aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2012-12-16 01:39:42 +0000
committerranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2012-12-16 01:39:42 +0000
commit88937b957b30b9e197858ebc3a3219079fd01f96 (patch)
treed42710bc11354294c11f589fc187194654bed4b4
parent63a62f35db409b3814d3be960fa23e7554a29197 (diff)
Added NAMESPACE and fixed the tests
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@96 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
-rw-r--r--DESCRIPTION4
-rw-r--r--NAMESPACE12
-rw-r--r--data/00Index2
-rw-r--r--tests/IM1xIPC81.R2
-rw-r--r--tests/IM1xIPC81.Rout.save54
-rw-r--r--tests/IM1xVibrio.R2
-rw-r--r--tests/IM1xVibrio.Rout.save46
-rw-r--r--tests/pyrithione.R4
-rw-r--r--tests/pyrithione.Rout.save72
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

Contact - Imprint