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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
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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
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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
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- 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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- 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
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Added example data IM1xIPC81.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@61 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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function.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@60 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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- 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
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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
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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
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dose level is smaller than 0.5.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@56 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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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
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- 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
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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
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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
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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
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filenames with ghostscript.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@45 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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to let people without the X11() device make pngs, too.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@43 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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checkplate function.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@41 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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to topleft instead of topright.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@40 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@36 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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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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git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@31 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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bug that prevented
fitting the weibull function in most cases in the last version. Also, the log EC50 is reported
as estimated with nlm from the fitted weibull model. Because of the important changes, mainly
in naming the different models which leads to incompatibility with the old drfit syntax,
I am increasing the minor version number to 0.04 with this release.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@30 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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- Addition of the weibull fit
- Renaming of lognorm to probit, logis to logit, and linearlogis to linlogit
- Fix of a bug that prevented the logis fit to work in recent version
- Different way of listing parameters in the output.
- Documentation of changes
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@29 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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R version 2.1.0.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@28 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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both for single substance plots and for overlay plots.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@27 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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units in drfit. Added cat output from drfit to keep track of which substance is currently
being worked on.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@26 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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that produce
misleading or wrong fits with all dose-response models.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@25 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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the "ok" column. They are not used for fitting, but they are plotted.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@21 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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parentheses () are not substituted any more. Only whitespace is substituted
by "_".
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@20 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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legend(s).
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@19 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@18 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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to the drfit function.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@16 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@14 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@13 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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drfit function, so only one fit is reported per substance.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@12 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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drfit function, so it now also works with larger datasets,
and if some substances have no data.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@11 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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the same colors are chosen for data and fited curves.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@9 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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is restricted. JR
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@7 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
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