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-rw-r--r--ChangeLog10
-rw-r--r--DESCRIPTION4
-rw-r--r--GNUmakefile32
-rw-r--r--tests/IM1xIPC81.Rout.save9
-rw-r--r--tests/IM1xVibrio.Rout.save9
-rw-r--r--tests/XY.Rout.save11
-rw-r--r--tests/antifoul.Rout.save11
-rw-r--r--tests/pyrithione.R2
-rw-r--r--tests/pyrithione.Rout.save67
9 files changed, 70 insertions, 85 deletions
diff --git a/ChangeLog b/ChangeLog
index 35a8a35..c29f20a 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,13 @@
+2014-07-28 Johannes Ranke
+
+ * DESCRIPTION: New verson 0.6.3
+
+ * inst/test: Reduced precision in pyrithione.R as results were
+ platform dependent. Updated all .Rout.save files
+
+ * inst/doc/index.html: Make the index contain valid html. Thanks to
+ Kurt Hornik for checking HTML validity in CRAN packages.
+
2014-03-18 Johannes Ranke
* DESCRIPTION, NAMESPACE: New verson 0.6.1, with the drc package as
diff --git a/DESCRIPTION b/DESCRIPTION
index 4bf9df4..ba4f425 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: drfit
-Version: 0.6.1
-Date: 2014-03-18
+Version: 0.6.3
+Date: 2014-07-28
Title: Dose-response data evaluation
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre"),
email = "jranke@uni-bremen.de"))
diff --git a/GNUmakefile b/GNUmakefile
index dfc1b7b..64aa9d4 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -1,6 +1,7 @@
PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
PKGSRC := $(shell basename $(PWD))
+TGZ := ../$(PKGNAME)_$(PKGVERS).tar.gz
# Specify the directory holding R binaries. To use an alternate R build (say a
# pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...`
@@ -8,31 +9,6 @@ PKGSRC := $(shell basename $(PWD))
# containing the first instance of R on the PATH.
RBIN ?= $(shell dirname "`which R`")
-.PHONY: help
-
-help:
- @echo "\nExecute development tasks for $(PKGNAME)\n"
- @echo "Usage: \`make <task>\` where <task> is one of:"
- @echo ""
- @echo "Development Tasks"
- @echo "-----------------"
- @echo " build Create the package"
- @echo " check Invoke build and then check the package"
- @echo " install Invoke build and then install the result"
- @echo ""
- @echo "Packaging Tasks"
- @echo "---------------"
- @echo " release Give some reminders"
- @echo ""
- @echo "Using R in: $(RBIN)"
- @echo "Set the RBIN environment variable to change this."
- @echo ""
-
-
-#------------------------------------------------------------------------------
-# Development Tasks
-#------------------------------------------------------------------------------
-
build:
cd ..;\
"$(RBIN)/R" CMD build $(PKGSRC)
@@ -44,3 +20,9 @@ install: build
check: build
cd ..;\
"$(RBIN)/R" CMD check --as-cran $(PKGNAME)_$(PKGVERS).tar.gz
+
+winbuilder: build
+ @echo "Uploading to R-release on win-builder"
+ curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-release/
+ @echo "Uploading to R-devel on win-builder"
+ curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/
diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
index 203ac66..3ed2681 100644
--- a/tests/IM1xIPC81.Rout.save
+++ b/tests/IM1xIPC81.Rout.save
@@ -1,7 +1,6 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -17,8 +16,6 @@ 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)
@@ -89,4 +86,4 @@ Waiting for profiling to be done...
>
> proc.time()
user system elapsed
- 0.852 0.024 0.869
+ 1.111 0.808 0.789
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
index e54ba59..4878972 100644
--- a/tests/IM1xVibrio.Rout.save
+++ b/tests/IM1xVibrio.Rout.save
@@ -1,7 +1,6 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -17,8 +16,6 @@ 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)
@@ -75,4 +72,4 @@ Waiting for profiling to be done...
>
> proc.time()
user system elapsed
- 0.864 0.024 0.879
+ 1.261 0.995 0.953
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
index fc5b0cd..a3f84c0 100644
--- a/tests/XY.Rout.save
+++ b/tests/XY.Rout.save
@@ -1,7 +1,7 @@
-R version 2.9.2 (2009-08-24)
-Copyright (C) 2009 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+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.
@@ -16,8 +16,6 @@ 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,logit=TRUE,weibull=TRUE,chooseone=FALSE)
@@ -45,3 +43,6 @@ Substance Y: Fitting data...
4 3.0096 2.03624
5 NA NA
>
+> proc.time()
+ user system elapsed
+ 0.609 0.379 0.491
diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save
index 6846b1e..ff69334 100644
--- a/tests/antifoul.Rout.save
+++ b/tests/antifoul.Rout.save
@@ -1,7 +1,7 @@
-R version 2.9.2 (2009-08-24)
-Copyright (C) 2009 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+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.
@@ -16,8 +16,6 @@ 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)
@@ -36,3 +34,6 @@ Waiting for profiling to be done...
1 0.19286 -0.16436 0.67637
2 0.22866 -0.39792 0.41696
>
+> proc.time()
+ user system elapsed
+ 0.743 0.555 0.612
diff --git a/tests/pyrithione.R b/tests/pyrithione.R
index 3a3ff23..87552aa 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","PyS"))
-print(rpyr,digits=4)
+print(rpyr,digits=2)
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
index eb92b80..f796a40 100644
--- a/tests/pyrithione.Rout.save
+++ b/tests/pyrithione.Rout.save
@@ -1,7 +1,6 @@
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -17,8 +16,6 @@ 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","PyS"))
@@ -75,36 +72,36 @@ Waiting for profiling to be done...
NaJ: Fitting data...
-> 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
+> print(rpyr,digits=2)
+ Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma
+1 Na Pyrithion 20 108 -2.11 2.0 linlogit -0.35 -0.43 -0.26 microM 0.21
+2 Pyridin 19 161 0.59 3.7 inactive NA NA NA microM NA
+3 PyNO 19 81 0.59 3.7 no fit NA NA NA microM 0.11
+4 (PT)2 19 81 -2.41 2.0 linlogit -0.42 -0.53 NA microM 0.21
+5 MSO2P 28 108 -1.71 3.7 inactive NA NA NA microM NA
+6 MSPHI 19 81 0.59 3.7 probit 3.66 3.55 3.88 microM 0.13
+7 PyS 18 80 -0.41 3.0 probit 2.68 NA NA microM 0.13
+8 Zn Pyrithion 27 81 -2.11 2.0 linlogit -0.41 -0.53 -0.30 microM 0.23
+9 Cu Pyrithion 19 79 -2.41 2.0 linlogit -0.31 -0.48 -0.15 microM 0.24
+10 Fe Pyrithion 19 81 -2.41 2.0 linlogit -0.35 -0.50 -0.21 microM 0.23
+11 MSPT 18 108 -0.41 3.0 probit 2.14 2.07 2.21 microM 0.23
+12 TBT 38 135 -2.71 2.4 linlogit -0.16 -0.26 -0.05 microM 0.19
+13 NaJ 10 108 0.59 3.3 inactive NA NA NA microM NA
+ a b c
+1 -0.35 2.12 -0.267
+2 NA NA NA
+3 NA NA NA
+4 -0.42 1.85 -0.515
+5 NA NA NA
+6 3.66 0.44 NA
+7 2.68 0.13 NA
+8 -0.41 1.74 0.611
+9 -0.31 1.02 -0.049
+10 -0.35 1.18 0.025
+11 2.14 0.21 NA
+12 -0.16 1.04 -0.024
+13 NA NA NA
>
> proc.time()
user system elapsed
- 1.556 0.044 1.595
+ 2.302 1.804 1.550

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