From 9b36a3d2055d3bfa4844ca43acc232f064856871 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 31 Mar 2017 12:10:59 +0200 Subject: Further improvement to checkcontrols() Static documentation rebuilt by pkgdown::build_site() --- R/checkcontrols.R | 65 +++++++--- check.log | 5 - docs/index.html | 2 +- docs/reference/IM1xIPC81.html | 196 ++++++++++++++++++++++++++++++ docs/reference/IM1xVibrio.html | 233 ++++++++++++++++++++++++++++++++++++ docs/reference/XY.html | 121 +++++++++++++++++++ docs/reference/antifoul.html | 4 +- docs/reference/checkcontrols.html | 25 ++-- docs/reference/checkexperiment.html | 4 +- docs/reference/checksubstance.html | 8 +- docs/reference/drcfit.html | 12 +- docs/reference/drdata.html | 8 +- docs/reference/drfit.html | 13 +- docs/reference/drplot.html | 14 +-- docs/reference/linlogitf.html | 149 +++++++++++++++++++++++ docs/reference/pyrithione.html | 125 +++++++++++++++++++ 16 files changed, 924 insertions(+), 60 deletions(-) create mode 100644 docs/reference/IM1xIPC81.html create mode 100644 docs/reference/IM1xVibrio.html create mode 100644 docs/reference/XY.html create mode 100644 docs/reference/linlogitf.html create mode 100644 docs/reference/pyrithione.html diff --git a/R/checkcontrols.R b/R/checkcontrols.R index df9a2f9..d996d18 100644 --- a/R/checkcontrols.R +++ b/R/checkcontrols.R @@ -1,5 +1,6 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc")) checkcontrols <- function(last = 10, id = NULL, db = "cytotox", + celltype = "IPC-81", enzymetype = "AChE", organism = "Vibrio fischeri", endpoint = "%", qcc = c("R", "xbar")) { @@ -14,8 +15,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox", if (db %in% c("cytotox","enzymes")) { if (is.null(id[1])) { - platequery <- paste("SELECT plate FROM controls", - "GROUP BY plate ORDER BY plate DESC LIMIT", last) + platequery <- "SELECT plate FROM" + if (db == "cytotox") { + platequery <- paste0(platequery, " cytotox WHERE celltype like + '", celltype, "'") + } + if (db == "enzymes") { + platequery <- paste0(platequery, " enzymes WHERE enzyme like + '", enzymetype, "'") + } + platequery <- paste(platequery, + "GROUP BY plate ORDER BY plate DESC LIMIT", last) plates <- RODBC::sqlQuery(channel, platequery)$plate } else { plates <- id @@ -25,26 +35,39 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox", controldata <- RODBC::sqlQuery(channel,controlquery) } else { if (is.null(id[1])) { - lastquery = paste0("SELECT experiment FROM ecotox ", - "WHERE type LIKE '", endpoint, "' ", + lastquery = paste0("SELECT experiment, type FROM ecotox ", + "WHERE organism LIKE '", organism, "'", + "AND type LIKE '", endpoint, "' ", "GROUP BY experiment ORDER BY experiment DESC LIMIT ", last) res <- RODBC::sqlQuery(channel, lastquery) if (nrow(res) == 0) { stop("No results for endpoint", endpoint) } else { + if (nlevels(res$type) > 1) { + stop("Found more than one endpoint type:\n", + paste(levels(res$type), collapse = ", "), "\n", + "Please specify an endpoint in your call to checkcontrols()") + } experiments <- res$experiment } } else { experiments <- id } - expquery <- paste("SELECT ", - "experimentator, substance, organism, conc, unit, response, ", + expquery <- paste0("SELECT ", + "experimentator, experiment, substance, organism, type, conc, unit, raw_response, ", "performed, ok ", "FROM ecotox ", "WHERE experiment IN (", paste(experiments, collapse = ", "), ") ", "AND organism LIKE '", organism, "' ", - "AND type LIKE '", endpoint, "'", sep = "") + "AND type LIKE '", endpoint, "'") expdata <- RODBC::sqlQuery(channel, expquery) + if (nlevels(expdata$type) > 1) { + stop("Found more than one endpoint type:\n", + paste(levels(expdata$type), collapse = ", "), "\n", + "Please specify an endpoint in your call to checkcontrols()") + } + # Use the raw response for QA + expdata$response <- expdata$raw_response } RODBC::odbcClose(channel) @@ -76,13 +99,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox", QA["Control (conc = 0)", 2],2) } + # The report + cat("\nDatabase", db, "\n") + if (db == "ecotox") { - endpoint_string = if(endpoint == "%") "any endpoint" else paste("endpoint", endpoint) - cat("\nExperiments ", paste(experiments, collapse = ", "), - " from database ecotox for ", endpoint_string, " for ", organism, ":\n\n", sep = "") + cat("Organism", organism, "\n") + cat("Endpoint", unique(expdata$type), "\n") + cat("\nExperiments ", paste(experiments, collapse = ", "), "\n\n") } else { - cat("\nPlates ", paste(plates, collapse = ", "), - " from database ", db, ":\n\n", sep = "") + if (db == "cytotox") cat ("Cell type", celltype, "\n") + if (db == "enzymes") cat ("Enzyme type", enzymetype, "\n") + cat("\nPlates", paste(plates, collapse = ", "), "\n\n") } print(QA) @@ -90,9 +117,17 @@ checkcontrols <- function(last = 10, id = NULL, db = "cytotox", op <- par(ask=TRUE) on.exit(par(op)) requireNamespace("reshape2") - controls_molten <- melt(controls[c("plate", "location", "response")], - id = c("plate", "location")) - controls_wide <- acast(controls_molten, formula = plate ~ location) + if (db == "ecotox") { + controls$row <- rownames(controls) + controls_molten <- melt(controls[c("experiment", "row", "response")], + id = c("experiment", "row")) + controls_wide <- acast(controls_molten, formula = experiment ~ row) + + } else { + controls_molten <- melt(controls[c("plate", "location", "response")], + id = c("plate", "location")) + controls_wide <- acast(controls_molten, formula = plate ~ location) + } if ("R" %in% qcc) { qcc(controls_wide, type = "R", nsigmas = 3, title = "Range chart", diff --git a/check.log b/check.log index 5d1e47c..2ad8764 100644 --- a/check.log +++ b/check.log @@ -2,12 +2,9 @@ * using R version 3.3.3 (2017-03-06) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 -* using option ‘--as-cran’ * checking for file ‘drfit/DESCRIPTION’ ... OK * this is package ‘drfit’ version ‘0.7.1’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers -Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -32,7 +29,6 @@ Maintainer: ‘Johannes Ranke ’ * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK -* checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK @@ -40,7 +36,6 @@ Maintainer: ‘Johannes Ranke ’ * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK -* checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK diff --git a/docs/index.html b/docs/index.html index f6c1903..6360f04 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ fitting dose-response curves to continuous dose-response data, calculating some toxicological parameters and plotting the results. Please consider using the more powerful and actively developed 'drc' package. Functions that are - fitted are the cumulative density function of the lognormal distribution + fitted are the cumulative density function of the log-normal distribution ('probit' fit), of the logistic distribution ('logit' fit), of the Weibull distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit), derived from the latter, which is used to describe data showing stimulation at diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html new file mode 100644 index 0000000..6ab98e7 --- /dev/null +++ b/docs/reference/IM1xIPC81.html @@ -0,0 +1,196 @@ + + + + + + + + +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

+
+ + +

This is the raw data documenting the influence of the alkyl + chain length in 3 position on the toxicity to the + promyelocytic leukemia rat cell line IPC-81. The substances + are named according to the UFT naming scheme of these + substances. IM13 BF4 means 1-methyl-3-propylimidazolium + tetrafluoroborate, IM14 BF4 means + 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 + BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. + This is a subset (only the BF4 anion) of the data + shown in Figure 3 in Ranke et al. (2004).

+ + + 
data(IM1xIPC81)
+ +

Format

+ +

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

+ +

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.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html new file mode 100644 index 0000000..79c3d95 --- /dev/null +++ b/docs/reference/IM1xVibrio.html @@ -0,0 +1,233 @@ + + + + + + + + +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

+
+ + +

This is the raw data documenting the influence of the alkyl chain length in 3 + position on the toxicity to the marine luminescent bacteria V. + fischeri. The substances are named according to the UFT naming scheme of + these substances. + IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, + IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and + IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.

+ + + 
data(IM1xVibrio)
+ +

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

+ +

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.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/XY.html b/docs/reference/XY.html new file mode 100644 index 0000000..a585270 --- /dev/null +++ b/docs/reference/XY.html @@ -0,0 +1,121 @@ + + + + + + + + +Dose-Response data for two substances X and Y — XY • drfit + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Dose-Response data for two substances X and Y

+
+ + +

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

+ + + 
data(XY)
+ +

Format

+ +

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: demo(XY)
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index f5bc9fd..92fd8e8 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -72,9 +72,9 @@ -

This data set shows the response of the rat leukaemic cell line IPC-81 to +

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

diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index 2b2eb8b..0e89c93 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -76,7 +76,9 @@ experiments from a specified database.

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

     
     
 Arguments

@@ -98,10 +100,19 @@
     "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
-      
The organism that was exposed to the chemical. Only important if the database
-    "ecotox" is used. Defaults to "Vibrio fischeri".

+      
Only important if database "ecotox" is used.

     
     
       endpoint
@@ -110,8 +121,8 @@
     
     
       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 
+      
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.

     
     
@@ -136,8 +147,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  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 e22705d..277bfd5 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -120,8 +120,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  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 0fbca62..60ae6e3 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -122,12 +122,12 @@
     
     
       whereClause
-      
With this argument, additional conditions for the SQL query can be set, 
+      
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 
+      
With the default value "%", all data in the database is retrieved for the
     specified substance.

     
     
@@ -153,8 +153,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  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 75a168a..e7de303 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -165,10 +165,10 @@
   
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 
+    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. 
+  
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.
     The name of the column depends on the requested confidence level.

@@ -176,11 +176,11 @@
   
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.
-    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 
+    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
-    parameters b from BC.4, LN.2, 
+    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.

@@ -236,7 +236,7 @@
 
     
Author

     
-  Johannes Ranke jranke@uni-bremen.de 
+  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 e369c5c..dd5be7b 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -95,7 +95,7 @@
     
       db
       
The database to be used. Currently, the databases "cytotox", "enzymes"
-    and "ecotox" of the UFT Department of Bioorganic Chemistry are 
+    and "ecotox" of the UFT Department of Bioorganic Chemistry are
     supported (default is "cytotox").

     
     
@@ -119,7 +119,7 @@
     
     
       whereClause
-      
With this argument, additional conditions for the SQL query can be set, 
+      
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).

     
@@ -222,8 +222,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  Johannes Ranke
+  jranke@uni-bremen.de
   http://www.uft.uni-bremen.de/chemie/ranke
 
   
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html
index 7acce23..2de949f 100644
--- a/docs/reference/drfit.html
+++ b/docs/reference/drfit.html
@@ -196,9 +196,8 @@
   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:

+  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

@@ -207,10 +206,10 @@
   
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 
+    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. 
+  
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.
     The name of the column depends on the requested confidence level.

@@ -277,8 +276,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  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 eff1338..9a678e1 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -72,7 +72,7 @@
     
 
     
-    
Produce graphics of dose-response data and dose-response relationships 
+    
Produce graphics of dose-response data and dose-response relationships
   either combined or separately, for one or more substances.

     
 
@@ -110,7 +110,7 @@
     
     
       ctype
-      
This argument decides if horizontal lines are drawn to show the scatter of 
+      
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
@@ -159,13 +159,13 @@
     
     
       postscript
-      
If TRUE, (a) postscript graph(s) will be created. Otherwise, and if 
+      
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 
+      
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.

     
@@ -177,7 +177,7 @@
     
     
       bw
-      
A boolean deciding if the plots will be black and white or not. Default 
+      
A boolean deciding if the plots will be black and white or not. Default
     is TRUE.

     
     
@@ -245,8 +245,8 @@
 
     
Author

     
-  Johannes Ranke 
-  jranke@uni-bremen.de 
+  Johannes Ranke
+  jranke@uni-bremen.de
   http://www.uft.uni-bremen.de/chemie/ranke
 
   
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
new file mode 100644
index 0000000..8b9ba0d
--- /dev/null
+++ b/docs/reference/linlogitf.html
@@ -0,0 +1,149 @@
+
+
+
+  
+  
+
+
+
+Linear-logistic function — linlogitf • drfit
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    

+      

+      
+
+      
+      

+
+      

+  

+    

+    
Linear-logistic function

+    

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

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

+    
+    
 Arguments

+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
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

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

+    
+
+  

+  
+

+
+      

+      

+  
Developed by Johannes Ranke.

+

+
+

+  
Site built with pkgdown.

+

+
+      

+   

+
+  
+
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
new file mode 100644
index 0000000..7496be2
--- /dev/null
+++ b/docs/reference/pyrithione.html
@@ -0,0 +1,125 @@
+
+
+
+  
+  
+
+
+
+Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    

+      

+      
+
+      
+      

+
+      

+  

+    

+    
Cytotoxicity data for different pyrithionates and related species

+    

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

+    
+
+    
data(pyrithione)

+        
+    
Format

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

+    
+    
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

+    
  ## Not run: demo(pyrithione)

+  

+  
+

+
+      
+   

+
+  
+
-- 
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