Changed the way confidence intervals are being calculated. Now

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

5 files changed, 115 insertions, 80 deletions

diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
index b67ed2a..b56b8c9 100644
--- a/tests/IM1xIPC81.Rout.save
+++ b/tests/IM1xIPC81.Rout.save
@@ -16,6 +16,7 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(drfit)
+Loading required package: MASS
 Loading required package: RODBC
 > data(IM1xIPC81)
 > rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
@@ -35,41 +36,45 @@ IM15 BF4: Fitting data...
 IM16 BF4: Fitting data...
 
 IM17 BF4: Fitting data...
+Waiting for profiling to be done...
 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...
+Waiting for profiling to be done...
 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...
+Waiting for profiling to be done...
 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...
+Waiting for profiling to be done...
 > 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
+   Substance ndl   n         lld      lhd    mtype   logED50      2.5%
+1   IM13 BF4   9  81  0.59176003 3.000000 inactive        NA        NA
+2   IM14 BF4  20 216 -0.01030017 3.176091   no fit        NA        NA
+3   IM15 BF4   9 135  0.59176003 3.000000 inactive        NA        NA
+4   IM16 BF4   9 108  0.59176003 3.000000 inactive        NA        NA
+5   IM17 BF4   9  81  0.59176003 3.000000 linlogit 2.5785719 2.5057219
+6   IM18 BF4   9 135  0.59176003 3.000000 linlogit 1.6806040 1.6229756
+7   IM19 BF4   9  81  0.59176003 3.000000 linlogit 1.6496121 1.5984793
+8 IM1-10 BF4  11 162 -0.01030017 3.000000 linlogit 0.7696961 0.6870081
+      97.5% unit     sigma         a        b          c
+1        NA   然        NA        NA       NA         NA
+2        NA   然        NA        NA       NA         NA
+3        NA   然        NA        NA       NA         NA
+4        NA   然        NA        NA       NA         NA
+5 2.6617385   然 0.2375857 2.5785719 2.300216 0.01468034
+6 1.7418917   然 0.2324871 1.6806040 2.237338 0.05719295
+7 1.7031463   然 0.1452716 1.6496121 1.976976 0.10956088
+8 0.8544213   然 0.2987708 0.7696961 1.936253 0.45808612
 > 
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
index 5d37703..bebdcea 100644
--- a/tests/IM1xVibrio.Rout.save
+++ b/tests/IM1xVibrio.Rout.save
@@ -16,42 +16,51 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(drfit)
+Loading required package: MASS
 Loading required package: RODBC
 > data(IM1xVibrio)
 > rIM1xVibrio <- drfit(IM1xVibrio)
 
 IM13 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM14 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM15 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM16 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM17 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM18 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM19 BF4: Fitting data...
+Waiting for profiling to be done...
 
 IM1-10 BF4: Fitting data...
+Waiting for profiling to be done...
 > 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
+   Substance ndl  n      lld     lhd  mtype    logED50       2.5%      97.5%
+1   IM13 BF4  13 22 -5.30103 4.69897 probit  3.9399128  3.8636215  4.0160099
+2   IM14 BF4  12 57 -4.30103 4.69897 probit  3.5442110  3.5030166  3.5855474
+3   IM15 BF4   7 20 -0.30103 4.69897 probit  3.1398488  3.1135935  3.1662394
+4   IM16 BF4  13 30 -4.30103 4.69897 probit  3.1804247  3.1435815  3.2176152
+5   IM17 BF4  10 20 -1.30103 4.69897 probit  2.4317301  2.3680656  2.4951179
+6   IM18 BF4  10 17 -2.30103 2.69897 probit  1.4015187  1.3146736  1.4880647
+7   IM19 BF4  13 22 -5.30103 2.69897 probit  0.7157942  0.6703743  0.7592458
+8 IM1-10 BF4  11 20 -6.30103 2.69897 probit -0.1790307 -0.2569430 -0.1037183
+  unit      sigma          a         b
+1   然 0.06302893  3.9399128 0.5763074
+2   然 0.05905375  3.5442110 0.6561300
+3   然 0.02695476  3.1398488 0.5526675
+4   然 0.04514079  3.1804247 0.4881559
+5   然 0.04773317  2.4317301 0.6386547
+6   然 0.05611347  1.4015187 0.8008513
+7   然 0.02956284  0.7157942 0.6969275
+8   然 0.04098662 -0.1790307 0.8019351
 > 
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
index 7bcc0df..d8098ae 100644
--- a/tests/XY.Rout.save
+++ b/tests/XY.Rout.save
@@ -16,6 +16,7 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(drfit)
+Loading required package: MASS
 Loading required package: RODBC
 > data(XY)
 > rXY <- drfit(XY)
@@ -23,15 +24,16 @@ Loading required package: RODBC
 Control: Fitting data...
 
 Substance X: Fitting data...
+Waiting for profiling to be done...
 
 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
+    Substance ndl  n  lld  lhd    mtype  logED50     2.5%    97.5% unit
+1     Control   1  6 -Inf -Inf inactive       NA       NA       NA mg/L
+2 Substance X   4 12    1    3   probit 2.161905 2.105861 2.214359 mg/L
+3 Substance Y   4 12    1    3   active       NA       NA       NA mg/L
+       sigma        a         b
+1         NA       NA        NA
+2 0.04131746 2.161905 0.5061306
+3         NA       NA        NA
 > 
diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save
index 5bc166c..9967240 100644
--- a/tests/antifoul.Rout.save
+++ b/tests/antifoul.Rout.save
@@ -16,18 +16,21 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(drfit)
+Loading required package: MASS
 Loading required package: RODBC
 > data(antifoul)
 > rantifoul <- drfit(antifoul)
 
 TBT: Fitting data...
+Waiting for profiling to be done...
 
 Zn Pyrithion: Fitting data...
+Waiting for profiling to be done...
 > 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
+     Substance ndl   n       lld     lhd  mtype    logED50       2.5%
+1          TBT  38 135 -2.709271 2.39794 probit -0.1643560 -0.2650411
+2 Zn Pyrithion  27  81 -2.107210 2.00000 probit -0.3979222 -0.5078291
+        97.5% unit     sigma          a         b
+1 -0.05648615   然 0.1928611 -0.1643560 0.6763882
+2 -0.29156056   然 0.2286560 -0.3979222 0.4169632
 > 
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
index fb11ca9..2a05dd8 100644
--- a/tests/pyrithione.Rout.save
+++ b/tests/pyrithione.Rout.save
@@ -16,70 +16,86 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(drfit)
+Loading required package: MASS
 Loading required package: RODBC
 > data(pyrithione)
 > rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
 
 Na Pyrithion: Fitting data...
+Waiting for profiling to be done...
+Error in prof$getProfile() : number of iterations exceeded maximum of 50
 
 Pyridin: Fitting data...
 
 PyNO: Fitting data...
 
 (PT)2: Fitting data...
+Waiting for profiling to be done...
 
 MSO2P: Fitting data...
 
 MSPHI: Fitting data...
+Waiting for profiling to be done...
 
 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
+Waiting for profiling to be done...
+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) 
 
 Zn Pyrithion: Fitting data...
+Waiting for profiling to be done...
 
 Cu Pyrithion: Fitting data...
+Waiting for profiling to be done...
 
 Fe Pyrithion: Fitting data...
+Waiting for profiling to be done...
 
 (PyS)2: Fitting data...
 Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp,  : 
 	singular gradient
+Waiting for profiling to be done...
 
 MSPT: Fitting data...
+Waiting for profiling to be done...
 
 TBT: Fitting data...
+Waiting for profiling to be done...
 
 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
+      Substance ndl   n       lld     lhd    mtype    logED50       2.5%
+1  Na Pyrithion  20 108 -2.107210 2.00000 linlogit -0.3461318         NA
+2       Pyridin  19 161  0.591760 3.69897 inactive         NA         NA
+3          PyNO  19  81  0.591760 3.69897   no fit         NA         NA
+4         (PT)2  19  81 -2.408240 2.00000 linlogit -0.4197042 -0.5326102
+5         MSO2P  28 108 -1.709271 3.69897 inactive         NA         NA
+6         MSPHI  19  81  0.591760 3.69897   probit  3.6625025  3.5548278
+7           PyS  18  80 -0.408240 3.00000   probit  2.6817944         NA
+8  Zn Pyrithion  27  81 -2.107210 2.00000 linlogit -0.4132886 -0.5293327
+9  Cu Pyrithion  19  79 -2.408240 2.00000 linlogit -0.3074717 -0.4753489
+10 Fe Pyrithion  19  81 -2.408240 2.00000 linlogit -0.3534573 -0.5003829
+11       (PyS)2  20  81 -0.408240 3.00000   probit  1.7840499  1.6726792
+12         MSPT  18 108 -0.408240 3.00000   probit  2.1384811  2.0709306
+13          TBT  38 135 -2.709271 2.39794 linlogit -0.1580954 -0.2602139
+14          NaJ  10 108  0.591760 3.30103 inactive         NA         NA
+         97.5% unit      sigma          a         b           c
+1           NA   然 0.20857751 -0.3461318 2.1188275 -0.26698926
+2           NA   然         NA         NA        NA          NA
+3           NA   然 0.09188853         NA        NA          NA
+4           NA   然 0.20509070 -0.4197042 1.8467290 -0.51505615
+5           NA   然         NA         NA        NA          NA
+6   3.88053203   然 0.12943273  3.6625025 0.4387540          NA
+7           NA   然 0.13401920  2.6817944 0.1250523          NA
+8  -0.29979846   然 0.22877916 -0.4132886 1.7424848  0.61079006
+9  -0.15442805   然 0.24494451 -0.3074717 1.0150650 -0.04897413
+10 -0.21459555   然 0.23383185 -0.3534573 1.1823561  0.02510663
+11  1.88824519   然 0.23298721  1.7840499 0.4098018          NA
+12  2.20511512   然 0.22881257  2.1384811 0.2112625          NA
+13 -0.05045493   然 0.19264079 -0.1580954 1.0406577 -0.02416082
+14          NA   然         NA         NA        NA          NA
 >