updateParscalesToBaseTrafo: Rename parscales to the names needed in the base trafo

In dlill/petab: PEtab support for R

Rename parscales to the names needed in the base trafo

Description

Rename parscales to the names needed in the base trafo

Usage

updateParscalesToBaseTrafo(scales_outer, est.grid)

Arguments

est.grid	data.table
parscales	setNames(PETABPars$parameterScale, PETABPars$parameterId)

Author(s)

Daniel Lill ([e-mail])

Examples

# Example 1: k1_A and k1_B are duplicated to two inner parameters 
est.grid <- data.frame(ID = 1:2,
                       condition = c("A", "B"),
                       k1 = c("k1_A", "k1_B"),
                       k1DUPE = c("k1_A", "k1_B"),
                       k3 = c("k3outer", NA),
                       stringsAsFactors = FALSE)
scales_outer <- c(k1_A = "log", k1_B = "log", k3outer = "lin")
updateParscalesToBaseTrafo(scales_outer, est.grid)

# Example 2: SHOULD FAIL k1_A and k1_B map to same inner parameter, but have idfferent scales
est.grid <- data.frame(ID = 1:2,
                       condition = c("A", "B"),
                       k1 = c("k1_A", "k1_B"),
                       k1DUPE = c("k1_A", "k1_B"),
                       k3 = c("k3outer", NA),
                       stringsAsFactors = FALSE)
scales_outer <- c(k1_A = "log", k1_B = "log10", k3outer = "lin")
updateParscalesToBaseTrafo(scales_outer, est.grid)

# Example 3: k4 is a parameter not in est.grid. It might be a parameter in fix.grid and should be returned as is
est.grid <- data.frame(ID = 1:2,
                       condition = c("A", "B"),
                       k1 = c("k1_A", "k1_B"),
                       k1DUPE = c("k1_A", "k1_B"),
                       k3 = c("k3outer", NA),
                       stringsAsFactors = FALSE)
scales_outer <- c(k1_A = "log", k1_B = "log", k3outer = "lin", k4 = "log")
updateParscalesToBaseTrafo(scales_outer, est.grid)

dlill/petab documentation built on Oct. 9, 2022, 3:07 p.m.