From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Feb 2021 16:41:31 +0100 Subject: Prepare for v1.0.0 - Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest --- docs/reference/mkindsg.html | 460 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 460 insertions(+) create mode 100644 docs/reference/mkindsg.html (limited to 'docs/reference/mkindsg.html') diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html new file mode 100644 index 00000000..74d3a26c --- /dev/null +++ b/docs/reference/mkindsg.html @@ -0,0 +1,460 @@ + + + + + + + + +A class for dataset groups for mkin — mkindsg • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+ + +
+

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
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