From 6178249bbb5e9de7cb7f34287ee7de28a68fed6c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Aug 2022 15:38:17 +0200 Subject: Change dev branch used for docs, update static docs --- docs/dev/reference/mkindsg.html | 689 +++++++++++++++++++--------------------- 1 file changed, 328 insertions(+), 361 deletions(-) (limited to 'docs/dev/reference/mkindsg.html') diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html index 67c6e5df..d19a7a1d 100644 --- a/docs/dev/reference/mkindsg.html +++ b/docs/dev/reference/mkindsg.html @@ -1,70 +1,15 @@ - - - - - - - -A class for dataset groups for mkin — mkindsg • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -A class for dataset groups for mkin — mkindsg • mkin - - - - - - - - - - - - - + + -
-
- -
- -
+

A class for dataset groups for mkin

- Source: R/mkinds.R + Source: R/mkinds.R
@@ -153,308 +92,336 @@ so that combined evaluations are desirable.

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, +

+ 
# 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

+

+
+
+

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

-
+
+

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
+
+
+
+
- - - + + -- cgit v1.2.1