Apply vachette transformations
apply_transformations(vachette_data, ...)
# S3 method for class 'vachette_data'
apply_transformations(
vachette_data,
tol.end = 0.001,
tol.noise = 1e-08,
step.x.factor = 1.5,
ngrid.fit = 100,
window = 17,
log_file = NULL,
...
)object of class vachette_data
Additional arguments
numeric; Relative tolerance to determine last x open end reference
numeric; Relative tolerance for landmark determination typical curves
numeric; x-axis extension factor to search for last x, i.e., to determine where close enough to asymptote
numeric; number of grid points in last query segment for matching last reference segment
integer; size (gridpoints) of Savitzky Golay smoothing window for landmark position determination
character; File path to direct console output e.g., "log.txt"
vachette_data object containing a list of vachette-transformed data.frames
obs <- read.csv(system.file(package = "vachette", "examples", "iv-obs.csv"))
typ <- read.csv(system.file(package = "vachette", "examples", "iv-typ-minmax.csv"))
vd <- vachette_data(
obs.data = obs,
typ.data = typ,
covariates = c(WT = 70),
mappings = c(OBS = "DV", x = "time"),
model.name = "IV"
)
#> `EVID` column found in obs.data, creating `dosenr` column in data for corresponding ref.dosenr value
#> `EVID` column found in typ.data, creating `dosenr` column in data for corresponding ref.dosenr value
vd <- apply_transformations(vd)
#>
#> ----------------------------------------------------------
#> --------------------- i.ucov = 1 ----------------------
#> ucov WT region region.type ref 1 30 1 open No
#> ----------------------------------------------------------
#> Remove noisy ends of the reference and query curves, if applicable
#> Some obs cannot be associated with query curve
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> No minimum or maximum detected
#> Points kept in y-range of 2.5% to 97.5% only
#> Polynomial order for open end curve fitting = 45
#> Searched for: inflec
#> Returned: NA
#> No inflection point found
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> No minimum or maximum detected
#> Points kept in y-range of 2.5% to 97.5% only
#> Polynomial order for open end curve fitting = 70
#> Searched for: inflec
#> Returned: NA
#> No inflection point found
#> First and last landmark available only
#> Removing 0 observations for i.ucov=1
#> No landmarks detected, x=0 assumed first landmark
#> Optimized last segment x.scaling 0.5163
#>
#> Reference
#> x type y1 0.1 start 1.960397e+012 102.0 end 2.777013e-08
#>
#> Query
#> x type y1 0.100 start 19.789242 197.451 end NA
#>
#> Zero observations cannot be transformed with proportional error model
#> 6 observations excluded for all i.ucov
#>
#> ----------------------------------------------------------
#> --------------------- i.ucov = 2 ----------------------
#> ucov WT region region.type ref 2 70 1 open Yes
#> ----------------------------------------------------------
#> Remove noisy ends of the reference and query curves, if applicable
#> Some obs cannot be associated with reference curve
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> No minimum or maximum detected
#> Points kept in y-range of 2.5% to 97.5% only
#> Polynomial order for open end curve fitting = 45
#> Searched for: inflec
#> Returned: NA
#> No inflection point found
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> Functions 'get_peaks()' and 'get_valeys()' have been deprecated: please use 'peaks()' and 'valleys()', or 'find_peaks()' and 'find_valleys()', instead.
#> No minimum or maximum detected
#> Points kept in y-range of 2.5% to 97.5% only
#> Polynomial order for open end curve fitting = 45
#> Searched for: inflec
#> Returned: NA
#> No inflection point found
#> First and last landmark available only
#> REFERENCE! No need to remove 0 observations for i.ucov=2
#> No landmarks detected, x=0 assumed first landmark
#> Optimized last segment x.scaling 1
#>
#> Reference
#> x type y1 0.1 start 1.960397e+012 102.0 end 2.777013e-08
#>
#> Query
#> x type y1 0.1 start 1.960397e+012 102.0 end 2.777013e-08
#>
#> *** LEFT Extension reference curve by exponential extrapolation ***
#> >> Applying NO-asymptote reference curve LEFT-side extrapolation
#> 15 observations excluded for all i.ucov