From 23528ad9b4f07434b3249f1e48ade1e0d07528bf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 02:11:57 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/IM1xIPC81.html | 28 ++++- docs/reference/IM1xVibrio.html | 28 ++++- docs/reference/XY.html | 28 ++++- docs/reference/antifoul.html | 30 ++++- docs/reference/checkcontrols.html | 30 ++++- docs/reference/checkexperiment.html | 30 ++++- docs/reference/checksubstance.html | 30 ++++- docs/reference/drcfit.html | 34 ++++-- docs/reference/drdata.html | 97 +++++++--------- docs/reference/drfit-package-1.png | Bin 60443 -> 64002 bytes docs/reference/drfit-package.html | 34 ++++-- docs/reference/drfit.html | 34 ++++-- docs/reference/drplot-1.png | Bin 0 -> 28404 bytes docs/reference/drplot-2.png | Bin 0 -> 26761 bytes docs/reference/drplot.html | 34 ++++-- docs/reference/index.html | 224 +++++++++++++++++++----------------- docs/reference/linlogitf.html | 30 ++++- docs/reference/pyrithione.html | 28 ++++- 18 files changed, 474 insertions(+), 245 deletions(-) create mode 100644 docs/reference/drplot-1.png create mode 100644 docs/reference/drplot-2.png (limited to 'docs/reference') diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index 2800440..d14afca 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -62,8 +68,12 @@ - drfit + + drfit + 0.7.1 + + @@ -87,12 +98,15 @@ -
+

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

+ +
+

This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the @@ -105,6 +119,7 @@ This is a subset (only the BF4 anion) of the data shown in Figure 3 in Ranke et al. (2004).

+ 
data(IM1xIPC81)
@@ -214,5 +229,8 @@
+ + + diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html index 22ab40e..594efe1 100644 --- a/docs/reference/IM1xVibrio.html +++ b/docs/reference/IM1xVibrio.html @@ -21,12 +21,15 @@ + + + - - - + + + + + + @@ -59,8 +65,12 @@ - drfit + + drfit + 0.7.1 +
+
@@ -84,12 +95,15 @@ -
+

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

+ +
+

This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the marine luminescent bacteria V. @@ -99,6 +113,7 @@ IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.

+ 
data(IM1xVibrio)
@@ -248,5 +263,8 @@
+ + + diff --git a/docs/reference/XY.html b/docs/reference/XY.html index 47ef324..2af3026 100644 --- a/docs/reference/XY.html +++ b/docs/reference/XY.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
+
@@ -79,16 +90,20 @@ -
+

Dose-Response data for two substances X and Y

+ +
+

This is just a sample Lemna growth rate data set for two substances arbitrarily named X and Y.

+ 
data(XY)
@@ -133,5 +148,8 @@
+ + + diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index 8dd00c9..d166ebd 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -21,19 +21,25 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ - drfit + + drfit + 0.7.1 +
+
@@ -81,18 +92,22 @@ -
+

Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

+ +
+

This data set shows the response of the rat leukaemic cell line IPC-81 to dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved from the "cytotox" database of the UFT Department of Bioorganic Chemistry on February 25, 2004

+ 
data(antifoul)
@@ -199,5 +214,8 @@
+ + + diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index 2ab3e4d..d3e4314 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
+
@@ -79,23 +90,27 @@ -
+

Check raw data from range of plates or experiments

+ +
+

Report control data from a specified range of microtiter plates or experiments from a specified database.

+ 
checkcontrols(last = 10, id = NULL, db = "cytotox",
                 celltype = "IPC-81", enzymetype = "AChE",
                 organism = "Vibrio fischeri",
                 endpoint = "%", qcc = c("R", "xbar"))
-

Arguments

+

Arguments

@@ -182,5 +197,8 @@ + + + diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html index 3ec5a09..0712cd4 100644 --- a/docs/reference/checkexperiment.html +++ b/docs/reference/checkexperiment.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,21 +90,25 @@ -
+

Check raw data from a specified experiment or microtiter plate

+ +
+

Report metadata from a specified experiment or microtiter plate from a specified database, box plot controls, and plot the dose-response data.

+ 
checkplate(id, db = "cytotox")
   checkexperiment(id, db = "ecotox", endpoint = "%")
-

Arguments

+

Arguments

@@ -155,5 +170,8 @@ + + + diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html index 184a757..3f07df2 100644 --- a/docs/reference/checksubstance.html +++ b/docs/reference/checksubstance.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,23 +90,27 @@ -
+

Check raw data for a specified substance

+ +
+

Report metadata for a specified substance from a specified database, and plot the data.

+ 
checksubstance(substance, db = "cytotox", experimentator = "%",
     celltype = "%", enzymetype = "%", organism = "%",
     endpoint = "%",
     whereClause = "1", ok = "%")
-

Arguments

+

Arguments

@@ -189,5 +204,8 @@ + + + diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index b208f4b..d08b4b0 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,22 +90,26 @@ -
+

Fit dose-response models using the drc package

+ +
+

Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation using the drc package

+ 
drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95,
   showED50 = FALSE, EDx = NULL)
-

Arguments

+

Arguments

@@ -215,9 +230,9 @@

See also

-

Further examples are given in help pages to the datasets +

Further examples are given in help pages to the datasets antifoul, IM1xIPC81 and - IM1xVibrio.

+ IM1xVibrio.

Examples

@@ -270,5 +285,8 @@ + + + diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index 6387e76..fc962be 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - drfit + + drfit + 0.7.1 + + @@ -78,21 +89,25 @@ -
+

Get dose-response data via RODBC

+ +
+

Get dose-response data from an adequate ODBC data source

+ 
drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
     enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
     whereClause = "1", ok = "'ok','no fit'")
-

Arguments

+

Arguments

@@ -165,55 +180,24 @@ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the respective data source with data source name (DSN) "cytotox". For my setting using unixodbc, I am using the file /etc/odbcinst.ini - containing:

- - - - - - - - - - - -
- [MySQL]
- Description = MySQL driver for ODBC
- Driver = /usr/local/lib/libmyodbc.so
- Setup = /usr/lib/odbc/libodbcmyS.so

and the file /etc/odbc.ini containing:

- - - - - - - - - - - - - - - - - - - - - - - -
- [cytotox]
- Description = Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
- Driver = MySQL
- Trace = Yes
- TraceFile = /tmp/odbc.log
- Database = cytotox
- Server = eckehaat
- Port = 3306
+ containing:

+ + + + + +
[MySQL]
Description=MySQL driver for ODBC
Driver=/usr/local/lib/libmyodbc.so
Setup=/usr/lib/odbc/libodbcmyS.so
[MySQL]
+

and the file /etc/odbc.ini containing:

+ + + + + + + + + +
[cytotox]
Description=Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
Driver=MySQL
Trace=Yes
TraceFile=/tmp/odbc.log
Database=cytotox
Server=eckehaat
Port=3306
[cytotox]

Examples

@@ -256,5 +240,8 @@
+ + + diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png index 64d831f..62e80fb 100644 Binary files a/docs/reference/drfit-package-1.png and b/docs/reference/drfit-package-1.png differ diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html index 1ce4fed..d2aa326 100644 --- a/docs/reference/drfit-package.html +++ b/docs/reference/drfit-package.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - drfit + + drfit + 0.7.1 +
+
@@ -78,15 +89,19 @@ -
+

Dose-response data evaluation

+ +
+

See ../DESCRIPTION

+

Details

@@ -102,9 +117,9 @@ of R for chemists.

See also

-

On CRAN, there is another, more statistically sophisticated package with +

On CRAN, there is another, more statistically sophisticated package with similar functionality called drc. I think the advantage of my package -is its user-friendliness.

+is its user-friendliness.

Examples

@@ -116,7 +131,7 @@ is its user-friendliness.

#> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 #> b #> 1 0.68 -#> 2 0.42
drplot(r,antifoul,overlay=TRUE,bw=FALSE)
+#> 2 0.42
drplot(r,antifoul,overlay=TRUE,bw=FALSE)
+ + + diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 4430a5b..4aa7935 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,16 +90,20 @@ -
+

Fit dose-response models

+ +
+

Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation

+ 
drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
@@ -96,7 +111,7 @@
   showED50 = FALSE,
   EDx = NULL, EDx.tolerance = 1e-4)
-

Arguments

+

Arguments

@@ -255,12 +270,12 @@

See also

-

Further examples are given in help pages to the datasets +

Further examples are given in help pages to the datasets antifoul, IM1xIPC81 and IM1xVibrio. Since version 0.6.1 of this package, there is a drop-in replacement function drcfit which internally uses the drc package and also gives - confidence intervals for EDx values via this package.

+ confidence intervals for EDx values via this package.

Examples

@@ -309,5 +324,8 @@ + + + diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png new file mode 100644 index 0000000..bcddcd1 Binary files /dev/null and b/docs/reference/drplot-1.png differ diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png new file mode 100644 index 0000000..75a75af Binary files /dev/null and b/docs/reference/drplot-2.png differ diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index b64d4e5..e5cbb22 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,22 +90,26 @@ -
+

Plot dose-response models

+ +
+

Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances.

+ 
drplot(drresults, data, dtype, alpha, ctype, path,
      fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript,
      pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos)
-

Arguments

+

Arguments

@@ -243,9 +258,7 @@ 
data(antifoul)
 r <- drfit(antifoul)
#> 
 #> TBT: Fitting data...
#> Waiting for profiling to be done...
#> 
-#> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
# NOT RUN {
-drplot(r,antifoul)
-# }
+#> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
drplot(r,antifoul)
+ + + diff --git a/docs/reference/index.html b/docs/reference/index.html index e3ecd24..2b1f884 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -21,13 +21,19 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - drfit + + drfit + 0.7.1 + + @@ -75,112 +86,108 @@ -
-
+
+
-

- Reference - version 0.7.1 -

+

Reference

-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-

All functions

-

-
-

data

-

Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

-

checkcontrols

-

Check raw data from range of plates or experiments

-

checkplate checkexperiment

-

Check raw data from a specified experiment or microtiter plate

-

drcfit

-

Fit dose-response models using the drc package

-

drdata

-

Get dose-response data via RODBC

-

drfit-package

-

Dose-response data evaluation

-

drfit

-

Fit dose-response models

-

drplot

-

Plot dose-response models

-

data

-

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

-

data

-

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

-

linlogitf

-

Linear-logistic function

-

data

-

Cytotoxicity data for different pyrithionates and related species

-

data

-

Dose-Response data for two substances X and Y

-
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+

All functions

+

+
+

IM1xIPC81

+

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

+

IM1xVibrio

+

Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

+

XY

+

Dose-Response data for two substances X and Y

+

antifoul

+

Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

+

checkcontrols()

+

Check raw data from range of plates or experiments

+

checkplate() checkexperiment()

+

Check raw data from a specified experiment or microtiter plate

+

drcfit()

+

Fit dose-response models using the drc package

+

drdata()

+

Get dose-response data via RODBC

+

drfit-package

+

Dose-response data evaluation

+

drfit()

+

Fit dose-response models

+

drplot()

+

Plot dose-response models

+

linlogitf()

+

Linear-logistic function

+

pyrithione

+

Cytotoxicity data for different pyrithionates and related species

+ + + diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index deed92a..1dddf50 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
+ @@ -79,20 +90,24 @@ -
+

Linear-logistic function

+ +
+

Helper function describing a special type of dose-response curves, showing a stimulus at subtoxic doses.

+ 
linlogitf(x,k,f,mu,b)
-

Arguments

+

Arguments

@@ -159,5 +174,8 @@ + + + diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index d7b6ced..1488ecb 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -21,18 +21,24 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ - drfit + + drfit + 0.7.1 + + @@ -80,17 +91,21 @@ -
+

Cytotoxicity data for different pyrithionates and related species

+ +
+

This data shows the cytotoxicity of pyrithione salts as well as the free pyrithione, its oxidation product and some other related compounds to the IPC-81 cell line.

+ 
data(pyrithione)
@@ -138,5 +153,8 @@
+ + + -- cgit v1.2.1