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2014-03-18Improvements on the EDx calculations in drcfit. However, in cases that there ↵ranke1-1/+1
is no hormesis in the data, drfit often fails to fit the linlogit model, and drcfit often fails to find the EDx values. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@100 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2014-02-25Feature-complete version of the new drfit package that can make useranke1-4/+5
of the drc package in order to obtain confidence intervals for EDx values. See ChangeLog for details. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@98 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2014-02-03- Some updates to the packagingranke1-5/+7
- Add the possibility to calculate EDx values - see ChangeLog for a full description git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@97 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2012-12-16Added NAMESPACE and fixed the testsranke1-2/+2
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@96 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2009-10-11Update of the tests to new numerical values at the fourth digit, and new ↵ranke1-2/+2
warning messages git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@95 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2009-10-11Update taking out a link to the package drc that was producing a warning in ↵ranke1-2/+2
the upcoming R 2.10 git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@94 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2008-04-09- Added the possibility to manipulate axes and plot.frameranke1-2/+2
- Adapted the test to the improved confidence interval fitting git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@93 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-11-23- Releasable version for CRANranke1-2/+2
- Changed usage of cat() to message() because the latter does not interfere with Sweave. Left cat() in checkexperiment.R and checksubstance.R git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@92 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-10-01Make drfit compatible with R 2.6.0, checked with prerelease from todayranke1-4/+5
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@91 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-09-21Testranke1-3/+3
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@90 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-03-29- Changed "µM" in all datasets to "microM", since non-Ascii charactersranke1-1/+1
cause a warning in the upcoming R 2.5.0 git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@89 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-03-29Updated the test results and took out the data for ranke1-1/+1
(PyS)2 from pyrithione.rda because it is fitted differently on amd64 and i386 (!). git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@88 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2007-03-29Now using the "port" algorithm for the model fitting ranke1-2/+2
by nls, because in some cases it converges when the default algorithm does not. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@87 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-08-28Fixed the line types in drplot. Now we get different lines ranke1-1/+1
for different fits (same substance), and plotting for multiple substances without overlay as needed for drfit-tox works again. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@86 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-08-28Fix for the weibull fitting. Now there is a warning if ranke1-2/+2
the log ED 50 can not be found, and the log ED50 is not reported. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@85 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-08-14- New version just published on my websiteranke1-2/+2
- Fixes in checkplate, checksubstance and checkexperiment - New arguments ltys, xlab and ylab in drplot, due to a request by Ewa Mulkiewicz git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@83 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-22Make the logit model work again, by setting a sensibleranke1-2/+2
starting value for the scale argument. Now all models get separate starting arguments, with hopefully effective default values. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@80 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-08- Corrected the use of the par() function, so no ranke1-2/+2
unnecessary devices are opened any more - Adjusted the .Rout.save files to kriemhilds version (R 2.3.0 from Debian unstable, i386) git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@78 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-05- Fix of the drfit() function for the case that the calculationranke1-2/+2
of the confidence interval fails - Updated version of the drfit-Rnews preprint git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@77 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-03Changed the way confidence intervals are being calculated. Nowranke1-4/+4
the function confint.nls from the MASS package is being used, after stumbling across the relevant paragraph of the MASS book. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@76 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-28I also removed the get(getOption("device"))()ranke1-1/+1
call from the checkexperiment function, and updated the INDEX. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@75 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-28- Fixed the drplot function, so the graphics parameter ask is adequately setranke1-2/+2
depending on the overlay argument, and set back to the previous value - Added a test for each datase - Added a demo for each dataset - Corrected many small bugs in the documentation and improved formatting of the .Rd files git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@74 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-26Added a note about the user-friendliness of this package.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@73 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-26Fixed the version number.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@72 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-26- drplot: Removed the call to get(getOption("device")), since it causedranke1-2/+2
problems when calling drplot from Sweave code chunks as well as in JGR. - drplot: Removed the output with cat, since it may be annoying to receive a message when a plot was requested - Small documentation adaptations and fixes git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@70 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-21Fix the version number again...ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@68 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-21Added the checkplate.R function, which is now just another wayranke1-1/+1
to call checkexperiment.R, and fixed DESCRIPTION and INDEX git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@67 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-21Working version of the checkexperiment function, ranke1-2/+2
including documentation, but R CMD check tells me that "use of NULL environment is deprecated" git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@66 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-21Finally committed the version that was submitted to ranke1-2/+2
CRAN on April 6 to the SVN repository. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@64 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-03- The drplot function now accepts custom xlim and ylim valuesranke1-2/+2
- Confidence intervals for the EC50 can now (again) be generated by drfit by giving the argument conf=TRUE - Update of the INDEX git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@62 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-01Corrected the split of the drift.R file. ranke1-1/+1
Added example data IM1xIPC81. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@61 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-03-30Split of the drfit.R file to have a separate file for eachranke1-1/+1
function. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@60 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-03-29- Added an error message for drplotranke1-2/+2
- Recalculated the XY data, so the response data is now calculated based on growth rates instead of simple frond numbers - Reduced the number of columns in the IM1xVibrio data git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@59 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-03-16Added the pyrithione and IM1x V. fischeri data with documentationranke1-13/+10
and cleaned the antioul data from some unnecessary components. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@58 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-03-06Added the drfit-package help page, a new sample data fileranke1-2/+2
and a preliminary version of the drfit-Rnews article. R/drfit.R - the possibility to directly write pdf graphs was added - the results dataframe now has numbered lines where it didn't The checkplate and checksubstance functions are now classified internal in their help files. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@57 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-02-27Now the model type (mtype) is set to "active" if the response at the lowestranke1-2/+2
dose level is smaller than 0.5. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@56 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-01-02- Added a little documentation of the sample data in inst/doc.ranke1-2/+2
- Added the possibility to show standard deviation or confidence interval for the mean of the control values, if present in the dose-response data. Also, control data (with dose=0) are not listed in the results data frame of drfit any more. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@54 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-12-22The calculation of dose-response curves in drfit was wrong if the number ofranke1-2/+2
dose levels was different from 9. Now, n is calculated as the rounded mean number of response data per dose level. The number of dose levels ndl is additionally reported. The test was removed because it didn't work properly. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@52 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-12-22Small improvement in the help file for the drfit function.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@51 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-12-21Added a simple test for the drfit function.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@50 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-12-21As usual, I didn't get the DESCRIPTION file right at first.ranke1-2/+2
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@49 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-12-21Changed the terminology from EC50 to ED50 reflecting that the package is meantranke1-1/+1
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
2005-11-25Fixed the check for dose == 0 in drplot() and improvedranke1-2/+2
the model naming in the result table given by drfit() git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@47 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-10-11Go back to the png device, since we get problems with "(" and ")" in theranke1-1/+1
filenames with ghostscript. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@45 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-10-11Fix version number again...ranke1-2/+2
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@44 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-10-10Fix Version number to sync with SVN.ranke1-2/+2
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@42 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-09-16Neue Version ohne deibianization.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@39 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-09-16Corrected the version number to be consistent with the repository.ranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@38 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-09-16Added the documentation for the drdata function update.ranke1-7/+8
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@37 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2005-08-02drplot: Added the pointsize argument for postscript and png graphsranke1-2/+2
drfit: Changed the order of fits in the case of chooseone=TRUE git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@34 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

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