A class for dataset groups for mkin

Source: R/mkinds.R

A container for working with datasets that share at least one compound, so that combined evaluations are desirable.

Time normalisation factors are initialised with a value of 1 for each dataset if no data are supplied.

# S3 method for mkindsg
print(x, data = FALSE, verbose = data, ...)

Arguments

x

An mkindsg object.

data

Should the mkinds objects be printed with their data?

verbose

Should the mkinds objects be printed?

...

Not used.

Public fields

title

A title for the dataset group

ds

A list of mkinds objects

observed_n

Occurrence counts of compounds in datasets

f_time_norm

Time normalisation factors

meta

A data frame with a row for each dataset, containing additional information in the form of categorical data (factors) or numerical data (e.g. temperature, moisture, or covariates like soil pH).

Methods

Public methods

Method new()

Create a new mkindsg object

Usage

mkindsg$new(title = "", ds, f_time_norm = rep(1, length(ds)), meta)

Arguments

title

The title

ds

A list of mkinds objects

f_time_norm

Time normalisation factors

meta

The meta data

Method clone()

The objects of this class are cloneable with this method.

Usage

mkindsg$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples


mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
print(mdsg)
#> <mkindsg> holding 5 mkinds objects
#> Title $title:  Experimental X 
#> Occurrence of observed compounds $observed_n:
#> parent     A1 
#>      5      5 
print(mdsg, verbose = TRUE)
#> <mkindsg> holding 5 mkinds objects
#> Title $title:  Experimental X 
#> Occurrence of observed compounds $observed_n:
#> parent     A1 
#>      5      5 
#> 
#> Datasets $ds:
#> <mkinds> with $title:  Soil 6 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#> 
#> <mkinds> with $title:  Soil 7 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 3, 7, 14, 30, 60, 90, 120, 180 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#> 
#> <mkinds> with $title:  Soil 8 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 1, 3, 8, 14, 27, 48, 70 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#> 
#> <mkinds> with $title:  Soil 9 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#> 
#> <mkinds> with $title:  Soil 10 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 8, 14, 21, 41, 63, 91, 120 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
print(mdsg, verbose = TRUE, data = TRUE)
#> <mkindsg> holding 5 mkinds objects
#> Title $title:  Experimental X 
#> Occurrence of observed compounds $observed_n:
#> parent     A1 
#>      5      5 
#> 
#> Datasets $ds:
#> <mkinds> with $title:  Soil 6 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#>    time parent   A1
#> 1     0   97.2   NA
#> 2     0   96.4   NA
#> 3     3   71.1  4.3
#> 4     3   69.2  4.6
#> 5     6   58.1  7.0
#> 6     6   56.6  7.2
#> 7    10   44.4  8.2
#> 8    10   43.4  8.0
#> 9    20   33.3 11.0
#> 10   20   29.2 13.7
#> 11   34   17.6 11.5
#> 12   34   18.0 12.7
#> 13   55   10.5 14.9
#> 14   55    9.3 14.5
#> 15   90    4.5 12.1
#> 16   90    4.7 12.3
#> 17  112    3.0  9.9
#> 18  112    3.4 10.2
#> 19  132    2.3  8.8
#> 20  132    2.7  7.8
#> 
#> <mkinds> with $title:  Soil 7 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 3, 7, 14, 30, 60, 90, 120, 180 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#>    time parent   A1
#> 1     0   93.6   NA
#> 2     0   92.3   NA
#> 3     3   87.0  3.9
#> 4     3   82.2  3.1
#> 5     7   74.0  6.9
#> 6     7   73.9  6.6
#> 7    14   64.2 10.4
#> 8    14   69.5  8.3
#> 9    30   54.0 14.4
#> 10   30   54.6 13.7
#> 11   60   41.1 22.1
#> 12   60   38.4 22.3
#> 13   90   32.5 27.5
#> 14   90   35.5 25.4
#> 15  120   28.1 28.0
#> 16  120   29.0 26.6
#> 17  180   26.5 25.8
#> 18  180   27.6 25.3
#> 
#> <mkinds> with $title:  Soil 8 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 1, 3, 8, 14, 27, 48, 70 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#>    time parent   A1
#> 1     0   91.9   NA
#> 2     0   90.8   NA
#> 3     1   64.9  9.6
#> 4     1   66.2  7.7
#> 5     3   43.5 15.0
#> 6     3   44.1 15.1
#> 7     8   18.3 21.2
#> 8     8   18.1 21.1
#> 9    14   10.2 19.7
#> 10   14   10.8 18.9
#> 11   27    4.9 17.5
#> 12   27    3.3 15.9
#> 13   48    1.6  9.5
#> 14   48    1.5  9.8
#> 15   70    1.1  6.2
#> 16   70    0.9  6.1
#> 
#> <mkinds> with $title:  Soil 9 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#>    time parent   A1
#> 1     0   99.8   NA
#> 2     0   98.3   NA
#> 3     1   77.1  4.2
#> 4     1   77.2  3.9
#> 5     3   59.0  7.4
#> 6     3   58.1  7.9
#> 7     8   27.4 14.5
#> 8     8   29.2 13.7
#> 9    14   19.1 14.2
#> 10   14   29.6 12.2
#> 11   27   10.1 13.7
#> 12   27   18.2 13.2
#> 13   48    4.5 13.6
#> 14   48    9.1 15.4
#> 15   70    2.3 10.4
#> 16   70    2.9 11.6
#> 17   91    2.0 10.0
#> 18   91    1.8  9.5
#> 19  120    2.0  9.1
#> 20  120    2.2  9.0
#> 
#> <mkinds> with $title:  Soil 10 
#> Observed compounds $observed:  parent, A1 
#> Sampling times $sampling_times:
#> 0, 8, 14, 21, 41, 63, 91, 120 
#> With a maximum of  2  replicates
#> Time unit:  days 
#> Observation unit:  \%AR 
#>    time parent   A1
#> 1     0   96.1   NA
#> 2     0   94.3   NA
#> 3     8   73.9  3.3
#> 4     8   73.9  3.4
#> 5    14   69.4  3.9
#> 6    14   73.1  2.9
#> 7    21   65.6  6.4
#> 8    21   65.3  7.2
#> 9    41   55.9  9.1
#> 10   41   54.4  8.5
#> 11   63   47.0 11.7
#> 12   63   49.3 12.0
#> 13   91   44.7 13.3
#> 14   91   46.7 13.2
#> 15  120   42.1 14.3
#> 16  120   41.3 12.1