Package 'rtematres'

This is the annotation features provided by rtematres

Description

You can semantically annotate data frames base on a tematres thesaurus.

Usage

annotate.dataframe(input)

Arguments

input

to be annotated takes a data frame

Value

a list wih annotation content

---

You can semantically annotate data frames base on a tematres thesaurus wih cleaning the dataset

Description

You can semantically annotate data frames base on a tematres thesaurus wih cleaning the dataset

Usage

annotate.dataframe.clean(input)

Arguments

input

to be annotated takes a data frame

Value

a list wih annotation content

---

A convenient wrapper to all tasks of the base api.

Description

As some of the task of the base api only take ids the wrapper does a conversion from a term to the id to communicate with the server. So you can use terms in all taks with this function.

rtematres A package to exploit controlled vocabularies from tematres servers

Usage

rtematres(task, verbose = F, term)

Arguments

task	The api task you like to execute.
verbose	Either true of false and determines the ammount of info that is returned by a query.
term	Is the term(s) you like to execute the task for.

Value

The function returns either a dataframe for information or a list of keywords and ids

Examples

## Not run: 
    rtematres(task = "fetchVocabularyData")
    rtematres(task = "fetchTopTerms")
    rtematres(task = "fetchCode", term = "tree")
    rtematres(task = "search", term = "measurement")
    rtematres(task = "fetch", term = "measurement")
    rtematres(task = "searchNotes", term = "measurement")
    rtematres(task = "suggest", term = "measurement")
    rtematres(task = "suggestDetails", term = "measurement")
    rtematres(task = "fetchSimilar", term = "t")
    rtematres(task = "letter", term = "t")
    rtematres(task = "fetchAlt", term = "tree" )
    rtematres(task = "fetchTerm", term = "tree")
    rtematres(task = "fetchTerms", term = c("Context", "tree") )
    rtematres(task = "fetchDown", term = "Context")
    rtematres(task = "fetchUp", term = "measurement")
    rtematres(task = "fetchRelated", term = "tree")
    rtematres(task = "fetchRelatedTerms", term = c("Context", "tree"))
    rtematres(task = "fetchNotes", term = "Context")
    rtematres(task = "fetchDirectTerms", term = "carbon")
    rtematres(task = "fetchURI", term = "carbon")
    rtematres(task = "fetchTargetTerms", term = "carbon")
    rtematres(task = "fetchSourceTerms", term = "Context")
    rtematres(task = "fetchLast")
  
## End(Not run)

---

Access to basic tematres server api

Description

Features the tasks of the tematres server api. With no sugar added. They are the basic building blocks for more convenient user functions.

Usage

rtematres.api(task = "availableTasks", argument)

Arguments

task	The api task you like to perform. Use the the task "availableTasks" to get an overview about the base api. It returns a data frame with descriptions and the arguments for the tasks.
argument	Is the argument for the api task. You find the information about the type of arguments when you call the task "availableTasks". It depends on the task if the argument is numeric or a character.

Value

The function returns either a dataframe for "availableTasks" or a list of information elements for a certain task.

Examples

## Not run: 
    rtematres.api(task = "availableTasks")
    rtematres.api(task = "fetchVocabularyData")
    rtematres.api(task = "fetchTopTerms")
    rtematres.api(task = "search", argument = "measurement")
    rtematres.api(task = "fetch", argument = "measurement")
    rtematres.api(task = "searchNotes", argument = "measurement")
    rtematres.api(task = "suggest", argument = "measurement")
    rtematres.api(task = "suggestDetails", argument = "measurement")
    rtematres.api(task = "fetchSimilar", argument = "tre")
    rtematres.api(task = "letter", argument = "t")
    rtematres.api(task = "fetchTerm", argument = 12)
    rtematres.api(task = "fetchDown", argument = 4 )
    rtematres.api(task = "fetchUp", argument = 4)
    rtematres.api(task = "fetchRelated", argument = 4)
    rtematres.api(task = "fetchAlt", argument = 12 )
    rtematres.api(task = "fetchCode", argument = "tree")
    rtematres.api(task = "fetchNotes", argument = 5 )
    rtematres.api(task = "fetchDirectTerms", argument = 12)
    rtematres.api(task = "fetchURI", argument = 12)
    rtematres.api(task = "fetchTargetTerms", argument = 12 )
    rtematres.api(task = "fetchSourceTerm", argument = "measurement")
    rtematres.api(task = "fetchTerms", argument = '12,13' )
    rtematres.api(task = "fetchRelatedTerms", argument = '12,13' )
    rtematres.api(task = "fetchLast")
 
## End(Not run)

---

Find common concept for categorial columns

Description

Search the thesaurus for concepts and extract their hirarchy. Then return the common concept if any.

Usage

rtematres.common(input)

Arguments

input

A categorial vector

Value

The function returns the common concept

Examples

## Not run: 
	rtematres.common(c("carbon", "nitrogen", "organic carbon"))
 
## End(Not run)

---

Convenient functions for various tasks

Description

Define a concepts

Usage

rtematres.define(term)

Arguments

term	The concept you are looking for

Details

The function retrieves the definition of a term. This works of course only given the case it has been described in the vocuabulary you query.

Value

It returns a text string describing the concept of interest

---

Locate concepts in hierarchy

Description

Search the thesaurus for concepts and extract their hirarchy. This envolves higher order and lower order terms.

Usage

rtematres.hierarchy(term)

Arguments

term	The concept you are looking for

Value

The function returns a character vector of concepts

Examples

## Not run: 
	rtematres.hierarchy("carbon")
 
## End(Not run)

---

Summarize information for a concept

Description

Summarizes information for a concept in one convenient function call. Currently it provides the definition, upstream and down stream concepts for the term you querry for and related concepts

Usage

rtematres.illuminate(input)

Arguments

input

A concept name as string

Value

The function returns a list containing the information

Examples

## Not run: 
    rtematres.illuminate(input = "carbon")
 
## End(Not run)

---

Set or query otions related to the rtematresdata R package.

Description

This function is used to query and set the options used by the rtematres package. For example you can set the URLs to your tematres server and the API.

Usage

rtematres.options(...)

Arguments

...	similar to options. see examples below.

Examples

#Tematres URLs
rtematres.options('tematres_url')
rtematres.options(tematres_url="http://www.example.com")

---

Search for concepts

Description

Search the thesaurus for concepts. This function is a wrapper and so it calls the appropriate funtions depending on the search task.

Usage

rtematres.search(term, includenotes = FALSE)

Arguments

term	The concept you are looking for
includenotes	Include definition texts in the search (true, false). Note that one is only working for searches containing > 2 characters. otherwise it is just ignored.

Value

The function returns a vecor or a list of results for the search

---

Create a summary for a vector

Description

Search the thesaurus for concepts in case of categorical textual vector. Create a five value summary for numerical columns.

Usage

rtematres.summary(input)

Arguments

input

A categorial vector

Value

The function returns a summary

Examples

## Not run: 
    rtematres.summary(input = iris$Species)
    lapply(iris, function(x) rtematres.summary(input = x))
 
## End(Not run)

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