Read datasets and relevant meta information from a spreadsheet file

diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index aeea435d..c5d5d820 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -12,7 +12,7 @@ articles: compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html -last_built: 2022-11-01T13:09Z +last_built: 2022-11-03T11:38Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 0b127b57..15c3a638 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -192,6 +192,10 @@ of an mmkin object

Create and work with nonlinear hierarchical models

read_spreadsheet()

+ +

nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>)

Create an nlme model for an mmkin row object

@@ -345,6 +349,10 @@ degradation models and one or more error models

tex_listing()

+ +

Wrap the output of a summary function in tex listing environment

f_time_norm_focus()

Normalisation factors for aerobic soil degradation according to FOCUS guidance

diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html new file mode 100644 index 00000000..70828765 --- /dev/null +++ b/docs/dev/reference/read_spreadsheet.html @@ -0,0 +1,176 @@ + +Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet • mkin + + +

+ + + +

+ + +

This function imports one dataset from each sheet of a spreadsheet file. +These sheets are selected based on the contents of a sheet 'Datasets', with +a column called 'Dataset Number', containing numbers identifying the dataset +sheets to be read in. In the second column there must be a grouping +variable, which will often be named 'Soil'. Optionally, time normalization +factors can be given in columns named 'Temperature' and 'Moisture'.

+ +

read_spreadsheet(
+  path,
+  valid_datasets = "all",
+  parent_only = TRUE,
+  normalize = TRUE
+)

+ +

Arguments

path: Absolute or relative path to the spreadsheet file
valid_datasets: Optional numeric index of the valid datasets, default is +to use all datasets
parent_only: Should only the parent data be used?
normalize: Should the time scale be normalized using temperature +and moisture normalisation factors in the sheet 'Datasets'?

Details

There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. +The first row read after the header read in from this sheet is assumed +to contain name and acronym of the parent compound.

The dataset sheets should be named using the dataset numbers read in from +the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, name +of the observed variable (e.g. the acronym of the parent compound or +one of its transformation products) should be in the first column, +the time values should be in the second colum, and the observed value +in the third column.

In case relevant covariate data are available, they should be given +in a sheet 'Covariates', containing one line for each value of the grouping +variable specified in 'Datasets'. These values should be in the first +column and the column must have the same name as the second column in +'Datasets'. Covariates will be read in from columns four and higher. +Their names should preferably not contain special characters like spaces, +so they can be easily used for specifying covariate models.

An similar data structure is defined as the R6 class mkindsg, but +is probably more complicated to use.

+ +

+ + +

+ + + + + + + + diff --git a/docs/dev/reference/tex_listing.html b/docs/dev/reference/tex_listing.html new file mode 100644 index 00000000..c82138b7 --- /dev/null +++ b/docs/dev/reference/tex_listing.html @@ -0,0 +1,140 @@ + +Wrap the output of a summary function in tex listing environment — tex_listing • mkin + + +

+ + + +

+ + +

This function can be used in a R markdown code chunk with the chunk +option results = "asis".

+ +

tex_listing(object, caption = NULL, label = NULL, clearpage = TRUE)

+ +

Arguments

object: The object for which the summary is to be listed
caption: An optional caption
label: An optional label
clearpage: Should a new page be started after the listing?

+ +

+ + +

+ + + + + + + + diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 2e2c4b14..17f86f6c 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -261,6 +261,9 @@ https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html + + https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html + https://pkgdown.jrwb.de/mkin/reference/reexports.html @@ -303,6 +306,9 @@ https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html + + https://pkgdown.jrwb.de/mkin/reference/tex_listing.html + https://pkgdown.jrwb.de/mkin/reference/tffm0.html -- cgit v1.2.1

mkin 1.1.1 (2022-07-12)

Read datasets and relevant meta information from a spreadsheet file

Arguments

Details

Wrap the output of a summary function in tex listing environment

Arguments