From ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 24 Mar 2017 15:22:07 +0100 Subject: Add pkgdown docu, change package build directory --- docs/reference/drdata.html | 245 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 245 insertions(+) create mode 100644 docs/reference/drdata.html (limited to 'docs/reference/drdata.html') diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html new file mode 100644 index 0000000..e369c5c --- /dev/null +++ b/docs/reference/drdata.html @@ -0,0 +1,245 @@ + + + + + + + + +Get dose-response data via RODBC — drdata • drfit + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Get dose-response data via RODBC

+
+ + +

Get dose-response data from an adequate ODBC data source

+ + + 
drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
+    enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
+    whereClause = "1", ok = "'ok','no fit'")
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
substances

A string or an array of strings with the substance names for + which dose-response data is to be retrieved.

experimentator

The name of the experimentator whose data is to be used. Default is " + which means that data from all experimentators are retrieved.

db

The database to be used. Currently, the databases "cytotox", "enzymes" + and "ecotox" of the UFT Department of Bioorganic Chemistry are + supported (default is "cytotox").

celltype

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.

enzymetype

Currently, only data for AChE, GR and GST are supported.

organism

The organism that was exposed to the chemical. Only important if the database + "ecotox" is used. Defaults to "Vibrio fischeri".

endpoint

The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "Luminescence".

whereClause

With this argument, additional conditions for the SQL query can be set, + e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The + default is 1 (in SQL syntax this means TRUE).

ok

With the default value "'ok','no fit'", only data that has been checked and + set to "ok" or "no fit" in the database is retrieved. The argument "no fit" + will result in not using the data for fitting, but it will be plotted. + Another sensible argument would be "'ok','no fit','?'", in order to + additionally retrieve data which has not yet been checked.

+ +

Value

+ +

+
data

A data frame with a factor describing the dose levels, the numeric dose + levels and a numeric column describing the response, as well as the entries + for plate, experimentator, performed (date of test performance), celltype, + unit (of the dose/concentration), and for the ok field in the database.

+ + +

Details

+ +

The function is currently only used for retrieving data from the + mysql database "cytotox" of the UFT Department of Bioorganic Chemistry. + Access to this database is limited to UFT staff. Additionally to the + installation of the RODBC package, it is required to set up a ODBC data + source with the name "cytotox", using an ODBC driver for mysql, probably + myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the + respective data source with data source name (DSN) "cytotox". For my + setting using unixodbc, I am using the file /etc/odbcinst.ini + containing:

+ + + + + + + + + + + +
+ [MySQL]
+ Description
= MySQL driver for ODBC
+ Driver =
/usr/local/lib/libmyodbc.so + Setup
= /usr/lib/odbc/libodbcmyS.so

and the file /etc/odbc.ini containing:

+ + + + + + + + + + + + + + + + + + + + + + + +
+ [cytotox]
+ Description
= Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
+ Driver =
MySQL + Trace
= Yes
+ TraceFile =
/tmp/odbc.log + Database
= cytotox
+ Server =
eckehaat + Port
= 3306
+ + +

Examples

+ 
# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+# cells
+## Not run: drdata(c("TBT","ZnPT2"))
+
+ +
+ + +
+ + + -- cgit v1.2.1