Create a Meth object representing a method comparison study

Creates a dataframe with columns meth, item, (repl) and y.

Meth(
  data = NULL,
  meth = "meth",
  item = "item",
  repl = NULL,
  y = "y",
  print = !is.null(data),
  keep.vars = !is.null(data)
)

Arguments

data: A data frame
meth: Vector of methods, numeric, character or factor. Can also be a number or character referring to a column in data.
item: Vector of items, numeric, character or factor. Can also be a number or character referring to a column in data.
repl: Vector of replicates, numeric, character or factor. Can also be a number or character referring to a column in data.
y: Vector of measurements. Can also be a character or numerical vector pointing to columns in data which contains the measurements by different methods or a dataframe with columns representing measurements by different methods. In this case the argument meth is ignored, and the names of the columns are taken as method names.
print: Logical: Should a summary result be printed?
keep.vars: Logical. Should the remaining variables from the dataframe data be transferred to the Meth object.

Value

The Meth function returns a Meth object which is a dataframe with columns meth, item, (repl) and y. summary.Meth returns a table classified by method and no. of replicate measurements, extended with columns of the total number of items, total number of observations and the range of the measurements.

Details

In order to perform analyses of method comparisons it is convenient to have a dataframe with classifying factors, meth, item, and possibly repl and the response variable y. This function creates such a dataframe, and gives it a class, Meth, for which there is a number of methods: summary - tabulation, plot - plotting and a couple of analysis methods.

If there are replicates in the values of item it is assumed that those observations represent replicate measurements and different replicate numbers are given to those.

Examples

data(fat)
# Different ways of selecting columns and generating replicate numbers
Sub1 <- Meth(fat,meth=2,item=1,repl=3,y=4,print=TRUE)
#> The following variables from the dataframe
#> "fat" are used as the Meth variables:
#> meth: Obs 
#> item: Id 
#> repl: Rep 
#>    y: Sub 
#>        #Replicates
#> Method          3 #Items #Obs: 258 Values:  min med max
#>     KL         43     43       129         0.39 1.7 4.2
#>     SL         43     43       129         0.51 1.7 4.1
Sub2 <- Meth(fat,2,1,3,4,print=TRUE)
#> The following variables from the dataframe
#> "fat" are used as the Meth variables:
#> meth: Obs 
#> item: Id 
#> repl: Rep 
#>    y: Sub 
#>        #Replicates
#> Method          3 #Items #Obs: 258 Values:  min med max
#>     KL         43     43       129         0.39 1.7 4.2
#>     SL         43     43       129         0.51 1.7 4.1
Sub3 <- Meth(fat,meth="Obs",item="Id",repl="Rep",y="Sub",print=TRUE)
#> The following variables from the dataframe
#> "fat" are used as the Meth variables:
#> meth: Obs 
#> item: Id 
#> repl: Rep 
#>    y: Sub 
#>        #Replicates
#> Method          3 #Items #Obs: 258 Values:  min med max
#>     KL         43     43       129         0.39 1.7 4.2
#>     SL         43     43       129         0.51 1.7 4.1
summary( Sub3 )
#>        #Replicates
#> Method          3 #Items #Obs: 258 Values:  min med max
#>     KL         43     43       129         0.39 1.7 4.2
#>     SL         43     43       129         0.51 1.7 4.1
plot( Sub3 )


# Use observation in different columns as methods
data( CardOutput )
head( CardOutput )
#>   Age        Diag VO2 Svo2 Scvo2 TCO  FCO Sex
#> 1  66      sepsis 207   63    62 4.9  5.3   M
#> 2  73      sepsis 300   75    78 7.4 10.2   M
#> 3  53      sepsis 289   69    70 8.1  8.7   F
#> 4  28 cardiogenic 150   70    71 3.1  3.7   F
#> 5  72 cardiogenic 350   66    68 5.7  7.6   M
#> 6  71      sepsis 150   70    72 3.1  3.7   M
sv <- Meth( CardOutput, y=c("Svo2","Scvo2") )
#> The following variables from the dataframe
#> "CardOutput" are used as the Meth variables:   
#>    y: Svo2 Scvo2 
#>         #Replicates
#> Method           1 #Items #Obs: 30 Values:  min med max
#>   Scvo2         15     15       15           61  71  84
#>   Svo2          15     15       15           62  70  82
# Note that replicates are generated if a non-unique item-id is used
sv <- Meth( CardOutput, y=c("Svo2","Scvo2"), item="Age" )
#> The following variables from the dataframe
#> "CardOutput" are used as the Meth variables: 
#> item: Age  
#>    y: Svo2 Scvo2 
#>         #Replicates
#> Method    1   2   3 #Items #Obs: 30 Values:  min med max
#>   Scvo2   8   2   1     11       15           61  71  84
#>   Svo2    8   2   1     11       15           62  70  82
str( sv )
#> Classes ‘Meth’ and 'data.frame':	30 obs. of  9 variables:
#>  $ meth: Factor w/ 2 levels "Scvo2","Svo2": 2 2 2 2 2 2 2 2 2 2 ...
#>  $ item: Factor w/ 11 levels "24","28","53",..: 7 10 3 2 9 8 8 3 5 11 ...
#>  $ repl: Factor w/ 3 levels "1","2","3": 1 1 1 1 1 1 2 2 1 1 ...
#>  $ y   : num  63 75 69 70 66 70 75 74 63 64 ...
#>  $ Diag: Factor w/ 3 levels "sepsis","cardiogenic",..: 1 1 1 2 2 1 1 1 1 2 ...
#>  $ VO2 : num  207 300 289 150 350 150 305 140 167 318 ...
#>  $ TCO : num  4.9 7.4 8.1 3.1 5.7 3.1 6.3 3.1 4.1 6.1 ...
#>  $ FCO : num  5.3 10.2 8.7 3.7 7.6 3.7 9.6 3.7 3.4 6.8 ...
#>  $ Sex : Factor w/ 2 levels "F","M": 2 2 1 1 2 2 1 2 1 1 ...
# A summary is not created if the the first argument (data=) is not used:
sv <- Meth( y=CardOutput[,c("Svo2","Scvo2")], item=CardOutput$VO2 )
#> 
#> NOTE: Replication numbers generated in the order of the data
summary(sv)
#>         #Replicates
#> Method      1     2 #Items #Obs: 30 Values:  min med max
#>   Scvo2    13     1     14       15           61  71  84
#>   Svo2     13     1     14       15           62  70  82

# Sample items
ssv <- sample.Meth( sv, how="item", N=8 )

# More than two methods
data( sbp )
plot( Meth( sbp ) )
#> The following variables from the dataframe
#> "sbp" are used as the Meth variables:
#> meth: meth 
#> item: item 
#> repl: repl 
#>    y: y 
#>        #Replicates
#> Method          3 #Items #Obs: 765 Values:  min med max
#>      J         85     85       255           74 120 228
#>      R         85     85       255           76 120 226
#>      S         85     85       255           77 135 228

# Creating non-unique replicate numbers per (meth,item) creates a warning:
data( hba1c )
hb1  <- with( hba1c,
              Meth( meth=dev, item=item, repl=d.ana-d.samp, y=y, print=TRUE ) )
#>         #Replicates
#> Method    6   7   8 #Items #Obs: 835 Values:  min med  max
#>   BR.V2   0  19  19     38       285          5.3 8.0 12.6
#>   BR.VC  19   0  19     38       266          5.3 8.1 12.1
#>   Tosoh   0  20  18     38       284          5.0 7.9 12.1
#> 
#> WARNING: You have chosen a replicate variable which is not unique
#>          within each (meth,item).
hb2  <- with( subset(hba1c,type=="Cap"),
              Meth( meth=dev, item=item, repl=d.ana-d.samp, y=y, print=TRUE ) )
#>         #Replicates
#> Method      3     4 #Items #Obs: 437 Values:  min med  max
#>   BR.V2     0    38     38       152          5.3 8.0 12.6
#>   BR.VC    19    19     38       133          5.3 8.2 12.1
#>   Tosoh     0    38     38       152          5.0 7.8 11.8