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2014-07-28Address platform dependence of tests/pyrithione.Rranke9-85/+70
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@102 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2014-07-28Add a doctype declaration to the index.ranke1-1/+3
- Thanks Kurt Hornik for checking for valid html - This is my first HTML 5 document git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@101 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2014-03-18Improvements on the EDx calculations in drcfit. However, in cases that there ↵ranke5-20/+29
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
2014-02-25More detailed documentation of the result dataframe returnedranke2-58/+148
by drfit and drcfit. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@99 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2014-02-25Feature-complete version of the new drfit package that can make useranke12-73/+508
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 packagingranke11-34/+163
- 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 testsranke9-86/+112
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 ↵ranke6-23/+23
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 ↵ranke2-4/+4
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.frameranke4-12/+23
- 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 CRANranke10-26/+68
- 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 todayranke3-16/+17
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 charactersranke9-38/+38
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 ranke6-58/+48
(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 ranke2-6/+6
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 ranke2-5/+9
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 ranke2-20/+28
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
2006-08-21New and hopefully final version of the drfit-Rnews article.ranke1-0/+0
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@84 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-08-14- New version just published on my websiteranke8-69/+141
- 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
2006-05-23Further reduced the digits in the pyrithione test, ranke2-32/+32
since it still differed between amd64 and i386. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@82 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-23Only print 5 digits in the tests, since I get some differencesranke10-98/+98
in the last digits between amd64 and i386. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@81 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-22Make the logit model work again, by setting a sensibleranke7-24/+38
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
2006-05-19This is now the officially accepted version of the article.ranke1-0/+0
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@79 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-05-08- Corrected the use of the par() function, so no ranke5-21/+15
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 calculationranke3-4/+6
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. Nowranke8-135/+181
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"))()ranke3-4/+10
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 setranke29-50/+419
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.ranke2-3/+4
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
2006-04-26Took out tabs from R help files, and fixed the formatting.ranke6-82/+82
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@71 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-26- drplot: Removed the call to get(getOption("device")), since it causedranke5-33/+28
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
2006-04-26Small documentation fixranke1-1/+1
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@69 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 wayranke3-8/+14
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, ranke5-148/+85
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
2006-04-21First chunk of work for making checkplate an aliasranke1-0/+101
to checkexperiment which will also work for the ecotox database. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@65 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-21Finally committed the version that was submitted to ranke9-84/+4
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
2006-04-05Small documentation fixranke1-13/+12
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@63 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-04-03- The drplot function now accepts custom xlim and ylim valuesranke6-23/+63
- 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. ranke6-289/+319
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 eachranke6-622/+620
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 drplotranke6-5/+11
- 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 documentationranke11-22/+68
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 fileranke11-49/+133
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 lowestranke3-112/+123
dose level is smaller than 0.5. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@56 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-01-02A fix for a bug that kept drplot from plotting if no control data ranke1-3/+2
are present in the dose-response data frame. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@55 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
2006-01-02- Added a little documentation of the sample data in inst/doc.ranke6-13/+92
- 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
2006-01-02datenranke3-0/+33
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@53 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

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