- Fixed the drplot function, so the graphics parameter ask is adequately set

  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

10 files changed, 307 insertions, 0 deletions

diff --git a/tests/IM1xIPC81.R b/tests/IM1xIPC81.R
new file mode 100644
index 0000000..075c84d
--- /dev/null
+++ b/tests/IM1xIPC81.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(IM1xIPC81)
+rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
+rIM1xIPC81
diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
new file mode 100644
index 0000000..b67ed2a
--- /dev/null
+++ b/tests/IM1xIPC81.Rout.save
@@ -0,0 +1,75 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(IM1xIPC81)
+> rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
+
+IM13 BF4: Fitting data...
+
+IM14 BF4: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp,  : 
+	singular gradient
+Error in numericDeriv(form[[3]], names(ind), env) : 
+	Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p) 
+
+IM15 BF4: Fitting data...
+
+IM16 BF4: Fitting data...
+
+IM17 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) : 
+	Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p) 
+
+IM18 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) : 
+	Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p) 
+
+IM19 BF4: Fitting data...
+Error in numericDeriv(form[[3]], names(ind), env) : 
+	Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p) 
+
+IM1-10 BF4: Fitting data...
+> rIM1xIPC81
+   Substance ndl   n         lld      lhd    mtype   logED50        std unit
+1   IM13 BF4   9  81  0.59176003 3.000000 inactive        NA         NA   然
+2   IM14 BF4  20 216 -0.01030017 3.176091   no fit        NA         NA   然
+3   IM15 BF4   9 135  0.59176003 3.000000 inactive        NA         NA   然
+4   IM16 BF4   9 108  0.59176003 3.000000 inactive        NA         NA   然
+5   IM17 BF4   9  81  0.59176003 3.000000 linlogit 2.5785719 0.03819482   然
+6   IM18 BF4   9 135  0.59176003 3.000000 linlogit 1.6806040 0.02982682   然
+7   IM19 BF4   9  81  0.59176003 3.000000 linlogit 1.6496121 0.02636274   然
+8 IM1-10 BF4  11 162 -0.01030017 3.000000 linlogit 0.7696961 0.04165397   然
+      sigma         a        b          c
+1        NA        NA       NA         NA
+2        NA        NA       NA         NA
+3        NA        NA       NA         NA
+4        NA        NA       NA         NA
+5 0.2375857 2.5785719 2.300216 0.01468034
+6 0.2324871 1.6806040 2.237338 0.05719295
+7 0.1452716 1.6496121 1.976976 0.10956088
+8 0.2987708 0.7696961 1.936253 0.45808611
+> 
diff --git a/tests/IM1xVibrio.R b/tests/IM1xVibrio.R
new file mode 100644
index 0000000..ed1a698
--- /dev/null
+++ b/tests/IM1xVibrio.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(IM1xVibrio)
+rIM1xVibrio <- drfit(IM1xVibrio)
+rIM1xVibrio
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
new file mode 100644
index 0000000..5d37703
--- /dev/null
+++ b/tests/IM1xVibrio.Rout.save
@@ -0,0 +1,57 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(IM1xVibrio)
+> rIM1xVibrio <- drfit(IM1xVibrio)
+
+IM13 BF4: Fitting data...
+
+IM14 BF4: Fitting data...
+
+IM15 BF4: Fitting data...
+
+IM16 BF4: Fitting data...
+
+IM17 BF4: Fitting data...
+
+IM18 BF4: Fitting data...
+
+IM19 BF4: Fitting data...
+
+IM1-10 BF4: Fitting data...
+> rIM1xVibrio
+   Substance ndl  n      lld     lhd  mtype    logED50        std unit
+1   IM13 BF4  13 22 -5.30103 4.69897 probit  3.9399128 0.03658457   然
+2   IM14 BF4  12 57 -4.30103 4.69897 probit  3.5442110 0.02060194   然
+3   IM15 BF4   7 20 -0.30103 4.69897 probit  3.1398488 0.01254468   然
+4   IM16 BF4  13 30 -4.30103 4.69897 probit  3.1804247 0.01801591   然
+5   IM17 BF4  10 20 -1.30103 4.69897 probit  2.4317301 0.03015341   然
+6   IM18 BF4  10 17 -2.30103 2.69897 probit  1.4015187 0.04053083   然
+7   IM19 BF4  13 22 -5.30103 2.69897 probit  0.7157942 0.02085130   然
+8 IM1-10 BF4  11 20 -6.30103 2.69897 probit -0.1790307 0.03623821   然
+       sigma          a         b
+1 0.06302893  3.9399128 0.5763074
+2 0.05905375  3.5442110 0.6561300
+3 0.02695476  3.1398488 0.5526675
+4 0.04514079  3.1804247 0.4881559
+5 0.04773317  2.4317301 0.6386547
+6 0.05611347  1.4015187 0.8008513
+7 0.02956284  0.7157942 0.6969275
+8 0.04098662 -0.1790307 0.8019351
+> 
diff --git a/tests/XY.R b/tests/XY.R
new file mode 100644
index 0000000..e295be4
--- /dev/null
+++ b/tests/XY.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(XY)
+rXY <- drfit(XY)
+rXY
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
new file mode 100644
index 0000000..7bcc0df
--- /dev/null
+++ b/tests/XY.Rout.save
@@ -0,0 +1,37 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(XY)
+> rXY <- drfit(XY)
+
+Control: Fitting data...
+
+Substance X: Fitting data...
+
+Substance Y: Fitting data...
+> rXY
+    Substance ndl  n  lld  lhd    mtype  logED50        std unit      sigma
+1     Control   1  6 -Inf -Inf inactive       NA         NA mg/L         NA
+2 Substance X   4 12    1    3   probit 2.161905 0.02425144 mg/L 0.04131746
+3 Substance Y   4 12    1    3   active       NA         NA mg/L         NA
+         a         b
+1       NA        NA
+2 2.161905 0.5061306
+3       NA        NA
+> 
diff --git a/tests/antifoul.R b/tests/antifoul.R
new file mode 100644
index 0000000..f9c1a9d
--- /dev/null
+++ b/tests/antifoul.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(antifoul)
+rantifoul <- drfit(antifoul)
+rantifoul
diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save
new file mode 100644
index 0000000..5bc166c
--- /dev/null
+++ b/tests/antifoul.Rout.save
@@ -0,0 +1,33 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(antifoul)
+> rantifoul <- drfit(antifoul)
+
+TBT: Fitting data...
+
+Zn Pyrithion: Fitting data...
+> rantifoul
+     Substance ndl   n       lld     lhd  mtype    logED50        std unit
+1          TBT  38 135 -2.709271 2.39794 probit -0.1643560 0.05349216   然
+2 Zn Pyrithion  27  81 -2.107210 2.00000 probit -0.3979222 0.05393693   然
+      sigma          a         b
+1 0.1928611 -0.1643560 0.6763882
+2 0.2286560 -0.3979222 0.4169632
+> 
diff --git a/tests/pyrithione.R b/tests/pyrithione.R
new file mode 100644
index 0000000..f05988d
--- /dev/null
+++ b/tests/pyrithione.R
@@ -0,0 +1,4 @@
+library(drfit)
+data(pyrithione)
+rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+rpyr
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
new file mode 100644
index 0000000..fb11ca9
--- /dev/null
+++ b/tests/pyrithione.Rout.save
@@ -0,0 +1,85 @@
+
+R : Copyright 2006, The R Foundation for Statistical Computing
+Version 2.3.0 (2006-04-24)
+ISBN 3-900051-07-0
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> library(drfit)
+Loading required package: RODBC
+> data(pyrithione)
+> rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+
+Na Pyrithion: Fitting data...
+
+Pyridin: Fitting data...
+
+PyNO: Fitting data...
+
+(PT)2: Fitting data...
+
+MSO2P: Fitting data...
+
+MSPHI: Fitting data...
+
+PyS: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp,  : 
+	step factor 0.000488281 reduced below 'minFactor' of 0.000976562
+
+Zn Pyrithion: Fitting data...
+
+Cu Pyrithion: Fitting data...
+
+Fe Pyrithion: Fitting data...
+
+(PyS)2: Fitting data...
+Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp,  : 
+	singular gradient
+
+MSPT: Fitting data...
+
+TBT: Fitting data...
+
+NaJ: Fitting data...
+> rpyr
+      Substance ndl   n       lld     lhd    mtype    logED50        std unit
+1  Na Pyrithion  20 108 -2.107210 2.00000 linlogit -0.3461318 0.04237833   然
+2       Pyridin  19 161  0.591760 3.69897 inactive         NA         NA   然
+3          PyNO  19  81  0.591760 3.69897   no fit         NA         NA   然
+4         (PT)2  19  81 -2.408240 2.00000 linlogit -0.4197031 0.05030460   然
+5         MSO2P  28 108 -1.709271 3.69897 inactive         NA         NA   然
+6         MSPHI  19  81  0.591760 3.69897   probit  3.6625025 0.06724673   然
+7           PyS  18  80 -0.408240 3.00000   probit  2.6817944 0.02031252   然
+8  Zn Pyrithion  27  81 -2.107210 2.00000 linlogit -0.4132885 0.06234927   然
+9  Cu Pyrithion  19  79 -2.408240 2.00000 linlogit -0.3074717 0.07918130   然
+10 Fe Pyrithion  19  81 -2.408240 2.00000 linlogit -0.3534572 0.07263386   然
+11       (PyS)2  20  81 -0.408240 3.00000   probit  1.7840499 0.05230663   然
+12         MSPT  18 108 -0.408240 3.00000   probit  2.1384811 0.03379904   然
+13          TBT  38 135 -2.709271 2.39794 linlogit -0.1580954 0.05474371   然
+14          NaJ  10 108  0.591760 3.30103 inactive         NA         NA   然
+        sigma          a         b           c
+1  0.20857751 -0.3461318 2.1188272 -0.26698979
+2          NA         NA        NA          NA
+3  0.09188853         NA        NA          NA
+4  0.20509070 -0.4197031 1.8466994 -0.51508088
+5          NA         NA        NA          NA
+6  0.12943273  3.6625025 0.4387540          NA
+7  0.13401920  2.6817944 0.1250523          NA
+8  0.22877916 -0.4132885 1.7424846  0.61078660
+9  0.24494451 -0.3074717 1.0150649 -0.04897422
+10 0.23383185 -0.3534572 1.1823558  0.02510613
+11 0.23298721  1.7840499 0.4098018          NA
+12 0.22881257  2.1384811 0.2112625          NA
+13 0.19264079 -0.1580954 1.0406576 -0.02416104
+14         NA         NA        NA          NA
+>