Added NAMESPACE and fixed the tests

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@96 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

9 files changed, 112 insertions, 86 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 636ad8a..b5bfb8a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.05-95
-Date: 2009-10-11
+Version: 0.05-96
+Date: 2012-10-29
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..0b39883
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,12 @@
+# Default NAMESPACE created by R
+# Remove the previous line if you edit this file
+
+# Export all names
+exportPattern(".")
+
+# Import all packages listed as Imports or Depends
+import(
+  stats,
+  MASS,
+  RODBC
+)
diff --git a/data/00Index b/data/00Index
deleted file mode 100644
index 6cdea42..0000000
--- a/data/00Index
+++ /dev/null
@@ -1,2 +0,0 @@
-antifoul                Dose-Response data for TBT and Zink Pyrithione
-                        in IPC-81 cells
diff --git a/tests/IM1xIPC81.R b/tests/IM1xIPC81.R
index 52b5653..475fcae 100644
--- a/tests/IM1xIPC81.R
+++ b/tests/IM1xIPC81.R
@@ -1,4 +1,4 @@
 library(drfit)
 data(IM1xIPC81)
 rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
-print(rIM1xIPC81,digits=5)
+print(rIM1xIPC81,digits=4)
diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
index db37e67..203ac66 100644
--- a/tests/IM1xIPC81.Rout.save
+++ b/tests/IM1xIPC81.Rout.save
@@ -1,7 +1,8 @@
 
-R version 2.9.2 (2009-08-24)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -31,7 +32,7 @@ Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp,  :
 Error in numericDeriv(form[[3L]], names(ind), env, ifelse(internalPars <  : 
   Missing value or an infinity produced when evaluating the model
 In addition: Warning message:
-In pnorm(q, mean, sd, lower.tail, log.p) : NaNs produced
+In pnorm(-log10(dose), -logED50, scale) : NaNs produced
 
 IM15 BF4: Fitting data...
 
@@ -45,7 +46,7 @@ Waiting for profiling to be done...
 Error in numericDeriv(form[[3L]], names(ind), env, ifelse(internalPars <  : 
   Missing value or an infinity produced when evaluating the model
 In addition: Warning message:
-In pnorm(q, mean, sd, lower.tail, log.p) : NaNs produced
+In pnorm(-log10(dose), -logED50, scale) : NaNs produced
 
 IM18 BF4: Fitting data...
 
@@ -53,7 +54,7 @@ Waiting for profiling to be done...
 Error in numericDeriv(form[[3L]], names(ind), env, ifelse(internalPars <  : 
   Missing value or an infinity produced when evaluating the model
 In addition: Warning message:
-In pnorm(q, mean, sd, lower.tail, log.p) : NaNs produced
+In pnorm(-log10(dose), -logED50, scale) : NaNs produced
 
 IM19 BF4: Fitting data...
 
@@ -61,28 +62,31 @@ Waiting for profiling to be done...
 Error in numericDeriv(form[[3L]], names(ind), env, ifelse(internalPars <  : 
   Missing value or an infinity produced when evaluating the model
 In addition: Warning message:
-In pnorm(q, mean, sd, lower.tail, log.p) : NaNs produced
+In pnorm(-log10(dose), -logED50, scale) : NaNs produced
 
 IM1-10 BF4: Fitting data...
 
 Waiting for profiling to be done...
-> print(rIM1xIPC81,digits=5)
-   Substance ndl   n       lld    lhd    mtype logED50    2.5%   97.5%   unit
-1   IM13 BF4   9  81  0.591760 3.0000 inactive      NA      NA      NA microM
-2   IM14 BF4  20 216 -0.010300 3.1761   no fit      NA      NA      NA microM
-3   IM15 BF4   9 135  0.591760 3.0000 inactive      NA      NA      NA microM
-4   IM16 BF4   9 108  0.591760 3.0000 inactive      NA      NA      NA microM
-5   IM17 BF4   9  81  0.591760 3.0000 linlogit  2.5786 2.50572 2.66174 microM
-6   IM18 BF4   9 135  0.591760 3.0000 linlogit  1.6806 1.62297 1.74189 microM
-7   IM19 BF4   9  81  0.591760 3.0000 linlogit  1.6496 1.59848 1.70315 microM
-8 IM1-10 BF4  11 162 -0.010300 3.0000 linlogit  0.7697 0.68701 0.85442 microM
-    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 0.23759 2.5786 2.3002 0.014680
-6 0.23249 1.6806 2.2373 0.057193
-7 0.14527 1.6496 1.9770 0.109561
-8 0.29877 0.7697 1.9363 0.458090
+> print(rIM1xIPC81,digits=4)
+   Substance ndl   n     lld   lhd    mtype logED50  2.5%  97.5%   unit  sigma
+1   IM13 BF4   9  81  0.5918 3.000 inactive      NA    NA     NA microM     NA
+2   IM14 BF4  20 216 -0.0103 3.176   no fit      NA    NA     NA microM     NA
+3   IM15 BF4   9 135  0.5918 3.000 inactive      NA    NA     NA microM     NA
+4   IM16 BF4   9 108  0.5918 3.000 inactive      NA    NA     NA microM     NA
+5   IM17 BF4   9  81  0.5918 3.000 linlogit  2.5786 2.506 2.6617 microM 0.2376
+6   IM18 BF4   9 135  0.5918 3.000 linlogit  1.6806 1.623 1.7419 microM 0.2325
+7   IM19 BF4   9  81  0.5918 3.000 linlogit  1.6496 1.598 1.7031 microM 0.1453
+8 IM1-10 BF4  11 162 -0.0103 3.000 linlogit  0.7697 0.687 0.8544 microM 0.2988
+       a     b       c
+1     NA    NA      NA
+2     NA    NA      NA
+3     NA    NA      NA
+4     NA    NA      NA
+5 2.5786 2.300 0.01468
+6 1.6806 2.237 0.05719
+7 1.6496 1.977 0.10956
+8 0.7697 1.936 0.45809
 > 
+> proc.time()
+   user  system elapsed 
+  0.852   0.024   0.869 
diff --git a/tests/IM1xVibrio.R b/tests/IM1xVibrio.R
index 8fb23d2..83aa878 100644
--- a/tests/IM1xVibrio.R
+++ b/tests/IM1xVibrio.R
@@ -1,4 +1,4 @@
 library(drfit)
 data(IM1xVibrio)
 rIM1xVibrio <- drfit(IM1xVibrio)
-print(rIM1xVibrio,digits=5)
+print(rIM1xVibrio,digits=4)
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
index ccfdc48..e54ba59 100644
--- a/tests/IM1xVibrio.Rout.save
+++ b/tests/IM1xVibrio.Rout.save
@@ -1,7 +1,8 @@
 
-R version 2.9.2 (2009-08-24)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -52,23 +53,26 @@ Waiting for profiling to be done...
 IM1-10 BF4: Fitting data...
 
 Waiting for profiling to be done...
-> print(rIM1xVibrio,digits=5)
-   Substance ndl  n      lld    lhd  mtype  logED50     2.5%    97.5%   unit
-1   IM13 BF4  13 22 -5.30103 4.6990 probit  3.93991  3.86362  4.01601 microM
-2   IM14 BF4  12 57 -4.30103 4.6990 probit  3.54421  3.50302  3.58555 microM
-3   IM15 BF4   7 20 -0.30103 4.6990 probit  3.13985  3.11359  3.16624 microM
-4   IM16 BF4  13 30 -4.30103 4.6990 probit  3.18042  3.14358  3.21762 microM
-5   IM17 BF4  10 20 -1.30103 4.6990 probit  2.43173  2.36807  2.49512 microM
-6   IM18 BF4  10 17 -2.30103 2.6990 probit  1.40152  1.31467  1.48806 microM
-7   IM19 BF4  13 22 -5.30103 2.6990 probit  0.71579  0.67038  0.75925 microM
-8 IM1-10 BF4  11 20 -6.30103 2.6990 probit -0.17903 -0.25694 -0.10372 microM
-     sigma        a       b
-1 0.063029  3.93991 0.57631
-2 0.059054  3.54421 0.65613
-3 0.026955  3.13985 0.55267
-4 0.045141  3.18042 0.48816
-5 0.047733  2.43173 0.63865
-6 0.056113  1.40152 0.80085
-7 0.029563  0.71579 0.69693
-8 0.040987 -0.17903 0.80194
+> print(rIM1xVibrio,digits=4)
+   Substance ndl  n    lld   lhd  mtype logED50    2.5%   97.5%   unit   sigma
+1   IM13 BF4  13 22 -5.301 4.699 probit  3.9399  3.8636  4.0160 microM 0.06303
+2   IM14 BF4  12 57 -4.301 4.699 probit  3.5442  3.5030  3.5855 microM 0.05905
+3   IM15 BF4   7 20 -0.301 4.699 probit  3.1398  3.1136  3.1662 microM 0.02695
+4   IM16 BF4  13 30 -4.301 4.699 probit  3.1804  3.1436  3.2176 microM 0.04514
+5   IM17 BF4  10 20 -1.301 4.699 probit  2.4317  2.3681  2.4951 microM 0.04773
+6   IM18 BF4  10 17 -2.301 2.699 probit  1.4015  1.3147  1.4881 microM 0.05611
+7   IM19 BF4  13 22 -5.301 2.699 probit  0.7158  0.6704  0.7592 microM 0.02956
+8 IM1-10 BF4  11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099
+        a      b
+1  3.9399 0.5763
+2  3.5442 0.6561
+3  3.1398 0.5527
+4  3.1804 0.4882
+5  2.4317 0.6387
+6  1.4015 0.8009
+7  0.7158 0.6969
+8 -0.1790 0.8019
 > 
+> proc.time()
+   user  system elapsed 
+  0.864   0.024   0.879 
diff --git a/tests/pyrithione.R b/tests/pyrithione.R
index baec676..3a3ff23 100644
--- a/tests/pyrithione.R
+++ b/tests/pyrithione.R
@@ -1,4 +1,4 @@
 library(drfit)
 data(pyrithione)
-rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
-print(rpyr,digits=3)
+rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI","PyS"))
+print(rpyr,digits=4)
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
index af67552..eb92b80 100644
--- a/tests/pyrithione.Rout.save
+++ b/tests/pyrithione.Rout.save
@@ -1,7 +1,8 @@
 
-R version 2.9.2 (2009-08-24)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -19,7 +20,7 @@ Type 'q()' to quit R.
 Loading required package: MASS
 Loading required package: RODBC
 > data(pyrithione)
-> rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
+> rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI","PyS"))
 
 Na Pyrithion: Fitting data...
 
@@ -47,6 +48,10 @@ Waiting for profiling to be done...
 PyS: Fitting data...
 
 Waiting for profiling to be done...
+Error in numericDeriv(form[[3L]], names(ind), env, ifelse(internalPars <  : 
+  Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+In pnorm(-log10(dose), -logED50, scale) : NaNs produced
 
 Zn Pyrithion: Fitting data...
 
@@ -70,33 +75,36 @@ Waiting for profiling to be done...
 
 NaJ: Fitting data...
 
-> print(rpyr,digits=3)
-      Substance ndl   n    lld lhd    mtype logED50   2.5%   97.5%   unit sigma
-1  Na Pyrithion  20 108 -2.107 2.0 linlogit  -0.346 -0.428 -0.2648 microM 0.209
-2       Pyridin  19 161  0.592 3.7 inactive      NA     NA      NA microM    NA
-3          PyNO  19  81  0.592 3.7   no fit      NA     NA      NA microM 0.107
-4         (PT)2  19  81 -2.408 2.0 linlogit  -0.420 -0.533      NA microM 0.205
-5         MSO2P  28 108 -1.709 3.7 inactive      NA     NA      NA microM    NA
-6         MSPHI  19  81  0.592 3.7   probit   3.663  3.555  3.8802 microM 0.129
-7           PyS  18  80 -0.408 3.0 linlogit   2.756     NA  2.8228 microM 0.146
-8  Zn Pyrithion  27  81 -2.107 2.0 linlogit  -0.413 -0.529 -0.2998 microM 0.229
-9  Cu Pyrithion  19  79 -2.408 2.0 linlogit  -0.307 -0.475 -0.1544 microM 0.245
-10 Fe Pyrithion  19  81 -2.408 2.0 linlogit  -0.353 -0.500 -0.2146 microM 0.234
-11         MSPT  18 108 -0.408 3.0   probit   2.138  2.071  2.2051 microM 0.229
-12          TBT  38 135 -2.709 2.4 linlogit  -0.158 -0.260 -0.0505 microM 0.193
-13          NaJ  10 108  0.592 3.3 inactive      NA     NA      NA microM    NA
-        a     b         c
-1  -0.346 2.119 -0.266998
-2      NA    NA        NA
-3      NA    NA        NA
-4  -0.420 1.847 -0.515071
-5      NA    NA        NA
-6   3.663 0.439        NA
-7   2.756 0.743 -0.000993
-8  -0.413 1.742  0.610900
-9  -0.307 1.015 -0.048966
-10 -0.353 1.182  0.025082
-11  2.138 0.211        NA
-12 -0.158 1.041 -0.024165
-13     NA    NA        NA
+> print(rpyr,digits=4)
+      Substance ndl   n     lld   lhd    mtype logED50    2.5%    97.5%   unit
+1  Na Pyrithion  20 108 -2.1072 2.000 linlogit -0.3461 -0.4276 -0.26479 microM
+2       Pyridin  19 161  0.5918 3.699 inactive      NA      NA       NA microM
+3          PyNO  19  81  0.5918 3.699   no fit      NA      NA       NA microM
+4         (PT)2  19  81 -2.4082 2.000 linlogit -0.4197 -0.5326       NA microM
+5         MSO2P  28 108 -1.7093 3.699 inactive      NA      NA       NA microM
+6         MSPHI  19  81  0.5918 3.699   probit  3.6625  3.5546  3.88019 microM
+7           PyS  18  80 -0.4082 3.000   probit  2.6818      NA       NA microM
+8  Zn Pyrithion  27  81 -2.1072 2.000 linlogit -0.4133 -0.5293 -0.29980 microM
+9  Cu Pyrithion  19  79 -2.4082 2.000 linlogit -0.3075 -0.4753 -0.15444 microM
+10 Fe Pyrithion  19  81 -2.4082 2.000 linlogit -0.3535 -0.5004 -0.21460 microM
+11         MSPT  18 108 -0.4082 3.000   probit  2.1385  2.0709  2.20511 microM
+12          TBT  38 135 -2.7093 2.398 linlogit -0.1581 -0.2602 -0.05047 microM
+13          NaJ  10 108  0.5918 3.301 inactive      NA      NA       NA microM
+    sigma       a      b        c
+1  0.2086 -0.3461 2.1188 -0.26700
+2      NA      NA     NA       NA
+3  0.1073      NA     NA       NA
+4  0.2051 -0.4197 1.8467 -0.51507
+5      NA      NA     NA       NA
+6  0.1294  3.6625 0.4387       NA
+7  0.1340  2.6818 0.1250       NA
+8  0.2288 -0.4133 1.7425  0.61081
+9  0.2449 -0.3075 1.0151 -0.04897
+10 0.2338 -0.3535 1.1823  0.02508
+11 0.2288  2.1385 0.2113       NA
+12 0.1926 -0.1581 1.0407 -0.02416
+13     NA      NA     NA       NA
 > 
+> proc.time()
+   user  system elapsed 
+  1.556   0.044   1.595