From d04bac001217855b4e9a1490a35bef3325441b55 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Jul 2023 08:24:12 +0200 Subject: Maintenance prompted by email from CRAN - Fix an improper use of 'packageVersion' - Update .Rbuildignore - Fix a link in the README - Static documentation rebuilt by pkgdown::build_site() --- docs/reference/IM1xIPC81.html | 285 ++++++++++------------ docs/reference/IM1xVibrio.html | 375 ++++++++++++++--------------- docs/reference/Rplot001.png | Bin 0 -> 1011 bytes docs/reference/Rplot002.png | Bin 0 -> 13725 bytes docs/reference/XY.html | 126 +++------- docs/reference/antifoul.html | 269 +++++++++------------ docs/reference/checkcontrols.html | 216 ++++++----------- docs/reference/checkexperiment.html | 186 +++++---------- docs/reference/checksubstance.html | 237 +++++++------------ docs/reference/drcfit.html | 369 +++++++++++++---------------- docs/reference/drdata.html | 263 +++++++-------------- docs/reference/drfit.html | 455 ++++++++++++++++-------------------- docs/reference/drplot-1.png | Bin 28331 -> 45593 bytes docs/reference/drplot-2.png | Bin 26640 -> 41522 bytes docs/reference/drplot.html | 369 +++++++++++------------------ docs/reference/index.html | 200 ++++------------ docs/reference/linlogitf.html | 177 +++++--------- docs/reference/pyrithione.html | 134 +++-------- 18 files changed, 1361 insertions(+), 2300 deletions(-) create mode 100644 docs/reference/Rplot001.png create mode 100644 docs/reference/Rplot002.png (limited to 'docs/reference') diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index bd9211c..2ae6a33 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -1,42 +1,5 @@ - - - - - - - -Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit - - - - - - - - - - - - - - + + -
-
- -
- -
+

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

@@ -127,115 +61,142 @@ shown in Figure 3 in Ranke et al. (2004).

- 
data(IM1xIPC81)
- - -

Format

+
+ 
data(IM1xIPC81)
+
+
+

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

- +
+
+

Source

Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404

+
-

Examples

- 
  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...
#> 
-#> IM16 BF4: Fitting data...
#> 
-#> IM17 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Warning: NaNs wurden erzeugt
#> 
-#> 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)
#> 
-#> IM13 BF4: Fitting data...
#> 
-#> IM14 BF4: Fitting data...
#> 
-#> IM15 BF4: Fitting data...
#> 
-#> IM16 BF4: Fitting data...
#> 
-#> IM17 BF4: Fitting data...
#> 
-#> IM18 BF4: Fitting data...
#> 
-#> IM19 BF4: Fitting data...
#> 
-#> IM1-10 BF4: Fitting data...

-  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    ED50 ED50 2.5% ED50 97.5%   EDx10
-#> 1     NA    NA      NA      NA        NA         NA      NA
-#> 2     NA    NA      NA      NA        NA         NA      NA
-#> 3     NA    NA      NA      NA        NA         NA      NA
-#> 4     NA    NA      NA      NA        NA         NA      NA
-#> 5 2.5786 2.300 0.01468 378.941   320.424    458.918 230.782
-#> 6 1.6806 2.237 0.05719  47.930    41.973     55.194  27.367
-#> 7 1.6496 1.977 0.10956  44.628    39.671     50.483  23.031
-#> 8 0.7697 1.936 0.45809   5.884     4.864      7.152   2.835
  print(rIM1xIPC81.drc,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 linlogit      NA     NA     NA microM 0.1529
-#> 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 2.4935 2.6497 microM 0.2376
-#> 6   IM18 BF4   9 135  0.5918 3.000 linlogit  1.6806 1.6168 1.7362 microM 0.2325
-#> 7   IM19 BF4   9  81  0.5918 3.000 linlogit  1.6496 1.5940 1.6990 microM 0.1453
-#> 8 IM1-10 BF4  11 162 -0.0103 3.000 linlogit  0.7697 0.6774 0.8458 microM 0.2988
-#>           a      b          c    ED50 ED50 2.5% ED50 97.5%   EDx10 EDx10 2.5%
-#> 1        NA     NA         NA      NA        NA         NA      NA         NA
-#> 2 5.390e+15 0.3148 -0.0001736      NA        NA         NA      NA         NA
-#> 3        NA     NA         NA      NA        NA         NA      NA         NA
-#> 4        NA     NA         NA      NA        NA         NA      NA         NA
-#> 5 1.281e+02 2.3001  0.0146821 378.964   311.555    446.372 230.790    202.915
-#> 6 2.079e+01 2.2373  0.0571925  47.930    41.382     54.478  27.367     23.809
-#> 7 1.342e+01 1.9773  0.1094542  44.630    39.260     50.000  23.036     20.614
-#> 8 2.258e+00 1.9362  0.4580784   5.884     4.758      7.011   2.835      2.181
-#>   EDx10 97.5%
-#> 1          NA
-#> 2          NA
-#> 3          NA
-#> 4          NA
-#> 5     258.665
-#> 6      30.925
-#> 7      25.459
-#> 8       3.489
-
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html index 70381ec..ae3fceb 100644 --- a/docs/reference/IM1xVibrio.html +++ b/docs/reference/IM1xVibrio.html @@ -1,70 +1,18 @@ - - - - - - - -Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio • drfit - - - - - - - - - - - - - - + + -
-
- -
- -
+

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

@@ -121,155 +55,190 @@ IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.

- 
data(IM1xVibrio)
- - -

Format

+
+ 
data(IM1xVibrio)
+
-

A dataframe containing the data as required for the drfit +

+

Format

+

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).

-

Source

- +
+
+

Source

Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404

+
-

Examples

- 
  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...
#> 
-#> IM15 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> IM16 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> IM17 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> IM18 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> IM19 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> IM1-10 BF4: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
  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    IM13 BF4  13 22 -5.301 4.699  logit  3.9461  3.8708  4.0211 microM 0.06188
-#> 3    IM14 BF4  12 57 -4.301 4.699 probit  3.5442  3.5030  3.5855 microM 0.05905
-#> 4    IM14 BF4  12 57 -4.301 4.699  logit  3.5465  3.5044  3.5885 microM 0.06030
-#> 5    IM15 BF4   7 20 -0.301 4.699 probit  3.1398  3.1136  3.1662 microM 0.02695
-#> 6    IM15 BF4   7 20 -0.301 4.699  logit  3.1387  3.1118  3.1659 microM 0.02723
-#> 7    IM16 BF4  13 30 -4.301 4.699 probit  3.1804  3.1436  3.2176 microM 0.04514
-#> 8    IM16 BF4  13 30 -4.301 4.699  logit  3.1814  3.1440  3.2190 microM 0.04553
-#> 9    IM17 BF4  10 20 -1.301 4.699 probit  2.4317  2.3681  2.4951 microM 0.04773
-#> 10   IM17 BF4  10 20 -1.301 4.699  logit  2.4353  2.3672  2.5026 microM 0.05050
-#> 11   IM18 BF4  10 17 -2.301 2.699 probit  1.4015  1.3147  1.4881 microM 0.05611
-#> 12   IM18 BF4  10 17 -2.301 2.699  logit  1.4051  1.3129  1.4966 microM 0.05898
-#> 13   IM19 BF4  13 22 -5.301 2.699 probit  0.7158  0.6704  0.7592 microM 0.02956
-#> 14   IM19 BF4  13 22 -5.301 2.699  logit  0.7172  0.6689  0.7635 microM 0.03210
-#> 15 IM1-10 BF4  11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099
-#> 16 IM1-10 BF4  11 20 -6.301 2.699  logit -0.1831 -0.2620 -0.1055 microM 0.04192
-#>          a      b      ED50 ED50 2.5% ED50 97.5%     EDx10    EDx20
-#> 1   3.9399 0.5763 8707.8956 7305.0279  1.038e+04 1.590e+03 2850.222
-#> 2   3.9461 0.3426 8832.9407 7426.2282  1.050e+04 1.561e+03 2959.147
-#> 3   3.5442 0.6561 3501.1558 3184.3196  3.851e+03 5.051e+02  981.759
-#> 4   3.5465 0.3911 3519.5779 3194.6808  3.877e+03 4.867e+02 1010.014
-#> 5   3.1398 0.5527 1379.9037 1298.9533  1.466e+03 2.701e+02  472.823
-#> 6   3.1387 0.3347 1376.4086 1293.7152  1.465e+03 2.532e+02  472.911
-#> 7   3.1804 0.4882 1515.0421 1391.8150  1.650e+03 3.588e+02  588.292
-#> 8   3.1814 0.2957 1518.4650 1393.2665  1.656e+03 3.401e+02  590.840
-#> 9   2.4317 0.6387  270.2279  233.3814  3.127e+02 4.105e+01   78.382
-#> 10  2.4353 0.3810  272.4409  232.9287  3.182e+02 3.965e+01   80.754
-#> 11  1.4015 0.8009   25.2069   20.6383  3.077e+01 2.372e+00    5.340
-#> 12  1.4051 0.4816   25.4135   20.5545  3.138e+01 2.222e+00    5.463
-#> 13  0.7158 0.6969    5.1975    4.6814  5.744e+00 6.647e-01    1.347
-#> 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,
-                            showED50 = TRUE, EDx = c(10, 20))
#> 
-#> IM13 BF4: Fitting data...
#> 
-#> IM14 BF4: Fitting data...
#> 
-#> IM15 BF4: Fitting data...
#> 
-#> IM16 BF4: Fitting data...
#> 
-#> IM17 BF4: Fitting data...
#> 
-#> IM18 BF4: Fitting data...
#> 
-#> IM19 BF4: Fitting data...
#> 
-#> IM1-10 BF4: Fitting data...
  print(rIM1xVibrio.drc, 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  3.8563  4.0100 microM 0.06303
-#> 2    IM13 BF4  13 22 -5.301 4.699  logit  3.9461  3.8637  4.0153 microM 0.06188
-#> 3    IM14 BF4  12 57 -4.301 4.699 probit  3.5442  3.5009  3.5836 microM 0.05905
-#> 4    IM14 BF4  12 57 -4.301 4.699  logit  3.5465  3.5023  3.5866 microM 0.06030
-#> 5    IM15 BF4   7 20 -0.301 4.699 probit  3.1398  3.1127  3.1654 microM 0.02695
-#> 6    IM15 BF4   7 20 -0.301 4.699  logit  3.1387  3.1109  3.1649 microM 0.02723
-#> 7    IM16 BF4  13 30 -4.301 4.699 probit  3.1804  3.1419  3.2158 microM 0.04514
-#> 8    IM16 BF4  13 30 -4.301 4.699  logit  3.1814  3.1424  3.2172 microM 0.04553
-#> 9    IM17 BF4  10 20 -1.301 4.699 probit  2.4317  2.3632  2.4909 microM 0.04773
-#> 10   IM17 BF4  10 20 -1.301 4.699  logit  2.4353  2.3618  2.4981 microM 0.05050
-#> 11   IM18 BF4  10 17 -2.301 2.699 probit  1.4015  1.3052  1.4803 microM 0.05611
-#> 12   IM18 BF4  10 17 -2.301 2.699  logit  1.4051  1.3023  1.4881 microM 0.05898
-#> 13   IM19 BF4  13 22 -5.301 2.699 probit  0.7158  0.6690  0.7580 microM 0.02956
-#> 14   IM19 BF4  13 22 -5.301 2.699  logit  0.7172  0.6672  0.7620 microM 0.03210
-#> 15 IM1-10 BF4  11 20 -6.301 2.699 probit -0.1790 -0.2628 -0.1088 microM 0.04099
-#> 16 IM1-10 BF4  11 20 -6.301 2.699  logit -0.1831 -0.2690 -0.1114 microM 0.04192
-#>            a       b      ED50 ED50 2.5% ED50 97.5%     EDx10 EDx10 2.5%
-#> 1  8707.5571 -0.7536 8707.5571 7183.0127  1.023e+04 1.590e+03  968.72501
-#> 2  8832.8773  1.2676 8832.8773 7306.8669  1.036e+04 1.561e+03  925.39582
-#> 3  3501.1967 -0.6619 3501.1967 3168.9639  3.833e+03 5.051e+02  395.26341
-#> 4  3519.5773  1.1105 3519.5773 3179.2923  3.860e+03 4.866e+02  371.84710
-#> 5  1379.9019 -0.7858 1379.9019 1296.3162  1.463e+03 2.701e+02  233.25320
-#> 6  1376.4086  1.2976 1376.4086 1290.8397  1.462e+03 2.531e+02  215.79719
-#> 7  1515.0427 -0.8896 1515.0427 1386.3308  1.644e+03 3.588e+02  283.79434
-#> 8  1518.4644  1.4686 1518.4644 1387.9173  1.649e+03 3.401e+02  262.20564
-#> 9   270.2279 -0.6800  270.2279  230.7905  3.097e+02 4.105e+01   27.78507
-#> 10  272.4526  1.1401  272.4526  230.0588  3.148e+02 3.966e+01   25.34948
-#> 11   25.2059 -0.5423   25.2059   20.1927  3.022e+01 2.372e+00    1.29116
-#> 12   25.4145  0.9017   25.4145   20.0576  3.077e+01 2.223e+00    1.09707
-#> 13    5.1971 -0.6231    5.1971    4.6665  5.728e+00 6.646e-01    0.49235
-#> 14    5.2141  1.0511    5.2141    4.6477  5.781e+00 6.446e-01    0.46046
-#> 15    0.6622 -0.5416    0.6622    0.5460  7.783e-01 6.213e-02    0.03513
-#> 16    0.6560  0.9018    0.6560    0.5383  7.737e-01 5.738e-02    0.03163
-#>    EDx10 97.5%    EDx20 EDx20 2.5% EDx20 97.5%
-#> 1    2.211e+03 2850.328  2.019e+03   3681.2703
-#> 2    2.196e+03 2958.988  2.092e+03   3826.1457
-#> 3    6.149e+02  981.743  8.254e+02   1138.0862
-#> 4    6.014e+02 1010.061  8.414e+02   1178.7611
-#> 5    3.070e+02  472.838  4.257e+02    520.0197
-#> 6    2.905e+02  472.906  4.239e+02    521.8955
-#> 7    4.337e+02  588.259  4.999e+02    676.6627
-#> 8    4.181e+02  590.824  4.972e+02    684.4677
-#> 9    5.431e+01   78.383  5.955e+01     97.2142
-#> 10   5.396e+01   80.763  5.975e+01    101.7713
-#> 11   3.454e+00    5.339  3.544e+00      7.1350
-#> 12   3.348e+00    5.463  3.489e+00      7.4370
-#> 13   8.369e-01    1.346  1.084e+00      1.6086
-#> 14   8.288e-01    1.394  1.106e+00      1.6832
-#> 15   8.912e-02    0.140  9.501e-02      0.1850
-#> 16   8.314e-02    0.141  9.588e-02      0.1862
-
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png new file mode 100644 index 0000000..17a3580 Binary files /dev/null and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png new file mode 100644 index 0000000..ddce484 Binary files /dev/null and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/XY.html b/docs/reference/XY.html index 4be91cb..689c125 100644 --- a/docs/reference/XY.html +++ b/docs/reference/XY.html @@ -1,65 +1,13 @@ - - - - - - - -Dose-Response data for two substances X and Y — XY • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Dose-Response data for two substances X and Y — XY • drfit - - - - + + -
-
- -
- -
+

Dose-Response data for two substances X and Y

@@ -111,44 +45,42 @@ arbitrarily named X and Y.

- 
data(XY)
- - -

Format

+
+ 
data(XY)
+
+
+

Format

A dataframe containing dose (concentration) and response data, as well as control values where the dose is zero.

+
-

Examples

- 
  if (FALSE) demo(XY)
-
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index b3e5604..e679ce3 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -1,67 +1,15 @@ - - - - - - - -Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul • drfit - - - - + + -
-
- -
- -
+

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

@@ -115,108 +49,121 @@ February 25, 2004

- 
data(antifoul)
- - -

Format

+
+ 
data(antifoul)
+
+
+

Format

A dataframe containing 135 and 81 data points for concentrations and responses for TBT and Zink Pyrithione, respectively. Some additional columns from the database are also present.

+
-

Examples

- 
rantifoul.ED50 <- drfit(antifoul,
-                        linlogit = TRUE, logit = TRUE, weibull = TRUE,
-                        chooseone = FALSE,
-                        showED50 = TRUE, EDx = c(10))
#> 
-#> TBT: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> 
-#> Zn Pyrithion: Fitting data...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
print(rantifoul.ED50, digits = 5)
#>      Substance ndl   n     lld    lhd    mtype  logED50     2.5%     97.5%
-#> 1          TBT  38 135 -2.7093 2.3979 linlogit -0.15809 -0.26021 -0.050475
-#> 2          TBT  38 135 -2.7093 2.3979   probit -0.16436 -0.26504 -0.056498
-#> 3          TBT  38 135 -2.7093 2.3979    logit -0.16012 -0.26116 -0.052591
-#> 4          TBT  38 135 -2.7093 2.3979  weibull -0.11507       NA        NA
-#> 5 Zn Pyrithion  27  81 -2.1072 2.0000 linlogit -0.41329 -0.52932 -0.299799
-#> 6 Zn Pyrithion  27  81 -2.1072 2.0000   probit -0.39792 -0.50783 -0.291563
-#> 7 Zn Pyrithion  27  81 -2.1072 2.0000    logit -0.40035 -0.51049 -0.293501
-#> 8 Zn Pyrithion  27  81 -2.1072 2.0000  weibull -0.38795       NA        NA
-#>     unit   sigma        a       b         c    ED50 ED50 2.5% ED50 97.5%
-#> 1 microM 0.19264 -0.15809 1.04065 -0.024165 0.69487   0.54927    0.89028
-#> 2 microM 0.19286 -0.16436 0.67637        NA 0.68493   0.54320    0.87801
-#> 3 microM 0.19199 -0.16012 0.41358        NA 0.69164   0.54808    0.88595
-#> 4 microM 0.18810  0.63743 1.28891        NA 0.76724        NA         NA
-#> 5 microM 0.22878 -0.41329 1.74249  0.610900 0.38611   0.29558    0.50142
-#> 6 microM 0.22866 -0.39792 0.41696        NA 0.40002   0.31058    0.51102
-#> 7 microM 0.22802 -0.40035 0.25395        NA 0.39779   0.30868    0.50874
-#> 8 microM 0.23008  0.47647 2.51561        NA 0.40931        NA         NA
-#>      EDx10
-#> 1 0.085214
-#> 2 0.093077
-#> 3 0.085340
-#> 4 0.053392
-#> 5 0.120233
-#> 6 0.116872
-#> 7 0.110068
-#> 8 0.121166

-rantifoul.drc <- drcfit(antifoul,
-                        linlogit = TRUE, logit = TRUE, weibull = TRUE,
-                        chooseone = FALSE,
-                        showED50 = TRUE, EDx = c(10))
#> 
-#> TBT: Fitting data...
#> 
-#> Zn Pyrithion: Fitting data...
print(rantifoul.drc, digits = 5)
#>      Substance ndl   n     lld    lhd    mtype  logED50     2.5%     97.5%
-#> 1          TBT  38 135 -2.7093 2.3979 linlogit       NA       NA        NA
-#> 2          TBT  38 135 -2.7093 2.3979   probit -0.16436 -0.28178 -0.072022
-#> 3          TBT  38 135 -2.7093 2.3979    logit -0.16012 -0.27782 -0.067603
-#> 4          TBT  38 135 -2.7093 2.3979  weibull -0.13012 -0.23786 -0.043860
-#> 5 Zn Pyrithion  27  81 -2.1072 2.0000 linlogit -0.41330 -0.54457 -0.312631
-#> 6 Zn Pyrithion  27  81 -2.1072 2.0000   probit -0.39792 -0.52005 -0.302705
-#> 7 Zn Pyrithion  27  81 -2.1072 2.0000    logit -0.40035 -0.52324 -0.304676
-#> 8 Zn Pyrithion  27  81 -2.1072 2.0000  weibull -0.37351 -0.49792 -0.276917
-#>     unit   sigma        a        b         c    ED50 ED50 2.5% ED50 97.5%
-#> 1 microM 0.19264  0.71806  1.04061 -0.024169      NA        NA         NA
-#> 2 microM 0.19286  0.68492 -0.64209        NA 0.68492   0.52267    0.84718
-#> 3 microM 0.19199  0.69165  1.05007        NA 0.69165   0.52744    0.85585
-#> 4 microM 0.18900 -0.13012  0.79816        NA 0.74111   0.57828    0.90394
-#> 5 microM 0.22878  0.30926  1.74257  0.611358 0.38610   0.28538    0.48682
-#> 6 microM 0.22866  0.40002 -1.04159        NA 0.40002   0.30196    0.49808
-#> 7 microM 0.22802  0.39779  1.71015        NA 0.39779   0.29975    0.49582
-#> 8 microM 0.23077 -0.37351  1.19152        NA 0.42315   0.31775    0.52855
-#>      EDx10 EDx10 2.5% EDx10 97.5%
-#> 1       NA         NA          NA
-#> 2 0.093074   0.040308     0.14584
-#> 3 0.085338   0.035963     0.13471
-#> 4 0.069958   0.026197     0.11372
-#> 5 0.120238   0.043513     0.19696
-#> 6 0.116878   0.048151     0.18561
-#> 7 0.110068   0.043085     0.17705
-#> 8 0.087066   0.017958     0.15617
-
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index 6fa239b..0228a63 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -1,65 +1,13 @@ - - - - - - - -Check raw data from range of plates or experiments — checkcontrols • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Check raw data from range of plates or experiments — checkcontrols • drfit - - - - + + -
-
- -
- -
+

Check raw data from range of plates or experiments

@@ -111,96 +45,88 @@ experiments from a specified database.

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

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
last

If id is not specified, this argument specifies the number of +

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

Arguments

+
last
+

If id is not specified, this argument specifies the number of plates/experiments that should be evaluated. The plates/experiments with - the hightest numbers are selected.

id

A numeric vector of integers, specifying the plates or experiments explicitly.

db

The database to be used. Currently, the microtiter plate databases + the hightest numbers are selected.

+ +
id
+

A numeric vector of integers, specifying the plates or experiments explicitly.

+ +
db
+

The database to be used. Currently, the microtiter plate databases "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are - supported, as well as the database of ecotoxicity experiments "ecotox".

celltype

Only important if database "cytotox" is used. Data for - "IPC-81", "C6", "NB4", "HeLa", "Jurkat" and "U937" are available.

enzymetype

Only important if database "enzymes" is used. - Data for "AChE", "GR" and "GST" are available.

organism

Only important if database "ecotox" is used.

endpoint

The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".

qcc

The type of quality control charts to be plotted. By default, an R chart - (showing ranges of control values within plates/experiments), and an - xbar chart (showing means) are generated.

+ supported, as well as the database of ecotoxicity experiments "ecotox".

-

Value

+
celltype
+

Only important if database "cytotox" is used. Data for + "IPC-81", "C6", "NB4", "HeLa", "Jurkat" and "U937" are available.

-

The function lists a report and shows two graphs.

+
enzymetype
+

Only important if database "enzymes" is used. + Data for "AChE", "GR" and "GST" are available.

-

Examples

- 
if (FALSE) checkcontrols(15)
-
- +
+

Value

+ + +

The function lists a report and shows two graphs.

+
+

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
if (FALSE) checkcontrols(15)
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html index 7acd323..a97ea52 100644 --- a/docs/reference/checkexperiment.html +++ b/docs/reference/checkexperiment.html @@ -1,65 +1,13 @@ - - - - - - - -Check raw data from a specified experiment or microtiter plate — checkexperiment • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Check raw data from a specified experiment or microtiter plate — checkexperiment • drfit - - - - + + -
-
- -
- -
+

Check raw data from a specified experiment or microtiter plate

@@ -111,78 +45,74 @@ specified database, box plot controls, and plot the dose-response data.

- 
checkplate(id, db = c("cytotox", "enzymes"))
-  checkexperiment(id, db = c("ecotox", "cytotox", "enzymes"), endpoint = "%",
-                  whereClause = "1")
- -

Arguments

- - - - - - - - - - - - - - - - - - -
id

The id of the experiment or the plate identifying it within the database.

db

The database to be used. Currently, the microtiter plate databases - "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are - supported, as well as the database of ecotoxicity experiments "ecotox".

endpoint

The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".

whereClause

With this argument, additional conditions for the SQL query can be set, - e.g. "duration = 48" (i.e. "Only retrieve data with duration 48"). The - default is 1 (in SQL syntax this means TRUE).

+
+ 
checkplate(id, db = c("cytotox", "enzymes"))
+  checkexperiment(id, db = c("ecotox", "cytotox", "enzymes"), endpoint = "%", 
+                  whereClause = "1")
+
-

Value

+
+

Arguments

+
id
+

The id of the experiment or the plate identifying it within the database.

-

The function lists a report and shows two graphs.

+
db
+

The database to be used. Currently, the microtiter plate databases + "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are + supported, as well as the database of ecotoxicity experiments "ecotox".

-

Examples

- 
# Check plate number 3 in the cytotox database
-if (FALSE) checkplate(3)
+  
endpoint

+
The endpoint that should be used for selecting the data. Only important if
+    the database "ecotox" is used. Defaults to "%".

 
-# Check data from experiment 1517 with duration 48 hours
-if (FALSE) checkexperiment(1517, whereClause = "duration = 48")
-
- +
+

Value

+ + +

The function lists a report and shows two graphs.

+
+

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
# Check plate number 3 in the cytotox database
+if (FALSE) checkplate(3)
+
+# Check data from experiment 1517 with duration 48 hours
+if (FALSE) checkexperiment(1517, whereClause = "duration = 48")
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html index 39bcd4a..54c5be6 100644 --- a/docs/reference/checksubstance.html +++ b/docs/reference/checksubstance.html @@ -1,65 +1,13 @@ - - - - - - - -Check raw data for a specified substance — checksubstance • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Check raw data for a specified substance — checksubstance • drfit - - - - + + -
-
- -
- -
+

Check raw data for a specified substance

@@ -111,104 +45,95 @@ the data.

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

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
substance

The name of the substance identifying it within the database. Matching is not - case-sensitive.

db

The database to be used. Currently, the databases "cytotox" and "enzymes" +

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

Arguments

+
substance
+

The name of the substance identifying it within the database. Matching is not + case-sensitive.

+ +
db
+

The database to be used. Currently, the databases "cytotox" and "enzymes" of the UFT Department of Bioorganic Chemistry are supported (default is - "cytotox").

experimentator

The name of the experimentator whose data is to be used. Default is "%", - which means that data from all experimentators are shown.

celltype

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + "cytotox").

+ +
experimentator
+

The name of the experimentator whose data is to be used. Default is "%", + which means that data from all experimentators are shown.

+ +
celltype
+

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported. Default is "%", i.e. data for any cell type will be - displayed.

enzymetype

Currently, only data for AChE, GR and GST are supported. The default value - is "%", i.e. data for any enzyme type will be displayed.

organism

The latin name of the tested organism, if the ecotox db was selected. The - default value is "%", i.e. data for any organism will be displayed.

endpoint

The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".

whereClause

With this argument, additional conditions for the SQL query can be set, - e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).

ok

With the default value "%", all data in the database is retrieved for the - specified substance.

- -

Value

- -

The function lists a report and shows one graph.

- -

Examples

- 
# Check substance IM14 BF4 in the cytotox database
-if (FALSE) checksubstance("IM14 BF4")
-
- +
+

Value

+ + +

The function lists a report and shows one graph.

+
+

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
# Check substance IM14 BF4 in the cytotox database
+if (FALSE) checksubstance("IM14 BF4")
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index 1930a24..8a76863 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -1,65 +1,13 @@ - - - - - - - -Fit dose-response models using the drc package — drcfit • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Fit dose-response models using the drc package — drcfit • drfit - - - - + + -
-
- -
- -
+

Fit dose-response models using the drc package

@@ -111,181 +45,206 @@ 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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
data

A data frame containing dose-response data. The data frame has to contain - at least a factor called “substance”, a numeric vector “dose” - with the dose values, a vector called “unit” containing the unit - used for the dose and a numeric vector “response” with the response +

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

Arguments

+
data
+

A data frame containing dose-response data. The data frame has to contain + at least a factor called “substance”, a numeric vector “dose” + with the dose values, a vector called “unit” containing the unit + 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.

-

If there is a column called “ok” and it is set to “no fit” in + 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.

probit

A boolean defining if cumulative density curves of normal distributions + the fitting procedure, although it will be plotted.

+ +
probit
+

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 - as a here, and parameter b from there is listed as b.

logit

A boolean defining if cumulative density curves of logistic distributions - plogis are fitted to the decadic logarithm of the dose. + ones used in drfit. Parameter e from LN.2 is listed + as a here, and parameter b from there is listed as b.

+ +
logit
+

A boolean defining if cumulative density curves of logistic distributions + 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 - as a here, and parameter b from LL.2 is listed as b.

weibull

A boolean defining if Weibull dose-response models + ones used in drfit. Parameter e from LL.2 is listed + as a here, and parameter b from LL.2 is listed as b.

+ +
weibull
+

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 + 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 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.

level

The level for the confidence interval listed for the log ED50.

chooseone

If TRUE (default), the models are tried in the order linlogit, probit, + result.

+ +
level
+

The level for the confidence interval listed for the log ED50.

+ +
chooseone
+

If TRUE (default), the models are tried in the order linlogit, probit, logit, weibull, and the first model that produces a valid fit is used. If FALSE, all models that are set to TRUE and that can be fitted will be - reported.

EDx

A vector of inhibition values x in percent for which the corresponding doses - EDx should be reported.

showED50

If set to TRUE, the ED50 and its confidence interval on the original dose - scale (not log scale) is included in the output.

- -

Value

- -

A dataframe with the attribute models holding a list of the fitted - dose-response models of class nls. The dataframe has at least + reported.

+ +
EDx
+

A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported.

+ +
showED50
+

If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output.

+ +
+
+

Value

+ + +

A dataframe with the attribute models holding a list of the fitted + dose-response models of class nls. The dataframe has at least one line for each substance.

+ +

The following variables are in the dataframe:

-
Substance

The name of the substance

-
ndl

The number of dose levels in the raw data

-
n

The total number of data points in the raw data used for the fit

-
lld

The decadic logarithm of the lowest dose

-
lhd

The total number of data points in the raw data used for the fit

-
mtype

If the data did not show a mean response < 0.5 at the highest dose level, - the modeltype is set to “inactive”. If the mean response at the - lowest dose is smaller than 0.5, the modeltype is set to “active”. +

Substance
+

The name of the substance

+ +
ndl
+

The number of dose levels in the raw data

+ +
n
+

The total number of data points in the raw data used for the fit

+ +
lld
+

The decadic logarithm of the lowest dose

+ +
lhd
+

The total number of data points in the raw data used for the fit

+ +
mtype
+

If the data did not show a mean response < 0.5 at the highest dose level, + the modeltype is set to “inactive”. If the mean response at the + lowest dose is smaller than 0.5, the modeltype is set to “active”. In both cases, no fitting procedure is carried out. If the fitted ED50 - is higher than the highest dose, “no fit” is given here.

-
logED50

The decadic logarithm of the ED50

-
low %

The lower bound of the confidence interval of log ED50. + is higher than the highest dose, “no fit” is given here.

+ +
logED50
+

The decadic logarithm of the ED50

+ +
low %
+

The lower bound of the confidence interval of log ED50. The name of the column depends on the requested confidence level.

-
high %

The higher bound of the confidence interval of log ED50. + +

high %
+

The higher bound of the confidence interval of log ED50. The name of the column depends on the requested confidence level.

-
unit

The unit used for the dose levels in the dose-response data

-
sigma

The square root of the estimated variance of the random error as returned + +

unit
+

The unit used for the dose levels in the dose-response data

+ +
sigma
+

The square root of the estimated variance of the random error as returned by summary.drc.

-
a

For the linlogit model, this is the parameter e from BC.4. + +

a
+

For the linlogit model, this is the parameter e from BC.4. For the probit and the logit model, this is the ED50. For the weibull model, this is parameter e from W1.2. Note that the Weibull model is fitted to the untransformed data.

-
b

For the linlogit, probit, logit and weibull models, these are the + +

b
+

For the linlogit, probit, logit and weibull models, these are the 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.

-
c

Only the “linlogit” fit produces a third parameter c, which is + 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 - confidence intervals are also included on the original dose scale. - If one or more response leves were specified in the argument EDx, - the corresponding dose levels are given in addition, together with their - confidence intervals as calculated by ED from the drc package. +

If the parameter showED50 was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale.

-

Note

+

If one or more response leves were specified in the argument EDx, + the corresponding dose levels are given in addition, together with their + confidence intervals as calculated by ED from the drc package.

+
+
+

Note

There is a demo for each dataset that can be accessed by - demo(dataset)

-

See also

- -

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

- -

Examples

- 
data(antifoul)
-r <- drcfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
#> 
-#> TBT: Fitting data...
#> 
-#> Zn Pyrithion: Fitting data...
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 -0.28 -0.072 microM  0.19 0.68
-#> 2 Zn Pyrithion  27  81 -2.1 2.0 probit   -0.40 -0.52 -0.303 microM  0.23 0.40
-#>       b ED50 ED50 2.5% ED50 97.5%  EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5%
-#> 1 -0.64 0.68      0.52       0.85 0.053     0.015      0.091 0.093      0.040
-#> 2 -1.04 0.40      0.30       0.50 0.082     0.023      0.142 0.117      0.048
-#>   EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5%
-#> 1        0.15  0.18       0.11        0.26
-#> 2        0.19  0.18       0.10        0.26
-
- +
+

See also

+

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

+
+

Author

-

Johannes Ranke jranke@uni-bremen.de +

Johannes Ranke jranke@uni-bremen.de The functionality of the drc package used under the hood in this function was written by Christian Ritz.

+
+ +
+

Examples

+ 
data(antifoul)
+r <- drcfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
+#> 
+#> TBT: Fitting data...
+#> 
+#> Zn Pyrithion: Fitting data...
+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 -0.28 -0.072 microM  0.19 0.68
+#> 2 Zn Pyrithion  27  81 -2.1 2.0 probit   -0.40 -0.52 -0.303 microM  0.23 0.40
+#>       b ED50 ED50 2.5% ED50 97.5%  EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5%
+#> 1 -0.64 0.68      0.52       0.85 0.053     0.015      0.091 0.093      0.040
+#> 2 -1.04 0.40      0.30       0.50 0.082     0.023      0.142 0.117      0.048
+#>   EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5%
+#> 1        0.15  0.18       0.11        0.26
+#> 2        0.19  0.18       0.10        0.26
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index 104e190..a34be4f 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -1,64 +1,12 @@ - - - - - - - -Get dose-response data via RODBC — drdata • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Get dose-response data via RODBC — drdata • drfit - - - - + + -
-
- -
- -
+

Get dose-response data via RODBC

@@ -109,75 +43,67 @@

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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
substances

A string or an array of strings with the substance names for - which dose-response data is to be retrieved. Matching is case-sensitive.

experimentator

The name of the experimentator whose data is to be used. Default is " - which means that data from all experimentators are retrieved.

db

The database to be used. Currently, the databases "cytotox", "enzymes" +

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

Arguments

+
substances
+

A string or an array of strings with the substance names for + which dose-response data is to be retrieved. Matching is case-sensitive.

+ +
experimentator
+

The name of the experimentator whose data is to be used. Default is " + which means that data from all experimentators are retrieved.

+ +
db
+

The database to be used. Currently, the databases "cytotox", "enzymes" and "ecotox" of the UFT Department of Bioorganic Chemistry are - supported (default is "cytotox").

celltype

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are - supported.

enzymetype

Currently, only data for AChE, GR and GST are supported.

organism

The organism that was exposed to the chemical. Only important if the database - "ecotox" is used. Defaults to "Vibrio fischeri".

endpoint

The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "Luminescence".

whereClause

With this argument, additional conditions for the SQL query can be set, + supported (default is "cytotox").

+ +
celltype
+

Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.

+ +
enzymetype
+

Currently, only data for AChE, GR and GST are supported.

+ +
organism
+

The organism that was exposed to the chemical. Only important if the database + "ecotox" is used. Defaults to "Vibrio fischeri".

+ +
endpoint
+

The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "Luminescence".

+ +
whereClause
+

With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The - default is 1 (in SQL syntax this means TRUE).

ok

With the default value "'ok','no fit'", only data that has been checked and + default is 1 (in SQL syntax this means TRUE).

+ +
ok
+

With the default value "'ok','no fit'", only data that has been checked and set to "ok" or "no fit" in the database is retrieved. The argument "no fit" will result in not using the data for fitting, but it will be plotted. Another sensible argument would be "'ok','no fit','?'", in order to - additionally retrieve data which has not yet been checked.

- -

Value

+ additionally retrieve data which has not yet been checked.

-

-
data

A data frame with a factor describing the dose levels, the numeric dose +

+
+

Value

+
data
+

A data frame with a factor describing the dose levels, the numeric dose levels and a numeric column describing the response, as well as the entries for plate, experimentator, performed (date of test performance), celltype, unit (of the dose/concentration), and for the ok field in the database.

-

Details

- +
+
+

Details

The function is currently only used for retrieving data from the mysql database "cytotox" of the UFT Department of Bioorganic Chemistry. Access to this database is limited to UFT staff. Additionally to the @@ -186,66 +112,45 @@ 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
- - - -

Examples

- 
  if (FALSE) {
-
-  # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
-  # cells
-  drdata(c("TBT", "ZnPT2"))
-
-  }
-
- +

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
  if (FALSE) {
+
+  # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+  # cells
+  drdata(c("TBT", "ZnPT2"))
+
+  }
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index d707a5f..ab2fbd0 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -1,65 +1,13 @@ - - - - - - - -Fit dose-response models — drfit • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Fit dose-response models — drfit • drfit - - - - + + -
-
- -
- -
+

Fit dose-response models

@@ -111,220 +45,241 @@ 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,
-  allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0,
-  showED50 = FALSE,
-  EDx = NULL, EDx.tolerance = 1e-4)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
data

A data frame containing dose-response data. The data frame has to contain - at least a factor called “substance”, a numeric vector “dose” - with the dose values, a vector called “unit” containing the unit - used for the dose and a numeric vector “response” with the response +

+ 
drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
+  weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
+  allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0,
+  showED50 = FALSE,
+  EDx = NULL, EDx.tolerance = 1e-4)
+
+ +
+

Arguments

+
data
+

A data frame containing dose-response data. The data frame has to contain + at least a factor called “substance”, a numeric vector “dose” + with the dose values, a vector called “unit” containing the unit + 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.

-

If there is a column called “ok” and it is set to “no fit” in + 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.

startlogED50

Especially for the linlogit model, a suitable log10 of the ED50 has to be + the fitting procedure, although it will be plotted.

+ +
startlogED50
+

Especially for the linlogit model, a suitable log10 of the ED50 has to be given by the user, since it is not correctly estimated for data showing - hormesis with the default estimation method.

probit

A boolean defining if cumulative density curves of normal distributions - pnorm are fitted against the decadic logarithm of the dose. - Default ist TRUE.

logit

A boolean defining if cumulative density curves of logistic distributions - plogis are fitted to the decadic logarithm of the dose. - Default is FALSE.

weibull

A boolean defining if the cumulative density curves of weibull distributions - (pweibull with additionall location parameter and scale=1) + hormesis with the default estimation method.

+ +
probit
+

A boolean defining if cumulative density curves of normal distributions + pnorm are fitted against the decadic logarithm of the dose. + Default ist TRUE.

+ +
logit
+

A boolean defining if cumulative density curves of logistic distributions + plogis are fitted to the decadic logarithm of the dose. + Default is FALSE.

+ +
weibull
+

A boolean defining if the cumulative density curves of weibull distributions + (pweibull with additionall location parameter and scale=1) are fitted to the decadic logarithm of the dose. Default is FALSE. Note that the weibull distribution is fitted here to the log transformed doses - which appears to be an uncommon approach.

linlogit

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

level

The level for the confidence interval listed for the log ED50.

linlogitWrong

An optional vector containing the names of the substances for which the - linlogit function produces a wrong fit.

allWrong

An optional vector containing the names of the substances for which all - functions produce a wrong fit.

chooseone

If TRUE (default), the models are tried in the order linlogit, probit, + which appears to be an uncommon approach.

+ +
linlogit
+

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

+ +
level
+

The level for the confidence interval listed for the log ED50.

+ +
linlogitWrong
+

An optional vector containing the names of the substances for which the + linlogit function produces a wrong fit.

+ +
allWrong
+

An optional vector containing the names of the substances for which all + functions produce a wrong fit.

+ +
chooseone
+

If TRUE (default), the models are tried in the order linlogit, probit, logit, weibull, and the first model that produces a valid fit is used. If FALSE, all models that are set to TRUE and that can be fitted will be - reported.

ps0

If the probit model is fitted, ps0 gives the possibility to adjust - the starting value for the scale parameter of pnorm.

ls0

If the logit model is fitted, ls0 gives the possibility to adjust - the starting value for the scale parameter of plogis.

ws0

If the weibull model is fitted, ws0 gives the possibility to adjust - the starting value for the shape parameter of pweibull.

b0,f0

If the linearlogistic model is fitted, b0 and f0 give the - possibility to adjust the starting values for the parameters b and f.

showED50

If set to TRUE, the ED50 and its confidence interval on the original dose - scale (not log scale) is included in the output.

EDx

A vector of inhibition values x in percent for which the corresponding doses - EDx should be reported.

EDx.tolerance

Tolerance of the effect level, expressed on the response scale from 0 to 1.

- -

Value

- -

A dataframe with the attribute models holding a list of the fitted - dose-response models of class nls. The dataframe has at least + reported.

+ +
ps0
+

If the probit model is fitted, ps0 gives the possibility to adjust + the starting value for the scale parameter of pnorm.

+ +
ls0
+

If the logit model is fitted, ls0 gives the possibility to adjust + the starting value for the scale parameter of plogis.

+ +
ws0
+

If the weibull model is fitted, ws0 gives the possibility to adjust + the starting value for the shape parameter of pweibull.

+ +
b0,f0
+

If the linearlogistic model is fitted, b0 and f0 give the + possibility to adjust the starting values for the parameters b and f.

+ +
showED50
+

If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output.

+ +
EDx
+

A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported.

+ +
EDx.tolerance
+

Tolerance of the effect level, expressed on the response scale from 0 to 1.

+ +
+
+

Value

+ + +

A dataframe with the attribute models holding a list of the fitted + dose-response models of class nls. The dataframe has at least one line for each substance.

-

For the “linlogit”, “logit” and “probit” models, the + + +

For the “linlogit”, “logit” and “probit” models, the parameter a that is reported coincides with the logED50, i.e the logED50 is one of the model parameters that is being fitted. Therefore, a confidence interval for the confidence level level is calculated using the confint.nls function and listed.

+ +

The following variables are in the dataframe:

-
Substance

The name of the substance

-
ndl

The number of dose levels in the raw data

-
n

The total number of data points in the raw data used for the fit

-
lld

The decadic logarithm of the lowest dose

-
lhd

The total number of data points in the raw data used for the fit

-
mtype

If the data did not show a mean response < 0.5 at the highest dose level, - the modeltype is set to “inactive”. If the mean response at the - lowest dose is smaller than 0.5, the modeltype is set to “active”. +

Substance
+

The name of the substance

+ +
ndl
+

The number of dose levels in the raw data

+ +
n
+

The total number of data points in the raw data used for the fit

+ +
lld
+

The decadic logarithm of the lowest dose

+ +
lhd
+

The total number of data points in the raw data used for the fit

+ +
mtype
+

If the data did not show a mean response < 0.5 at the highest dose level, + the modeltype is set to “inactive”. If the mean response at the + lowest dose is smaller than 0.5, the modeltype is set to “active”. In both cases, no fitting procedure is carried out. If the fitted ED50 - is higher than the highest dose, “no fit” is given here.

-
logED50

The decadic logarithm of the ED50

-
low %

The lower bound of the confidence interval of log ED50. + is higher than the highest dose, “no fit” is given here.

+ +
logED50
+

The decadic logarithm of the ED50

+ +
low %
+

The lower bound of the confidence interval of log ED50. The name of the column depends on the requested confidence level.

-
high %

The higher bound of the confidence interval of log ED50. + +

high %
+

The higher bound of the confidence interval of log ED50. The name of the column depends on the requested confidence level.

-
unit

The unit used for the dose levels in the dose-response data

-
sigma

The square root of the estimated variance of the random error as returned - by summary.nls.

-
a

For the “linlogit”, “logit” and “probit” models, the + +

unit
+

The unit used for the dose levels in the dose-response data

+ +
sigma
+

The square root of the estimated variance of the random error as returned + by summary.nls.

+ +
a
+

For the “linlogit”, “logit” and “probit” models, the 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” + “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” 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.

- If the parameter showED50 was set to TRUE, the ED50 values and their - confidence intervals are also included on the original dose scale. + 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.

- If one or more response leves were specified in the argument EDx, - the corresponding dose levels are given in addition. +
c
+

Only the “linlogit” fit produces a third parameter c which is + the variable f from the linlogitf function.

-

Note

+

If the parameter showED50 was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale.

-

There is a demo for each dataset that can be accessed by - demo(dataset)

-

See also

-

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

If one or more response leves were specified in the argument EDx, + the corresponding dose levels are given in addition.

+
+
+

Note

+

There is a demo for each dataset that can be accessed by + demo(dataset)

+
+
+

See also

+

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 + drcfit which internally uses the drc package and also gives confidence intervals for EDx values via this package.

- -

Examples

- 
data(antifoul)
-r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
#> 
-#> 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 ED50 ED50 2.5% ED50 97.5%  EDx5 EDx10 EDx20
-#> 1 0.68 0.68      0.54       0.88 0.053 0.093  0.18
-#> 2 0.42 0.40      0.31       0.51 0.082 0.117  0.18
-
- +

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
data(antifoul)
+r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
+#> 
+#> 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 ED50 ED50 2.5% ED50 97.5%  EDx5 EDx10 EDx20
+#> 1 0.68 0.68      0.54       0.88 0.053 0.093  0.18
+#> 2 0.42 0.40      0.31       0.51 0.082 0.117  0.18
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png index 99ba8f4..23ff15d 100644 Binary files a/docs/reference/drplot-1.png and b/docs/reference/drplot-1.png differ diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png index 22e0bbf..3299a71 100644 Binary files a/docs/reference/drplot-2.png and b/docs/reference/drplot-2.png differ diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index ebdcdd7..b07ae34 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -1,65 +1,13 @@ - - - - - - - -Plot dose-response models — drplot • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Plot dose-response models — drplot • drfit - - - - + + -
-
- -
- -
+

Plot dose-response models

@@ -111,191 +45,172 @@ 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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
drresults

A data frame as returned from drfit.

data

A data frame as returned from drdata. The data frame has to +

+ 
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

+
drresults
+

A data frame as returned from drfit.

+ +
data
+

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 "dose" with the numeric dose values and a factor called "dosefactor" - containing the dose as a factor.

dtype

A string describing if the raw data should be plotted ("raw"), or an error + containing the dose as a factor.

+ +
dtype
+

A string describing if the raw data should be plotted ("raw"), or an error bar should be constructed from the standard deviations of the responses at each dose level ("std", default value) or from the confidence intervals - ("conf"). If you don't want to see the data, set it to "none".

alpha

The confidence level, defaulting to 0.95, only used if dtype "conf" has been - chosen.

ctype

This argument decides if horizontal lines are drawn to show the scatter of + ("conf"). If you don't want to see the data, set it to "none".

+ +
alpha
+

The confidence level, defaulting to 0.95, only used if dtype "conf" has been + chosen.

+ +
ctype
+

This argument decides if horizontal lines are drawn to show the scatter of the control values (dose = 0), if there are more than three of them. Defaults to "none", further allowed values are "std" and "conf" for displaying the standard deviation of the controls or the confidence - interval for the mean of the controls.

path

The path where graphic files should be put if any are produced. Defaults - to "./" i.e. the current working directory of R.

fileprefix

A string which will form the beginning of each filename, if graphic files - are created. Defaults to "drplot".

overlay

If TRUE, all output will be put into one graph, otherwise a separate graph - will be created for each substance.

xlim

The plot limits (min,max) on the dose axis.

ylim

The plot limits (min,max) on the response axis.

xlab

The axis title for the x axis. Defaults to "Concentration in" unit.

ylab

The axis title for the y axis. Defaults to "Normalized response".

axes

Specifies if axes should be drawn. Default is TRUE, as in - plot.default

frame.plot

Specifies if the plot should be framed. Default is TRUE, as in - plot.default

postscript

If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + interval for the mean of the controls.

+ +
path
+

The path where graphic files should be put if any are produced. Defaults + to "./" i.e. the current working directory of R.

+ +
fileprefix
+

A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot".

+ +
overlay
+

If TRUE, all output will be put into one graph, otherwise a separate graph + will be created for each substance.

+ +
xlim
+

The plot limits (min,max) on the dose axis.

+ +
ylim
+

The plot limits (min,max) on the response axis.

+ +
xlab
+

The axis title for the x axis. Defaults to "Concentration in" unit.

+ +
ylab
+

The axis title for the y axis. Defaults to "Normalized response".

+ +
axes
+

Specifies if axes should be drawn. Default is TRUE, as in + plot.default

+ +
frame.plot
+

Specifies if the plot should be framed. Default is TRUE, as in + plot.default

+ +
postscript
+

If TRUE, (a) postscript graph(s) will be created. Otherwise, and if the pdf and png arguments are also FALSE, graphics will be - displayed with a screen graphics device.

pdf

If TRUE, (a) pdf graph(s) will be created. Otherwise, and if + displayed with a screen graphics device.

+ +
pdf
+

If TRUE, (a) pdf graph(s) will be created. Otherwise, and if the postscript, and png arguments are also FALSE, graphics will be - displayed with a screen graphics device.

png

If TRUE, (a) png graph(s) will be created. Otherwise, and if the + displayed with a screen graphics device.

+ +
png
+

If TRUE, (a) png graph(s) will be created. Otherwise, and if the postscript and pdf arguments are also FALSE, graphics will be displayed - with a screen graphics device.

bw

A boolean deciding if the plots will be black and white or not. Default - is TRUE.

pointsize

The pointsize used for pdf, png and postscript graphics.

colors

This is a vector of colors, defaulting to 1:8, used for plotting the data.

ltys

This is a vector of line types for the dose-response models, defaulting to 1:8.

pchs

This is a vector of character types for the data. The default uses built-in + with a screen graphics device.

+ +
bw
+

A boolean deciding if the plots will be black and white or not. Default + is TRUE.

+ +
pointsize
+

The pointsize used for pdf, png and postscript graphics.

+ +
colors
+

This is a vector of colors, defaulting to 1:8, used for plotting the data.

+ +
ltys
+

This is a vector of line types for the dose-response models, defaulting to 1:8.

+ +
pchs
+

This is a vector of character types for the data. The default uses built-in characters 1:n with n being the number of substances for which data are plotted - for overlays, or always 1 when no overlay plot is generated.

lpos

An optional argument defaulting to "topright" specifying the position + for overlays, or always 1 when no overlay plot is generated.

+ +
lpos
+

An optional argument defaulting to "topright" specifying the position of the legend by being passed to the legend function. See the help for the - legend function for all possiblities.

devoff

If set to FALSE, the device will not be closed after creation of an overlay - pdf, png or postscript graph, so texts and other elements can - be added.

+ legend function for all possiblities.

-

Value

+
devoff
+

If set to FALSE, the device will not be closed after creation of an overlay + pdf, png or postscript graph, so texts and other elements can + be added.

-

-
results

You will get plots of data and/or the fitted dose-response curves, on the +

+
+

Value

+
results
+

You will get plots of data and/or the fitted dose-response curves, on the screen and/or as postscript/pdf/png files, depending on the parameters.

-

Note

- +
+
+

Note

There is a demo for each dataset that can be accessed by - demo(dataset)

- -

Examples

- 
data(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)
-
- +

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+ +
+

Examples

+ 
data(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)
+
+
+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index cbd742c..bcafa3f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,62 +1,12 @@ - - - - - - - -Function reference • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • drfit - - - - + + -
-
- -
- -
+

Reference

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

Main functions

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

Main functions

+

drfit()

Fit dose-response models

+

drcfit()

Fit dose-response models using the drc package

+

drplot()

Plot dose-response models

-

Get and check data from a drfit database

-

These functions only work if you have such a database

+
+

Get and check data from a drfit database

+

These functions only work if you have such a database

+

checkcontrols()

Check raw data from range of plates or experiments

+

checkplate() checkexperiment()

Check raw data from a specified experiment or microtiter plate

+

drdata()

Get dose-response data via RODBC

-

Datasets and example evaluations

+
+

Datasets and example evaluations

+

antifoul

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

+

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

+

pyrithione

Cytotoxicity data for different pyrithionates and related species

+

XY

Dose-Response data for two substances X and Y

-

Helper functions

+
+

Helper functions

+

linlogitf()

Linear-logistic function

- +
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index f72ca49..00fb4f1 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -1,65 +1,13 @@ - - - - - - - -Linear-logistic function — linlogitf • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Linear-logistic function — linlogitf • drfit - - - - + + -
-
- -
- -
+

Linear-logistic function

@@ -111,73 +45,66 @@ at subtoxic doses.

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

Arguments

- - - - - - - - - - - - - - - - - - - - - - -
x

In this context, the x variable is the dose.

k

In the drfit functions, k is set to 1.

f

One of the parameters describing the curve shape.

mu

The parameter describing the location of the curve (log ED50).

b

One of the parameters describing the curve shape.

- -

Value

- -

The response at dose x.

-

References

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

Arguments

+
x
+

In this context, the x variable is the dose.

-

van Ewijk, P. H. and Hoekstra, J. A. (1993) Ecotox Environ Safety - 25 25-32

+
k
+

In the drfit functions, k is set to 1.

-
- +
+

Value

+ + +

The response at dose x.

+
+
+

References

+

van Ewijk, P. H. and Hoekstra, J. A. (1993) Ecotox Environ Safety + 25 25-32

+
+

Author

Johannes Ranke - jranke@uni-bremen.de

+ jranke@uni-bremen.de

+
+
+
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index 0175c25..cc8668e 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -1,66 +1,14 @@ - - - - - - - -Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit - - - - - - - - - - - - - - + + -
-
- -
- -
+

Cytotoxicity data for different pyrithionates and related species

@@ -113,51 +47,49 @@ IPC-81 cell line.

- 
data(pyrithione)
- - -

Format

+
+ 
data(pyrithione)
+
-

A dataframe containing the data as required for the drfit +

+

Format

+

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

-

Source

- +
+
+

Source

Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004) Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with antifouling biocide zinc pyrithione and structural analogues. Green Chemistry 6(5) 259-266

+
-

Examples

- 
  if (FALSE) demo(pyrithione)
-
- +
-
- - + + -- cgit v1.2.1