From d09233dd6cd6cf60d3b00b30ee59ec148bba3187 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 15 Sep 2018 20:03:55 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/authors.html | 2 +- docs/index.html | 4 ++-- docs/pkgdown.yml | 2 +- docs/reference/IM1xIPC81.html | 8 ++++---- docs/reference/IM1xVibrio.html | 8 ++++---- docs/reference/XY.html | 8 +------- docs/reference/antifoul.html | 12 +++--------- docs/reference/checkcontrols.html | 6 +++--- docs/reference/checkexperiment.html | 7 +++---- docs/reference/checksubstance.html | 7 ++++--- docs/reference/drcfit.html | 19 +++++++++---------- docs/reference/drdata.html | 18 ++++++++++-------- docs/reference/drfit-package.html | 6 +++--- docs/reference/drfit.html | 17 ++++++++--------- docs/reference/drplot.html | 9 ++++----- docs/reference/index.html | 2 +- docs/reference/linlogitf.html | 3 +-- docs/reference/pyrithione.html | 4 ++-- 18 files changed, 64 insertions(+), 78 deletions(-) (limited to 'docs') diff --git a/docs/authors.html b/docs/authors.html index 514359f..cb71793 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ drfit - 0.7.1 + 0.7.2 diff --git a/docs/index.html b/docs/index.html index 98afd7d..333c303 100644 --- a/docs/index.html +++ b/docs/index.html @@ -19,7 +19,7 @@ distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving - dose-response data retrieved from a database accessed via 'RODBC' are included. + dose-response data retrieved from a database accessed via 'odbc' are included. As an alternative to the original fitting methods, the algorithms from the 'drc' package can be used."> @@ -40,7 +40,7 @@ drfit - 0.7.1 + 0.7.2 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 6e67788..7908647 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 1.19.2.4 +pandoc: 2.2.1 pkgdown: 1.1.0 pkgdown_sha: ~ articles: [] diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index d14afca..3ac5ef7 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -70,7 +70,7 @@ drfit - 0.7.1 + 0.7.2 @@ -126,7 +126,7 @@

Format

A dataframe containing the data as required for the - drfit function. An additional column contains + drfit function. An additional column contains the tested organism (name of the cell line).

Source

@@ -140,7 +140,7 @@

Examples

- 
  rIM1xIPC81 <- drfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
#> 
+    
  rIM1xIPC81 <- drfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
#> 
 #> IM13 BF4: Fitting data...
#> 
 #> IM14 BF4: Fitting data...
#> Warning: NaNs wurden erzeugt
#> 
 #> IM15 BF4: Fitting data...
#> 
@@ -149,7 +149,7 @@
 #> IM18 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Warning: NaNs wurden erzeugt
#> 
 #> IM19 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Warning: NaNs wurden erzeugt
#> 
 #> IM1-10 BF4: Fitting data...
#> Waiting for profiling to be done...

-  rIM1xIPC81.drc <- drcfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
#> 
+  rIM1xIPC81.drc <- drcfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
#> 
 #> IM13 BF4: Fitting data...
#> 
 #> IM14 BF4: Fitting data...
#> 
 #> IM15 BF4: Fitting data...
#> 
diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html
index 594efe1..0dde6b0 100644
--- a/docs/reference/IM1xVibrio.html
+++ b/docs/reference/IM1xVibrio.html
@@ -67,7 +67,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     

 
@@ -119,7 +119,7 @@
         
     
Format

 
-    
A dataframe containing the data as required for the drfit
+    
A dataframe containing the data as required for the drfit
   function. Additional columns contain the species tested (luminescent bacteria
   Vibrio fischeri, organism), and a field specifying if the data is
   regarded valid (ok).

@@ -133,7 +133,7 @@
     
 
     
Examples

-    
  rIM1xVibrio <- drfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+    
  rIM1xVibrio <- drfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
                        showED50 = TRUE, EDx = c(10, 20))
#> 
 #> IM13 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
 #> IM14 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
@@ -176,7 +176,7 @@
 #> 14  0.7172 0.4132    5.2141    4.6652  5.801e+00 6.446e-01    1.394
 #> 15 -0.1790 0.8019    0.6622    0.5534  7.876e-01 6.212e-02    0.140
 #> 16 -0.1831 0.4816    0.6560    0.5470  7.843e-01 5.738e-02    0.141

-  rIM1xVibrio.drc <- drcfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+  rIM1xVibrio.drc <- drcfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
                             showED50 = TRUE, EDx = c(10, 20))
#> 
 #> IM13 BF4: Fitting data...
#> 
 #> IM14 BF4: Fitting data...
#> 
diff --git a/docs/reference/XY.html b/docs/reference/XY.html
index 2af3026..53770a3 100644
--- a/docs/reference/XY.html
+++ b/docs/reference/XY.html
@@ -62,7 +62,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     

 
@@ -112,10 +112,6 @@
     
A dataframe containing dose (concentration) and response data, as well as
   control values where the dose is zero.

     
-    
Source

-
-    
http://www.uft.uni-bremen.de/chemie

-    
 
     
Examples

     
  
# NOT RUN {
@@ -127,8 +123,6 @@
     
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index d166ebd..7ea336a 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -64,7 +64,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     

 
@@ -117,13 +117,9 @@
   for TBT and Zink Pyrithione, respectively. Some additional columns from the
   database are also present.

     
-    
Source

-
-    
http://www.uft.uni-bremen.de/chemie

-    
 
     
Examples

-    
rantifoul.ED50 <- drfit(antifoul,
+    
rantifoul.ED50 <- drfit(antifoul,
                         linlogit = TRUE, logit = TRUE, weibull = TRUE,
                         chooseone = FALSE,
                         showED50 = TRUE, EDx = c(10))
#> 
@@ -155,7 +151,7 @@
 #> 6 0.116872
 #> 7 0.110068
 #> 8 0.121166

-rantifoul.drc <- drcfit(antifoul,
+rantifoul.drc <- drcfit(antifoul,
                         linlogit = TRUE, logit = TRUE, weibull = TRUE,
                         chooseone = FALSE,
                         showED50 = TRUE, EDx = c(10))
#> 
@@ -193,8 +189,6 @@
     
diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html
index d3e4314..30baaed 100644
--- a/docs/reference/checkcontrols.html
+++ b/docs/reference/checkcontrols.html
@@ -62,7 +62,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     

 
@@ -105,7 +105,8 @@
     
     

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

@@ -180,7 +181,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
 
   

 
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
index 0712cd4..937b8dc 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -62,7 +62,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
@@ -105,8 +105,8 @@
     
     
 
-    
checkplate(id, db = "cytotox")
-  checkexperiment(id, db = "ecotox", endpoint = "%")

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

     
     
Arguments

     
@@ -153,7 +153,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 3f07df2..9f5899c 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -62,7 +62,7 @@
       
         drfit
-        0.7.1
+        0.7.2
       
 
@@ -105,7 +105,9 @@
     
     
 
-    
checksubstance(substance, db = "cytotox", experimentator = "%",
+    
checksubstance(substance,
+    db = c("cytotox", "enzymes", "ecotox"),
+    experimentator = "%",
     celltype = "%", enzymetype = "%", organism = "%",
     endpoint = "%",
     whereClause = "1", ok = "%")

@@ -187,7 +189,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
 
   
 
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index d08b4b0..b4c299b 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -62,7 +62,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
@@ -120,7 +120,7 @@
     used for the dose and a numeric vector “response” with the response
     values of the test system normalized between 0 and 1. Such a data frame can
     be easily obtained if a compliant RODBC data source is available for use in
-    conjunction with the function drdata.

+    conjunction with the function drdata.

 
If there is a column called “ok” and it is set to “no fit” in
     a specific line, then the corresponding data point will be excluded from
     the fitting procedure, although it will be plotted.

@@ -130,7 +130,7 @@
       

@@ -139,7 +139,7 @@
     plogis are fitted to the decadic logarithm of the dose.
     Default is FALSE.
     Again the parameter definitions used in the model are different to the
-    ones used in drfit. Parameter e from LL.2 is listed
+    ones used in drfit. Parameter e from LL.2 is listed
     as a here, and parameter b from LL.2 is listed as b.

@@ -147,12 +147,12 @@
       
+    drfit, due to a different model specification.

@@ -212,7 +212,7 @@
     parameters b from BC.4, LN.2,
     LL.2 and W1.2, respectively.
     Note that the parameter definitions (and in the case of Weibull, the model
-    used) are different to the ones used in drfit.

+    used) are different to the ones used in drfit.
c
Only the “linlogit” fit produces a third parameter c, which is
     the parameter f from the BC.4 function.

   If the parameter showED50 was set to TRUE, the ED50 values and their
@@ -231,8 +231,8 @@
     
See also
Further examples are given in help pages to the datasets
-  antifoul, IM1xIPC81 and
-  IM1xVibrio.

+  antifoul, IM1xIPC81 and
+  IM1xVibrio.
Examples

@@ -266,7 +266,6 @@
     
Author

     
   Johannes Ranke jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
   The functionality of the drc package used under the hood in this function
   was written by Christian Ritz.
 
diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html
index fc962be..438f32c 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -61,7 +61,7 @@
       
         drfit
-        0.7.1
+        0.7.2
       
 
@@ -103,8 +103,9 @@
     
     
 
-    
drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
-    enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
+    
drdata(substances, experimentator = "%", db = "cytotox",
+    celltype = "IPC-81", enzymetype = "AChE", organism = "Vibrio fischeri",
+    endpoint = "Luminescence",
     whereClause = "1", ok = "'ok','no fit'")

     
     
Arguments

@@ -201,10 +202,12 @@
     
 
     
Examples

-    
# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
-# cells
-
# NOT RUN {
-drdata(c("TBT","ZnPT2"))
+    
  
# NOT RUN {
+  # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+  # cells
+  drdata(c("TBT", "ZnPT2"))
+
+
 # }

   
   
 
diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html
index d2aa326..270cf91 100644
--- a/docs/reference/drfit-package.html
+++ b/docs/reference/drfit-package.html
@@ -61,7 +61,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
@@ -124,14 +124,14 @@ is its user-friendliness.

 
     
Examples

     
data(antifoul)
-r <- drfit(antifoul)
#> 
+r <- drfit(antifoul)
#> 
 #> TBT: Fitting data...
#> Waiting for profiling to be done...
#> 
 #> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
format(r,digits=2)
#>      Substance ndl   n  lld lhd  mtype logED50  2.5%  97.5%   unit sigma     a
 #> 1          TBT  38 135 -2.7 2.4 probit   -0.16 -0.27 -0.056 microM  0.19 -0.16
 #> 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)

   
   
 
@@ -122,7 +122,7 @@
     used for the dose and a numeric vector “response” with the response
     values of the test system normalized between 0 and 1. Such a data frame can
     be easily obtained if a compliant RODBC data source is available for use in
-    conjunction with the function drdata.

+    conjunction with the function drdata.

 
If there is a column called “ok” and it is set to “no fit” in
     a specific line, then the corresponding data point will be excluded from
     the fitting procedure, although it will be plotted.

@@ -156,7 +156,7 @@
     

@@ -249,13 +249,13 @@
     parameter a coincides with the logED50.  In the case of the
     “weibull” model, a is a location parameter.
b
Parameter b in the case of the “linlogit” fit is the variable
-    b from the linlogitf function. In the case of “probit”
+    b from the linlogitf function. In the case of “probit”
     fit it is the standard deviation of the fitted normal distribution, in the
     case of the “logit” fit it is the scale parameter in the
     plogis function, and in the “weibull” fit it is the
     shape parameter of the fitted pweibull function.
c
Only the “linlogit” fit produces a third parameter c which is
-    the variable f from the linlogitf function.

+    the variable f from the linlogitf function.

   If the parameter showED50 was set to TRUE, the ED50 values and their
   confidence intervals are also included on the original dose scale.
 
@@ -271,10 +271,10 @@
     
See also
Further examples are given in help pages to the datasets
-  antifoul, IM1xIPC81 and
-  IM1xVibrio.
+  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
+  drcfit which internally uses the drc package and also gives
   confidence intervals for EDx values via this package.

     
 
@@ -307,7 +307,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
index e5cbb22..24d69a8 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -62,7 +62,7 @@
       
         drfit
-        0.7.1
+        0.7.2
       
 
@@ -114,11 +114,11 @@
     
-      
+      
-      

 
   
 
       
     
A boolean defining if cumulative density curves of normal distributions
     are fitted against the decadic logarithm of the dose.  Default ist TRUE.
     Note that the parameter definitions used in the model are different to the
-    ones used in drfit. Parameter e from LN.2 is listed
+    ones used in drfit. Parameter e from LN.2 is listed
     as a here, and parameter b from there is listed as b.

     

     

     

     
A boolean defining if Weibull dose-response models
     (W1.2 are fitted to the untransformed dose. Default is FALSE.
     Note that the results differ from the ones obtained with
-    drfit, due to a different model specification.

     

     

       linlogit
       
A boolean defining if the linear-logistic function
-    linlogitf as defined by van Ewijk and Hoekstra 1993 is
+    linlogitf as defined by van Ewijk and Hoekstra 1993 is
     fitted to the data. Default is FALSE. Obtaining the ED50 (and EDx values
     in general) uses ED internally and does not always give a
     result.

   
 
     
     
 
     
       
     

       linlogit
       
A boolean defining if the linear-logistic function
-    linlogitf as defined by van Ewijk and Hoekstra 1993 is
+    linlogitf as defined by van Ewijk and Hoekstra 1993 is
     fitted to the data. Default is FALSE.

     

     

   
   
 
     
 
   
 
       
     

     

       drresults
A data frame as returned from drfit.
A data frame as returned from drfit.

     

     

       data
A data frame as returned from drdata. The data frame has to
+      
A data frame as returned from drdata. The data frame has to
     contain at least a factor called "substance", a vector called "unit"
     containing the unit used for the dose, a column "response" with the
     response values of the test system normalized between 0 and 1, a column
@@ -256,7 +256,7 @@
 
     
Examples

     
data(antifoul)
-r <- drfit(antifoul)
#> 
+r <- drfit(antifoul)
#> 
 #> TBT: Fitting data...
#> Waiting for profiling to be done...
#> 
 #> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
drplot(r,antifoul)

   
@@ -276,7 +276,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
 
   
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2b1f884..b05e223 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
index 1dddf50..ba854f0 100644
--- a/docs/reference/linlogitf.html
+++ b/docs/reference/linlogitf.html
@@ -62,7 +62,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
@@ -157,7 +157,6 @@
     
   Johannes Ranke
   jranke@uni-bremen.de
-  http://www.uft.uni-bremen.de/chemie/ranke
 
   
 
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
index 1488ecb..4e608d3 100644
--- a/docs/reference/pyrithione.html
+++ b/docs/reference/pyrithione.html
@@ -63,7 +63,7 @@
       
       
         drfit
-        0.7.1
+        0.7.2
       
     
 
@@ -111,7 +111,7 @@
         
     
Format

 
-    
A dataframe containing the data as required for the drfit
+    
A dataframe containing the data as required for the drfit
   function.

     
     
Source

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