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| url: ~ | ||
| url: https://pharmaverse.github.io/sdtm.oak | ||
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| template: | ||
| bootstrap: 5 | ||
| bootswatch: flatly | ||
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| navbar: | ||
| title: "sdtm.oak" |
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| --- | ||
| title: "Algorithms & Sub-Algorithms" | ||
| output: rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{Algorithms} | ||
| %\VignetteEncoding{UTF-8} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| editor_options: | ||
| markdown: | ||
| wrap: 72 | ||
| --- | ||
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| ## Core Concept | ||
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| SDTM mappings are defined as algorithms that transform the collected | ||
| (eCRF, eDT) source data into the target SDTM data model. Mapping | ||
| algorithms are the backbone of the sdtm.oak - SDTM data transformation | ||
| engine. | ||
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| **Key Points:** | ||
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| - Algorithms can be re-used across multiple SDTM domains. | ||
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| - Algorithms are pre-specified for data collection standards in MDR | ||
| (if applicable) | ||
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| - Programming language agnostic - this concept does not rely on a | ||
| specific programming language for implementation. The OAK team | ||
| implemented them as R functions. | ||
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| Here is an example of reusing an algorithm across multiple domains, | ||
| variables, and also to a non-standard | ||
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|  | ||
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| ## List of Algorithms | ||
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| ```{r echo = FALSE, results = "asis"} | ||
| library(knitr) | ||
| algorithms <- data.frame( | ||
| `Algorithm Name` = c( | ||
| "ASSIGN_NO_CT", | ||
| "ASSIGN_CT", | ||
| "AE_AEREL", | ||
| "HARDCODE_CT", | ||
| "HARDCODE_NO_CT", | ||
| "DATASET_LEVEL", | ||
| "NOTSUBMITTED", | ||
| "IF_THEN_ELSE", | ||
| "MERGE", | ||
| "RELREC", | ||
| "MULTIPLE_RESPONSES", | ||
| "SPLIT_TO_SUPPQUAL", | ||
| "REMOVE_DUP", | ||
| "GROUP_BY" | ||
| ), | ||
| `Description` = c( | ||
| paste( | ||
| "One-to-one mapping between the raw source and a target", | ||
| "SDTM variable that has no controlled terminology restrictions.", | ||
| "Just a simple assignment", | ||
| "statement. This algorithm will also handle the concatenation of", | ||
| "multiple items into a target SDTM variable." | ||
| ), | ||
| paste( | ||
| "One-to-one mapping between the raw source and a target ", | ||
| "SDTM variable that is subject to controlled terminology restrictions.", | ||
| "A simple assign statement and applying controlled terminology.", | ||
| "This will be used only if the SDTM variable has an associated", | ||
| "controlled terminology." | ||
| ), | ||
| paste( | ||
| "Algorithm that is currently unique to AE.AEREL,", | ||
| "particularly when more than one drug is used in the study.<br> If any collected study drug", | ||
| "causalities are 'Yes' then AE.AEREL is Y. <br>If all collected study", | ||
| "drug causalities are 'NA' then AE.AEREL is NA. <br>If no study drug", | ||
| "causalities are 'Yes' but there is at least one causality of 'No'", | ||
| "then AE.AEREL is N. <br>Individual study drug causality responses are", | ||
| "stored in AERELn in SUPPAE." | ||
| ), | ||
| paste( | ||
| "Mapping a hardcoded value to a target SDTM variable that is subject to terminology restrictions.", | ||
| "This will be used only if the SDTM variable has an associated", | ||
| "controlled terminology." | ||
| ), | ||
| paste( | ||
| "Mapping a hardcoded value to a target SDTM variable that has no terminology restrictions." | ||
| ), | ||
| paste( | ||
| "Indicates a dataset-level mapping. These mappings will", | ||
| "be applied to all SDTM records created from that source.", | ||
| "Also called a eCRF-level mappings in eCRF and dataset-level", | ||
| "mappings in eDT" | ||
| ), | ||
| paste( | ||
| "Instruction that `sdtm.oak` should not map the collected item to SDTM at all." | ||
| ), | ||
| paste( | ||
| "Represents the If then else statement. This can be an if statement", | ||
| "with no else or with the else condition. This algorithm will be", | ||
| "used for the annotations where a condition has to be evaluated", | ||
| "before a mapping is performed. A sub-algorithm is required. If the", | ||
| "condition resolves to `TRUE`, the sub-algorithm will be executed." | ||
| ), | ||
| paste( | ||
| "To indicate a join condition with a secondary source or multiple sources.", | ||
| "Merges are expressed at the domain level only", | ||
| "(not at data point or variable level).", | ||
| "This is a sub-algorithm and can only be used with algorithm DATASET_LEVEL." | ||
| ), | ||
| paste( | ||
| "Associate two domains based on the variables in each domain and how those are related.", | ||
| "Specifies the name of two domains that are related via RELREC." | ||
| ), | ||
| paste( | ||
| "Consolidate the responses from more than one source variable into one target variable.", | ||
| "Used when multiple responses may be given for a single SDTM column.", | ||
| "`sdtm.oak` will populate all target variable(s) after determining the number of responses provided." | ||
| ), | ||
| paste( | ||
| "Consolidates the responses from more than one", | ||
| "source variable into more than one target variable", | ||
| "(always a suppqual/non-standard variable).", | ||
| "There is no 'parent' target variable that is populated with 'MULTIPLE'." | ||
| ), | ||
| paste( | ||
| "Sub-algorithm at the domain level that indicates some source records may", | ||
| "be removed during the `sdtm.oak` mapping process if determined to be duplicate records." | ||
| ), | ||
| paste( | ||
| "Sub-algorithm used at the domain level to group source records", | ||
| "before mapping to SDTM. This is used in the event we need to collapse data", | ||
| "collected across multiple rows into one row in SDTM but it is not a simple", | ||
| "un-duplication effort. For example, the way infusion study drug", | ||
| "administration data requires us to create 1 SDTM record in EC from 1 or more source", | ||
| "records in the mixed log form. When there is more than one source record,", | ||
| "we need to take the earliest collected infusion start date (for ECSTDTC) and", | ||
| "the latest collected infusion end date within an eCRF instance." | ||
| ) | ||
| ), | ||
| `Example` = c( | ||
| paste( | ||
| "MH.MHTERM<br>", | ||
| "VS.VSDTC<br>", | ||
| "MH.MHTERM = [LNGCAHX1.HSTYP] || ' ' || 'NON-METASTATIC LUNG CANCER'<br>", | ||
| "CM.CMINDC = [MD9.MDCIND] || ' ' || [MD9.MDCINDSP]" | ||
| ), | ||
| paste("VS.VSPOS<br>", "VS.VSLAT"), | ||
| paste("For AE.AEREL and AERELn in SUPPAE"), | ||
| paste( | ||
| "MH.MHPRESP = 'Y'<br>", | ||
| "VS.VSTEST = 'Systolic Blood Pressure'<br>", | ||
| "VS.VSORRESU = 'mmHg'<br>" | ||
| ), | ||
| paste("FA.FASCAT = 'COVID-19 PROBABLE CASE'<br>", | ||
| "CM.CMTRT = 'FLUIDS'"), | ||
| paste( | ||
| "VS = 'Vital Signs'<br>", | ||
| "MH.MHCAT = 'PROSTATE CANCER HISTORY'<br>" | ||
| ), | ||
| paste(""), | ||
| paste( | ||
| "If 'Ongoing' then MH.MHENRTPT = 'ONGOING' <br> Else MH.MHENRTPT = 'BEFORE'<br> <br>", | ||
| "If [HX1.STATUS] is present then MH.MHENTPT = 'FIRST DOSE OF STUDY DRUG'<br> <br>", | ||
| "If checked then MH.MHSTTPT = 'SCREENING' <br> Else NOT SUBMITTED <br><br>", | ||
| "VS.VSMETHOD when VS.VSTESTCD = 'TEMP'", | ||
| "(Though the annotation text does not have the If condition,", | ||
| "we need to map VSMETHOD only if the VSTESTCD is TEMP. The IF_THEN_ELSE will be", | ||
| "used as the Algorithm for such cases even the 'If' condition is not explicitly", | ||
| "defined in the annotation text)" | ||
| ), | ||
| paste("AE = 'Adverse Events' on the early phase SAE eCRF"), | ||
| paste("BE record related to BS record via RELREC"), | ||
| paste( | ||
| "AE.AERELNST/ AERELNSn IN SUPPAE<br> <br>", | ||
| "DM.RACE, if only one value is selected.<br>", | ||
| "DM.RACE = MULTIPLE, if more than one value is selected.<br>", | ||
| "RACEn in SUPPDM where n = 1 to N selected values" | ||
| ), | ||
| paste( | ||
| "If both Filipino and Samoan are checked,", | ||
| "CRACE1 will be 'FILIPINO' and CRACE2 will be 'SAMOAN'.<br>", | ||
| "If only Chinese is checked, CRACE1 will be 'CHINESE'." | ||
| ), | ||
| paste("AE = 'Adverse Events' on early phase SAE form"), | ||
| paste("EC = 'Exposure as Collected'") | ||
| ) | ||
| ) | ||
| knitr::kable(algorithms) | ||
| ``` | ||
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| ## Sub-algorithms | ||
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| sdtm.oak supports two levels for defining algorithms. For example, there | ||
| are some SDTM mappings where a certain action has to be taken only when | ||
| a condition is met. In such cases, the primary algorithm checks for the | ||
| condition, and the sub-algorithm executes the mappings when the | ||
| condition is met. | ||
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| Currently, sub-algorithms must be provided for these main algorithms. | ||
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| - IF_THEN_ELSE | ||
| - DATASET_LEVEL | ||
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| Algorithms can be interchangeably used as algorithms and as | ||
| sub-algorithms as seen below (not an exhaustive list) | ||
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|  | ||
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| The permutation & combination of algorithms & sub-algorithms creates | ||
| endless possibilities to accommodate different types of mappings. |
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