From 1691fa45fe0c96040b3bac694e6a725a21d80586 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 30 Oct 2024 16:47:48 +0000 Subject: [PATCH] Built site for sdtm.oak: 0.1.0@966ab97 --- articles/events_domain.html | 52 +++++++++++++++++----------------- articles/findings_domain.html | 28 +++++++++--------- pkgdown.yml | 2 +- reference/Rplot001.png | Bin 1011 -> 0 bytes 4 files changed, 41 insertions(+), 41 deletions(-) delete mode 100644 reference/Rplot001.png diff --git a/articles/events_domain.html b/articles/events_domain.html index 6410e825..fa9d739e 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" )

-
- +
+

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

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

-
-

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() )

-
- +
+

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

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

-
-

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() ) }

-
-

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())

-
- +
+

Add Labels and Attributes diff --git a/articles/findings_domain.html b/articles/findings_domain.html index 65fddf65..064f0cda 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" ))

-
- +
+

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" ))

-
- +
+

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))

-
- +
+

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

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

-
- +
+

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

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

-
- +
+

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

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

-
- +
+

Add Labels and Attributes diff --git a/pkgdown.yml b/pkgdown.yml index 75306bd1..5e991651 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: 2024-09-12T22:51Z +last_built: 2024-10-30T16:46Z urls: reference: https://pharmaverse.github.io/sdtm.oak/reference article: https://pharmaverse.github.io/sdtm.oak/articles diff --git a/reference/Rplot001.png b/reference/Rplot001.png deleted file mode 100644 index 17a358060aed2a86950757bbd25c6f92c08c458f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1011 zcmeAS@N?(olHy`uVBq!ia0y~yV0-|=9Be?5+AI5}0x7m6Z+90U4Fo@(ch>_c&H|6f zVg?3oArNM~bhqvg0|WD9PZ!6KiaBo&GBN^{G%5UFpXcEKVvd5*5Eu=C0SJK)8A6*F U7`aXvEC5;V>FVdQ&MBb@00SN#Z2$lO