R: Get discretised data

discretized {opm}

R Documentation

Get discretised data

Description

Get the discretised kinetic data or the discretisation settings used. (See do_disc for generating discretised data.)

Usage

  ## S4 method for signature 'MOPMX'
disc_settings(object, join = NULL) 
  ## S4 method for signature 'NULL'
disc_settings(object, ...) 
  ## S4 method for signature 'OPMD'
disc_settings(object, join = NULL) 
  ## S4 method for signature 'OPMS'
disc_settings(object, join = NULL) 
  ## S4 method for signature 'character'
disc_settings(object, ...) 
  ## S4 method for signature 'logical'
disc_settings(object, ...) 
  ## S4 method for signature 'numeric'
disc_settings(object, ...) 

  ## S4 method for signature 'MOPMX'
discretized(object, ...) 
  ## S4 method for signature 'OPMD'
discretized(object, full = FALSE,
    in.parens = TRUE, max = opm_opt("max.chars"), ...) 
  ## S4 method for signature 'OPMS'
discretized(object, ...)

Arguments

`object`	`OPMD`, `OPMS` or `MOPMX` object. `disc_settings` methods for other classes are helpers for generating raw settings lists.
`full`	Logical scalar passed to `wells`. This and the following arguments affect the names of the resulting vector.
`in.parens`	Logical scalar also passed to that function.
`max`	Numeric scalar also passed to that function.
`join`	Empty or character scalar. Works like the eponymous argument of `aggr_settings`; see there for details.
`...`	Optional arguments passed between the methods or to `wells`.

Value

Logical vector or matrix in the case of discretized, named list in the case of disc_settings. See the examples for details.

Examples

# 'OPM' methods
(x <- discretized(vaas_1))[1:3] # => logical vector

##   A01   A02   A03 
## FALSE  TRUE  TRUE

stopifnot(is.logical(x), !is.matrix(x), length(x) == dim(x)[2L])
stopifnot(names(x) == colnames(aggregated(vaas_1)))
(x <- discretized(vaas_1, full = TRUE))[1:3] # => with full names

## A01 (Negative Control)          A02 (Dextrin)        A03 (D-Maltose) 
##                  FALSE                   TRUE                   TRUE

stopifnot(names(x) == colnames(aggregated(vaas_1, full = TRUE)))

# settings
(x <- disc_settings(vaas_1)) # => named list

## $method
## [1] "kmeans"
## 
## $options
## $options$cutoffs
## [1] 129.0670 241.2105
## 
## $options$datasets
## [1] 1
## 
## $options$parameter
## [1] "A"
## 
## 
## $software
## [1] "opm"
## 
## $version
## [1] "0.7-0"

stopifnot(is.list(x), !is.null(names(x)))
(x <- disc_settings(vaas_1, join = "yaml")) # matrix, one row per plate

##      method  
## [1,] "kmeans"
##      options                                                                
## [1,] "---\ncutoffs:\n- 129.06705\n- 241.2105\ndatasets: 1\nparameter: A\n\n"
##      software version
## [1,] "opm"    "0.7-0"

stopifnot(is.matrix(x), is.character(x), nrow(x) == 1)

# 'OPMS' methods
(x <- discretized(vaas_4))[, 1:3] # => logical matrix

##        A01   A02   A03
## [1,] FALSE    NA FALSE
## [2,]    NA  TRUE  TRUE
## [3,] FALSE FALSE FALSE
## [4,] FALSE FALSE FALSE

stopifnot(is.logical(x), is.matrix(x), ncol(x) == dim(x)[2L])
stopifnot(colnames(x) == colnames(aggregated(vaas_1)))

# settings
summary(x <- disc_settings(vaas_4)) # => list of named lists, one per plate

##      Length Class  Mode
## [1,] 4      -none- list
## [2,] 4      -none- list
## [3,] 4      -none- list
## [4,] 4      -none- list

stopifnot(is.list(x), is.null(names(x)), length(x) == length(vaas_4))
stopifnot(duplicated(x)[-1])
(x <- disc_settings(vaas_4, join = "json")) # matrix, one row per plate

##      method  
## [1,] "kmeans"
## [2,] "kmeans"
## [3,] "kmeans"
## [4,] "kmeans"
##      options                                                                             
## [1,] "{\"cutoffs\":[111.8537965869,230.912480834744],\"datasets\":4,\"parameter\":\"A\"}"
## [2,] "{\"cutoffs\":[111.8537965869,230.912480834744],\"datasets\":4,\"parameter\":\"A\"}"
## [3,] "{\"cutoffs\":[111.8537965869,230.912480834744],\"datasets\":4,\"parameter\":\"A\"}"
## [4,] "{\"cutoffs\":[111.8537965869,230.912480834744],\"datasets\":4,\"parameter\":\"A\"}"
##      software version
## [1,] "opm"    "0.7-0"
## [2,] "opm"    "0.7-0"
## [3,] "opm"    "0.7-0"
## [4,] "opm"    "0.7-0"

stopifnot(is.matrix(x), is.character(x), nrow(x) == 4)