From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- docs/dev/reference/mkindsg.html | 450 ---------------------------------------- 1 file changed, 450 deletions(-) delete mode 100644 docs/dev/reference/mkindsg.html (limited to 'docs/dev/reference/mkindsg.html') diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html deleted file mode 100644 index 6e221a23..00000000 --- a/docs/dev/reference/mkindsg.html +++ /dev/null @@ -1,450 +0,0 @@ - -A class for dataset groups for mkin — mkindsg • mkin - - -
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A class for dataset groups for mkin

- Source: R/mkinds.R - -
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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.

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

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x
-

An mkindsg object.

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data
-

Should the mkinds objects be printed with their data?

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verbose
-

Should the mkinds objects be printed?

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...
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Not used.

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Public fields

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title
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A title for the dataset group

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ds
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A list of mkinds objects

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observed_n
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Occurrence counts of compounds in datasets

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f_time_norm
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Time normalisation factors

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meta
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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).

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Methods

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Public methods

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Method new()

-

Create a new mkindsg object

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Usage

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

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Arguments

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title
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The title

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ds
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A list of mkinds objects

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f_time_norm
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Time normalisation factors

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meta
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The meta data

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Method clone()

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The objects of this class are cloneable with this method.

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Usage

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mkindsg$clone(deep = FALSE)

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Arguments

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deep
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Whether to make a deep clone.

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Examples

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-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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