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.
Usage
# S3 method for class 'mkindsg'
print(x, data = FALSE, verbose = data, ...)Note
Currently, no functions making use of the defined class structure are available in this package. Refer to D24_2014 for an example dataset in this structure, with some example evaluations.
Public fields
titleA title for the dataset group
dsA list of mkinds objects
observed_nOccurrence counts of compounds in datasets
f_time_normTime normalisation factors
metaA 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).
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