From db9ae6a0c9cecb92048fde6f06af1da183c09b5f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 19 Nov 2020 15:41:24 +0100 Subject: Depend on parallel, doc improvements By depending on parallel instead of importing it, functions to set up and stop a cluster are always available when mkin is loaded. The use of multicore processing in mmkin on Windows is now documented in the help file, which brings mkin closer to a version 1.0 #9. --- docs/dev/reference/mkindsg.html | 460 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 460 insertions(+) create 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 new file mode 100644 index 00000000..3e4dfb39 --- /dev/null +++ b/docs/dev/reference/mkindsg.html @@ -0,0 +1,460 @@ + + + + + + + + +A class for dataset groups for mkin — mkindsg • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

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 
+#> Occurrene of observed compounds $observed_n:
+#> parent     A1 
+#>      5      5 
print(mdsg, verbose = TRUE)
+
#> <mkindsg> holding 5 mkinds objects
+#> Title $title:  Experimental X 
+#> Occurrene 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 
+#> Occurrene 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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