       )
     ),
-    datanames = dataname
+    datanames = c(dataname, parentname)
   )
 }