From 699448335d6fc5668b569577cb38a628c258eaec Mon Sep 17 00:00:00 2001 From: ranke Date: Wed, 21 Dec 2005 15:33:22 +0000 Subject: Changed the terminology from EC50 to ED50 reflecting that the package is meant for dose-response analysis in general and not only for concentration-response analysis. This is the first revision that has been prepared with the knowledge of the existence of the drc package for dose-response curve analysis. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@48 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- chm/00Index.html | 28 ---------- chm/Rchm.css | 25 --------- chm/antifoul.html | 49 ------------------ chm/checkplate.html | 68 ------------------------ chm/drdata.html | 147 ---------------------------------------------------- chm/drfit.chm | Bin 30423 -> 0 bytes chm/drfit.hhp | 18 ------- chm/drfit.html | 99 ----------------------------------- chm/drfit.toc | 59 --------------------- chm/drplot.html | 143 -------------------------------------------------- chm/logo.jpg | Bin 8793 -> 0 bytes 11 files changed, 636 deletions(-) delete mode 100644 chm/00Index.html delete mode 100644 chm/Rchm.css delete mode 100644 chm/antifoul.html delete mode 100755 chm/checkplate.html delete mode 100644 chm/drdata.html delete mode 100644 chm/drfit.chm delete mode 100644 chm/drfit.hhp delete mode 100644 chm/drfit.html delete mode 100644 chm/drfit.toc delete mode 100644 chm/drplot.html delete mode 100644 chm/logo.jpg (limited to 'chm') diff --git a/chm/00Index.html b/chm/00Index.html deleted file mode 100644 index 066b05a..0000000 --- a/chm/00Index.html +++ /dev/null @@ -1,28 +0,0 @@ -Dose-response data evaluation - - -

Dose-response data evaluation -

- -
- - - - - -

Help pages for package `drfit' version 0.03-9

- - - - - - - - - - - - - -
antifoulDose-Response data for TBT and Zink Pyrithione in IPC-81 cells
checkplateCheck raw data from a specified microtiter plate
drdataGet dose-response data
drfitFit dose-response models
drplotPlot dose-response models
- diff --git a/chm/Rchm.css b/chm/Rchm.css deleted file mode 100644 index badd579..0000000 --- a/chm/Rchm.css +++ /dev/null @@ -1,25 +0,0 @@ -BODY{ background: white; - color: black } - -A:link{ background: white; - color: blue } -A:visited{ background: white; - color: rgb(50%, 0%, 50%) } - -H1{ background: white; - color: rgb(55%, 55%, 55%); - font-family: monospace; - font-size: large; - text-align: center } - -H2{ background: white; - color: rgb(0%, 0%, 100%); - font-family: monospace; - text-align: center } - -H3{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace } - -IMG.toplogo{ vertical-align: middle } - diff --git a/chm/antifoul.html b/chm/antifoul.html deleted file mode 100644 index 810c5e9..0000000 --- a/chm/antifoul.html +++ /dev/null @@ -1,49 +0,0 @@ -Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells - - - - -
antifoul(drfit)R Documentation
- - - - - -

Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

- - -

Description

- -

-This data set shows the response of the rat leukaemic cell line IPC-81 to -dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved -from the "cytotox" database of the UFT Department of Bioorganic Chemistry on -February 25, 2004 -

- - -

Usage

- -
data(antifoul)
- - -

Format

- -

-A dataframe containing 135 and 81 data points for concentrations and responses -for TBT and Zink Pyrithione, respectively. Additional data from the database is -also present. -

- - -

Source

- -

-http://www.uft.uni-bremen.de/chemie -

- - - -
[Package Contents]
- - diff --git a/chm/checkplate.html b/chm/checkplate.html deleted file mode 100755 index d545656..0000000 --- a/chm/checkplate.html +++ /dev/null @@ -1,68 +0,0 @@ -Check raw data from a specified microtiter plate - - - - -
checkplate(drfit)R Documentation
- - - - - -

Check raw data from a specified microtiter plate

- - -

Description

- -

-Report metadata from a specified microtiter plate from a specified database, box -plot positive and negative (blind) controls, and show the response data on the -plate. -

- - -

Usage

- -
-  checkplate(plate,db="cytotox")
-
- - -

Arguments

- - - - - - -
plate -The number of the plate identifying it within the database.
db -The database to be used. Currently only "cytotox" of the UFT Department of -Bioorganic Chemistry is supported.
- -

Value

- -

-The function lists a report and shows two graphs.

- -

Author(s)

- -

-Johannes Ranke -jranke@uni-bremen.de -http://www.uft.uni-bremen.de/chemie/ranke -

- - -

Examples

- -
-# Check plate number 1 in the cytotox database
-## Not run: data <- checkplate(1)
-
- - - -
[Package Contents]
- - diff --git a/chm/drdata.html b/chm/drdata.html deleted file mode 100644 index a2ef9d9..0000000 --- a/chm/drdata.html +++ /dev/null @@ -1,147 +0,0 @@ -Get dose-response data - - - - -
drdata(drfit)R Documentation
- - - - - -

Get dose-response data

- - -

Description

- -

-Get dose-response data from a remote mysql server -

- - -

Usage

- -
-  drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81", 
-    whereClause = "1", ok = "'ok'")
-
- - -

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.
db -The database to be used. Currently only "cytotox" of the UFT Department of -Bioorganic Chemistry is supported.
celltype -Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.
whereClause -With this argument, additional conditions for the SQL query can be set, -e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).
ok -With the default value "'ok'", only data that has been checked and set to "ok" -in the database is retrieved. Another sensible argument would be "'ok','?'", in -order to additionally retrieve data which has not yet been checked.
- -

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
-. -

- - -

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.
- -

Author(s)

- -

-Johannes Ranke -jranke@uni-bremen.de -http://www.uft.uni-bremen.de/chemie/ranke -

- - -

Examples

- -
-# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
-## Not run: data <- drdata(c("TBT","Zn Pyrithion"))
-
- - - -
[Package Contents]
- - diff --git a/chm/drfit.chm b/chm/drfit.chm deleted file mode 100644 index d88cbb3..0000000 Binary files a/chm/drfit.chm and /dev/null differ diff --git a/chm/drfit.hhp b/chm/drfit.hhp deleted file mode 100644 index 40a9b74..0000000 --- a/chm/drfit.hhp +++ /dev/null @@ -1,18 +0,0 @@ -[OPTIONS] -Auto Index=Yes -Contents file=drfit.toc -Compatibility=1.1 or later -Compiled file=drfit.chm -Default topic=00Index.html -Display compile progress=No -Full-text search=Yes -Full text search stop list file=..\..\..\gnuwin32\help\R.stp - - -[FILES] -00Index.html -antifoul.html -checkplate.html -drdata.html -drfit.html -drplot.html diff --git a/chm/drfit.html b/chm/drfit.html deleted file mode 100644 index 23dd70f..0000000 --- a/chm/drfit.html +++ /dev/null @@ -1,99 +0,0 @@ -Fit dose-response models - - - - -
drfit(drfit)R Documentation
- - - - - -

Fit dose-response models

- - -

Description

- -

-Fit dose-response relationships to dose-response data and calculate -biometric results for (eco)toxicity evaluation -

- - -

Usage

- -
-  drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE, 
-    linearlogis = FALSE, b0 = 2, f0 = 0)
-
- - -

Arguments

- - - - - - - - - - - - - - -
data -A data frame as returned from drdata. The data frame has to -contain at least a factor called "substance", a vector called "unit" -containing the unit used for the dose, a column "response" with the -response values of the test system normalized between 0 and 1 and a column -"dose" with the numeric dose values. For later use of the -drplot function, a factor called "dosefactor" also has to be -present, containing the dose as a factor. -
startlogEC50 -Especially for the linearlogis model, a suitable log10 of the EC50 has to be given -by the user, since it is not correctly estimated for data showing hormesis with -the default estimation method.
lognorm -A boolean defining if cumulative density curves of normal distributions -are fitted to the data. Default ist TRUE.
logis -A boolean defining if cumulative densitiy curves of logistic distributions -are fitted to the data. Default is FALSE.
linearlogis -A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra -1993 is fitted to the data. Default is FALSE.
b0,f0 -If the linearlogistic model is fitted, b0 and f0 give the possibility to -adapt the starting values for the parameters b and f.
- -

Value

- - - - -
results -A data frame containing at least one line for each substance. If the data did not -show a mean response < 0.5 at the highest dose level, the modeltype is set to "none". -Every successful fit is reported in one line. Parameters of the fitted curves are only -reported if the fitted EC50 is not higher than the highest dose.
- -

Author(s)

- -

-Johannes Ranke -jranke@uni-bremen.de -http://www.uft.uni-bremen.de/chemie/ranke -

- - -

Examples

- -
-data(antifoul)
-r <- drfit(antifoul)
-format(r,digits=2)
-
- - - -
[Package Contents]
- - diff --git a/chm/drfit.toc b/chm/drfit.toc deleted file mode 100644 index e80cc53..0000000 --- a/chm/drfit.toc +++ /dev/null @@ -1,59 +0,0 @@ - - - - diff --git a/chm/drplot.html b/chm/drplot.html deleted file mode 100644 index 84cf12e..0000000 --- a/chm/drplot.html +++ /dev/null @@ -1,143 +0,0 @@ -Plot dose-response models - - - - -
drplot(drfit)R Documentation
- - - - - -

Plot dose-response models

- - -

Description

- -

-Produce graphics of dose-response data and dose-response relationships -either combined or separately, for one or more substances. -

- - -

Usage

- -
-  drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
-    postscript, color, datacolors, fitcolors)
-
- - -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - -
drresults -A data frame as returned from drfit. -
data -A data frame as returned from drdata. If data is to be -plotted, the data frame has to contain at least a factor called -"substance", a vector called "unit" containing the unit used for the dose, -a column "response" with the response values of the test system normalized -between 0 and 1, a column "dose" with the numeric dose values and a factor -called "dosefactor" containing the dose as a factor. If plotting of the data is -not required, data can be set to FALSE. -
dtype -A string describing if the raw data should be plotted ("raw"), or -an error bar should be constructed from the standard deviations of the -responses at each dose level ("std", default value) or from the confidence -intervals ("conf"). Of course, dtype only makes a difference, if a valid data -object has been referenced. -
alpha -The confidence level, defaulting to 0.95, only used if dtype "conf" has been -chosen. -
path -The path where graphic files should be put if any are produced. Defaults -to "./" i.e. the current working directory of R. -
fileprefix -A string which will form the beginning of each filename, if graphic files are -created. Defaults to "drplot". -
overlay -If TRUE, all output will be put into one graph, otherwise a separate graph -will be created for each substance. In the latter case, on-screen display -(postscript=FALSE) only works correctly for data plots. Dose-response models -will all be put into the last graph in this case. -
postscript -If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be -displayed with a screen graphics device. -
color -If TRUE, a sensible selection of colors will be attempted. If false, everything -will be drawn in black -
datacolors -This is a vector of colors, defaulting to 1:8, used for plotting the data. -
fitcolors -Here you can specify a palette for the colors of the dose-response fits. The -default value is "default", which produces the default palette, if the -number of fits to be plotted is 8 or less. Otherwise, rainbow colors -will be plotted. Unless there is more than one fit per substance to be plotted, -or the number of fits is larger than 8, the fitcolors will match the -datacolors. -
- -

Value

- - - - -
results -You will get plots of data and/or the fitted dose-response curves, on the -screen and/or as postscript files, depending on the parameters. -
- -

Note

- -

-Turn off the colors if you don't like them and don't want to fiddle with -them. Treatment of legends is quite bad. Be sure all devices are closed -(e.g. by calling dev.off()) before calling drplot again. -

- - -

Author(s)

- -

-Johannes Ranke -jranke@uni-bremen.de -http://www.uft.uni-bremen.de/chemie/ranke -

- - -

Examples

- -
-data(antifoul)
-r <- drfit(antifoul)
-## Not run: drplot(r,antifoul)
-
- - - -
[Package Contents]
- - diff --git a/chm/logo.jpg b/chm/logo.jpg deleted file mode 100644 index b8e2149..0000000 Binary files a/chm/logo.jpg and /dev/null differ -- cgit v1.2.1