From d04bac001217855b4e9a1490a35bef3325441b55 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Jul 2023 08:24:12 +0200 Subject: Maintenance prompted by email from CRAN - Fix an improper use of 'packageVersion' - Update .Rbuildignore - Fix a link in the README - Static documentation rebuilt by pkgdown::build_site() --- docs/reference/drdata.html | 263 +++++++++++++++------------------------------ 1 file changed, 84 insertions(+), 179 deletions(-) (limited to 'docs/reference/drdata.html') diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index 104e190..a34be4f 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -1,64 +1,12 @@ - - - - - - - -Get dose-response data via RODBC — drdata • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Get dose-response data via RODBC — drdata • drfit - - - - + + -
-
- -
- -
+

Get dose-response data via RODBC

@@ -109,75 +43,67 @@

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. Matching is case-sensitive.

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" +

+ 
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. Matching is case-sensitive.

+ +
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, + 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 + 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

+ additionally retrieve data which has not yet been checked.

-

-
data

A data frame with a factor describing the dose levels, the numeric dose +

+
+

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

- +
+
+

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 @@ -186,66 +112,45 @@ 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

- 
  if (FALSE) {
-
-  # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
-  # cells
-  drdata(c("TBT", "ZnPT2"))
-
-  }
-
- +

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
  if (FALSE) {
+
+  # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+  # cells
+  drdata(c("TBT", "ZnPT2"))
+
+  }
+
+
+
-
- - + + -- cgit v1.2.1