From c325d745f801ca7d724b91302963919431042b46 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 31 Jul 2024 23:31:21 +0000 Subject: [PATCH] Built site for sdtm.oak: 0.1.0@453926b --- articles/events_domain.html | 52 +++++++++++++++++------------------ articles/findings_domain.html | 28 +++++++++---------- pkgdown.yml | 2 +- 3 files changed, 41 insertions(+), 41 deletions(-) diff --git a/articles/events_domain.html b/articles/events_domain.html index a2287ff8..83024621 100644 --- a/articles/events_domain.html +++ b/articles/events_domain.html @@ -120,8 +120,8 @@

Raw data

The raw dataset is presented below:

-
- +
+

Programming workflow @@ -190,8 +190,8 @@

Create oak_id_vars pat_var = "PATNUM", raw_src = "cm_raw" )

-
-

Read in the DM domain

+
+

Read in the DM domain

 dm <- read.csv(system.file("raw_data/dm.csv",
   package = "sdtm.oak"
@@ -208,8 +208,8 @@ 
Read in CT<
 study_ct <- read.csv(system.file("raw_data/sdtm_ct.csv",
   package = "sdtm.oak"
 ))
-
- +
+

Map Topic Variable @@ -232,8 +232,8 @@

Map Topic Variable= "MDRAW", tgt_var = "CMTRT" )

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- +
+

Map Rest of the Variables @@ -255,8 +255,8 @@

assign_no_ct= "CMGRPID", id_vars = oak_id_vars() )

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-

The CMGRPID is added to the corresponding CMTRT based on the +

+

The CMGRPID is added to the corresponding CMTRT based on the ‘oak_id_vars’. When calling the function, the parameter ‘id_vars = oak_id_vars()’ matches the raw dataset ‘oak_id_vars’ to the ‘oak_id_vars’ in the cm domain created in the previous step. It’s @@ -283,8 +283,8 @@

assign_ct= "C71620", id_vars = oak_id_vars() ) -
- +
+

assign_datetime @@ -305,8 +305,8 @@

assign_datetime raw_unk = c("UN", "UNK"), id_vars = oak_id_vars() )

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- +
+

hardcode_ct and condition_add @@ -336,8 +336,8 @@

hardcode_ct and condition_add= "C66728", id_vars = oak_id_vars() )

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-

The condition_add function adds additional metadata to +

+

The condition_add function adds additional metadata to the records in the raw dataset that meets the condition. Refer to the function documentation for more details. hardcode_ct function uses the additional metadata to find the records that meet the @@ -363,8 +363,8 @@

hardcode_no_ct and condition_add tgt_val = "SCREENING", id_vars = oak_id_vars() ) -
- +
+

condition_add involving target domain @@ -397,8 +397,8 @@

condition_add involving target domain= oak_id_vars() ) }

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-

Remember to use additional curly braces in the function call when +

+

Remember to use additional curly braces in the function call when using the condition_add function on the target dataset. This is necessary because the input target dataset is represented as a . and is passed on from the previous step using the @@ -452,8 +452,8 @@

condition_add involving raw dataset and target do id_vars = oak_id_vars() ) } -
-

Another way to achieve the same outcome is by moving the +

+

Another way to achieve the same outcome is by moving the ‘condition_by’ call up one level, as illustrated below: it is not required to use the {magrittr} pipe %>% or curly braces in this case.

@@ -582,8 +582,8 @@

condition_add involving raw dataset and target do tgt_var = "CMPNCD", id_vars = oak_id_vars() ) -
- +
+
@@ -631,8 +631,8 @@

Create SDTM derived variables) %>% # Add code for derive Baseline flag. dplyr::select("STUDYID", "DOMAIN", "USUBJID", everything())

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- +
+

Add Labels and Attributes diff --git a/articles/findings_domain.html b/articles/findings_domain.html index 7a0a79d4..671502e9 100644 --- a/articles/findings_domain.html +++ b/articles/findings_domain.html @@ -149,8 +149,8 @@

Read in datavs_raw <- read.csv(system.file("raw_data/vitals_raw_data.csv", package = "sdtm.oak" ))

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- +
+

Create oak_id_vars @@ -161,8 +161,8 @@

Create oak_id_vars pat_var = "PATNUM", raw_src = "vitals" )

-
-

Read in the DM domain

+
+

Read in the DM domain

Read in CT @@ -175,8 +175,8 @@

Read in CT< study_ct <- read.csv(system.file("raw_data/sdtm_ct.csv", package = "sdtm.oak" ))

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- +
+

Map Topic Variable @@ -198,8 +198,8 @@

Map Topic Variable# Filter for records where VSTESTCD is not empty. # Only these records need qualifier mappings. dplyr::filter(!is.na(.data$VSTESTCD))

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- +
+

Map Rest of the Variables @@ -245,8 +245,8 @@

Map Rest of the Variables ct_clst = "C71148", id_vars = oak_id_vars() )

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- +
+

Repeat Map Topic and Map Rest @@ -561,8 +561,8 @@

Repeat Map Topic and Map Rest= "VISITNUM", id_vars = oak_id_vars() )

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- +
+

Create SDTM derived variables @@ -586,8 +586,8 @@

Create SDTM derived variables= "VSDY" ) %>% dplyr::select("STUDYID", "DOMAIN", "USUBJID", everything())

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- +
+

Add Labels and Attributes diff --git a/pkgdown.yml b/pkgdown.yml index 8f861bdd..e75a6b30 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -8,7 +8,7 @@ articles: findings_domain: findings_domain.html iso_8601: iso_8601.html study_sdtm_spec: study_sdtm_spec.html -last_built: 2024-07-31T21:59Z +last_built: 2024-07-31T23:30Z urls: reference: https://pharmaverse.github.io/sdtm.oak/reference article: https://pharmaverse.github.io/sdtm.oak/articles