From 77ecdf16dedcbf0db47e5eead6568e514159a127 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Nov 2022 13:54:53 +0100 Subject: Update docs --- docs/dev/reference/index.html | 8 ++ docs/dev/reference/read_spreadsheet.html | 176 +++++++++++++++++++++++++++++++ docs/dev/reference/tex_listing.html | 140 ++++++++++++++++++++++++ 3 files changed, 324 insertions(+) create mode 100644 docs/dev/reference/read_spreadsheet.html create mode 100644 docs/dev/reference/tex_listing.html (limited to 'docs/dev/reference') 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()

+ +

Read datasets and relevant meta information from a spreadsheet file

+

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 + + +
+
+ + + +
+
+
+

Read datasets and relevant meta information from a spreadsheet file

+ Source: R/read_spreadsheet.R + +
+ +
+

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.

+
+ +
+ +
+ + +
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 2.0.6.

+
+ +
+ + + + + + + + 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 + + +
+
+ + + +
+
+
+

Wrap the output of a summary function in tex listing environment

+ Source: R/tex_listing.R + +
+ +
+

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?

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