AllExpDetails: All possible experimental details for 'extractExpDetails'

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

All possible experimental details for extractExpDetails

Description

INTERNAL USE: All possible experimental details that can be extracted from a simulator output file using extractExpDetails. This version includes columns used only internally with coding. For the more user-friendly version, see ExpDetailDefinitions.

Usage

AllExpDetails

Format

A data.frame with columns:

Detail

the experimental detail name to use with extractExpDetails for the argument exp_details

Notes

an explanation of what the experimental detail is

ReportTableText

Similar to Notes except more formally written and includes no coding info; info on that detail that will go in the report table

Regex_row

When searching the specified column, what regular expression should be used for finding the correct row.

Class

Data class

DataSource

Where did this info come from? simulator output sheet this detail is extracted from or whether it's from the workspace or database file or calculated

NameCol

the index of the column in the simulator output tab that will be searched for matches to the text in the column "Regex_row".

ValueCol

index of the column in the simulator output tab that contains the value used for this detail. This applies when the column doesn't move, e.g., not Input Sheet compound-specific details.

ColsChangeWithCmpd

TRUE or FALSE for whether NameCol and/or ValueCol change depending on what compound ID it is

CmpdsForWhichDeetAvail

Compounds for which this detail is available. Many compound-specific details are available for all compounds (entry here is "all"), but some are only available for the substrate (entry here would be "substrate") or only for the substrate and inhibitor 1 ("substrate, inhibitor 1").

CDSInputMatch

compound data sheet item on the "Simcyp Inputs and QC" tab that matches this experimental detail

SimulatorSection

For matching with the CDS, in which section does this detail belong? Options: Absorption, Distribution, Elimination, Interaction, Phys Chem and Blood Binding.

ADAMParameter

TRUE or FALSE for whether the parameter only comes into play when it's an ADAM model

SimulatorAvailability

Is this detail available for Simcyp Discovery simulations? Options are "Simulator only", "Discovery only", or "Simulator and Discovery". This is used to determine which details to check and which regex to use for those details.

OffsetRows

When there just isn't good regex in the specific row for this detail, we need to look for a value and then go down this number of rows to get to the actual value we want.

SortOrder

Order in which this detail should show up in the output from annotateDetails

Level1, Level2, etc.

the level in the XML file where the information lives

XMLswitch

If there is a switch involved in the XML file, what is the tag to use for checking on that switch

SwitchTo

If the XML switch is turned to "1" or "true" in the XML file, this is the tag to switch to for looking up the value for this detail.

CodingNotes

Notes specifically to coders

SimcypParameterType

For extracting data from database files or workspaces, what kind of parameter is this? Options are "compound", "general", "population", or "other" and will affect where to find the info needed

SimcypTag

tag used for identifying this parameter in the database or workspace file

SimcypSubcategory

when a subcategory applies in the Simcyp package, what is it? Not currently used, but I wanted a placeholder for better, more seamless data extraction with the Simcyp package.

CompoundID

CompoundID (a.k.a. compound position in the Simulator). This only applies for siutations when that detail is ONLY for a specific CompoundID, which sometimes happens with database or workspace info in particular.

Suffix

suffix to append for this detail when it's for a specific compound ID

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.