drFit: Function to run the dose-response curve fit and EC50...
In grofit: The package was developed to fit fit many growth curves obtained under different conditions.
Description
Usage
Arguments
Details
Value
See Also
Examples
Description
The function serves to estimate several dose-response curves at once. The function calls the functions drFitSpline and drBootSpline to generate a table with estimates for EC50 and respecting statistics.
Usage
1
drFit(gcFitData, control = grofit.control())
Arguments
gcFitData
Data frame containing the data for the dose-response curve estimation. It must follow the convention: 1. column: string, naming the experiment for which a dose-response curve shall be estimated; 2. column: string, additional information about the experiment; 3. column: numeric, concentration of substrate; 4. column: logical, reliability flag, 5. column: string, naming a parametric model, 6. column: logical, indicating wether a logarithmic transformation was applied to the time points of the growth data; 7. column: logical, indicating wether a logarithmic transformation was applied to the growth values of the growth data; 8.-55. characteristic growth parameters obtained from growth curve fit.
control
Object of class grofit.control containing a list of options generated by the function grofit.control.
Details
The function is meant to process the result from the fit of several growth curves performed by gcFit. It therefore expects a certain input format. For each of the distinct experiments specified by the names in the first column, the function relates the concentration (3. column) to a characteristic growth parameter (8.-55. columns). The choice of the parameter depends on the option parameter specified by the grofit.control function. The concentration and parameter are passed to drFitSpline and drBootSpline, which perform the dose-response curve estimation and bootstrapping.
Value
Generates an object of class drFit
raw.data
Data that passed to the function as gcFitData.
drTable
Data frame, 1. column: string, naming the experiment; 2. column: logical, indicating wether a logarithmic transformation was applied to concentration data; 3. column, logical, indicating wether a logarithmic transformation was applied to growth parameter; 4. column, numeric, number of bootstrap samples used; 5.-8. column: numeric, estimated EC50 value and respecting reponse value (5.-6.), also in original scale if a transformation is applied (7.-8.); 9.-10. column: numeric, mean and standard dev. from bootstrap sample; 11.-14. column: 90 and 95 percent confidence interval from bootstrap sample; 15. column: mean EC50 of bootstrap sample in original scale; 16.-19. 90 and 95 percent confidence interval in original scale.
drBootSplines
List of all drBootSpline objects generated by the call of drBootSpline for each distinct experiments. Note: access to each object via double brace: LIST[[1]], LIST[[2]]...
drFittedSplines
list of all drFitSpline objects generated by the call of drFitSpline for each distinct experiments. Note: access to each object via double brace: LIST[[1]], LIST[[2]]...
control
Object of class grofit.control containing list of options passed to the function as control.
See Also
drFitSpline, drBootSpline, drBootSpline, summary.drFit, plot.drFit
Examples
1
2
3
4
5
6
7
8
9
10
# generate random growth curve data set
foo <- ran.data(100, 25)
time <- foo$time
data <- foo$data
# fit dose response curves
drData <- gcFit(time, data, control = grofit.control(interactive = FALSE))
# use the output of gcFit as an input for drFit
drFit.result <- drFit(summary(drData))
print(summary(drFit.result))
plot(drFit.result)
Example output
= 1. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 2. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 3. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 4. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 5. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 6. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 7. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 8. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 9. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 10. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 11. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 12. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 13. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 14. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 15. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 16. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 17. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 18. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 19. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 20. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 21. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 22. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 23. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 24. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 25. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 26. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 27. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 28. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 29. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 30. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 31. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 32. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 33. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 34. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 35. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 36. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 37. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 38. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 39. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 40. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 41. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 42. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 43. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 44. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 45. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 46. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 47. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 48. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 49. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 50. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 51. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 52. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 53. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 54. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 55. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 56. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 57. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 58. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 59. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 60. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 61. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 62. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 63. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 64. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 65. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 66. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 67. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 68. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 69. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 70. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 71. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 72. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 73. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 74. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 75. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 76. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 77. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 78. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 79. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 80. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 81. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 82. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 83. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 84. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 85. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 86. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 87. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 88. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 89. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 90. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 91. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 92. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 93. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 94. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 95. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 96. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 97. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 98. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 99. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 100. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
=== EC 50 Estimation ==============================
---------------------------------------------------
--> Checking data ...
--> Number of distinct tests found: 3
--> Valid datasets per test:
TestID Number
Test I 33
Test II 33
Test III 34
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test I
xEC50 0.408862716541835 yEC50 0.590201471483502
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test II
xEC50 0.413431965989584 yEC50 0.597833857919661
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test III
xEC50 0.439740559760571 yEC50 0.569581272690095
Test log.x log.y Samples EC50 yEC50 EC50.orig yEC50.orig
1 Test I FALSE FALSE 0 0.4088627 0.5902015 0.4088627 0.5902015
2 Test II FALSE FALSE 0 0.4134320 0.5978339 0.4134320 0.5978339
3 Test III FALSE FALSE 0 0.4397406 0.5695813 0.4397406 0.5695813
meanEC50 sdEC50 ci90EC50.lo ci90EC50.up ci95EC50.lo ci95EC50.up meanEC50.orig
1 NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA
ci90EC50.orig.lo ci90EC50.orig.up ci95EC50.orig.lo ci95EC50.orig.up
1 NA NA NA NA
2 NA NA NA NA
3 NA NA NA NA
grofit documentation built on May 30, 2017, 4:08 a.m.
R Package Documentation
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Description Usage Arguments Details Value See Also Examples
Description
The function serves to estimate several dose-response curves at once. The function calls the functions drFitSpline and drBootSpline to generate a table with estimates for EC50 and respecting statistics.
Usage
1 | drFit(gcFitData, control = grofit.control())
|
Arguments
gcFitData |
Data frame containing the data for the dose-response curve estimation. It must follow the convention: 1. column: string, naming the experiment for which a dose-response curve shall be estimated; 2. column: string, additional information about the experiment; 3. column: numeric, concentration of substrate; 4. column: logical, reliability flag, 5. column: string, naming a parametric model, 6. column: logical, indicating wether a logarithmic transformation was applied to the time points of the growth data; 7. column: logical, indicating wether a logarithmic transformation was applied to the growth values of the growth data; 8.-55. characteristic growth parameters obtained from growth curve fit. |
control |
Object of class |
Details
The function is meant to process the result from the fit of several growth curves performed by gcFit. It therefore expects a certain input format. For each of the distinct experiments specified by the names in the first column, the function relates the concentration (3. column) to a characteristic growth parameter (8.-55. columns). The choice of the parameter depends on the option parameter specified by the grofit.control function. The concentration and parameter are passed to drFitSpline and drBootSpline, which perform the dose-response curve estimation and bootstrapping.
Value
Generates an object of class drFit
raw.data |
Data that passed to the function as |
drTable |
Data frame, 1. column: string, naming the experiment; 2. column: logical, indicating wether a logarithmic transformation was applied to concentration data; 3. column, logical, indicating wether a logarithmic transformation was applied to growth parameter; 4. column, numeric, number of bootstrap samples used; 5.-8. column: numeric, estimated EC50 value and respecting reponse value (5.-6.), also in original scale if a transformation is applied (7.-8.); 9.-10. column: numeric, mean and standard dev. from bootstrap sample; 11.-14. column: 90 and 95 percent confidence interval from bootstrap sample; 15. column: mean EC50 of bootstrap sample in original scale; 16.-19. 90 and 95 percent confidence interval in original scale. |
drBootSplines |
List of all |
drFittedSplines |
list of all |
control |
Object of class |
See Also
drFitSpline, drBootSpline, drBootSpline, summary.drFit, plot.drFit
Examples
1 2 3 4 5 6 7 8 9 10 | # generate random growth curve data set
foo <- ran.data(100, 25)
time <- foo$time
data <- foo$data
# fit dose response curves
drData <- gcFit(time, data, control = grofit.control(interactive = FALSE))
# use the output of gcFit as an input for drFit
drFit.result <- drFit(summary(drData))
print(summary(drFit.result))
plot(drFit.result)
|
Example output
= 1. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 2. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 3. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 4. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 5. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 6. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 7. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 8. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 9. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 10. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 11. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 12. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 13. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 14. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 15. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 16. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 17. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 18. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 19. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 20. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 21. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 22. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 23. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 24. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 25. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 26. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 27. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 28. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 29. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 30. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 31. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 32. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 33. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 34. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 35. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 36. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 37. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 38. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 39. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 40. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 41. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 42. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 43. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 44. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 45. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 46. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 47. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 48. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 49. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 50. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 51. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 52. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 53. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 54. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 55. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 56. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 57. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 58. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 59. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 60. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 61. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 62. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 63. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 64. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 65. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 66. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 67. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 68. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 69. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 70. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 71. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 72. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 73. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 74. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 75. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 76. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 77. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 78. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 79. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 80. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 81. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 82. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 83. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 84. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 85. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 86. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 87. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 88. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 89. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 90. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 91. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 92. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 93. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 94. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 95. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 96. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 97. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... ERROR in nls(). For further information see help(gcFitModel)
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 98. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... OK
= 99. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
= 100. growth curve =================================
----------------------------------------------------
--> Try to fit model logistic....... OK
--> Try to fit model richards....... OK
--> Try to fit model gompertz....... OK
--> Try to fit model gompertz.exp... ERROR in nls(). For further information see help(gcFitModel)
=== EC 50 Estimation ==============================
---------------------------------------------------
--> Checking data ...
--> Number of distinct tests found: 3
--> Valid datasets per test:
TestID Number
Test I 33
Test II 33
Test III 34
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test I
xEC50 0.408862716541835 yEC50 0.590201471483502
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test II
xEC50 0.413431965989584 yEC50 0.597833857919661
=== Dose response curve estimation ================
--- EC 50 -----------------------------------------
--> Test III
xEC50 0.439740559760571 yEC50 0.569581272690095
Test log.x log.y Samples EC50 yEC50 EC50.orig yEC50.orig
1 Test I FALSE FALSE 0 0.4088627 0.5902015 0.4088627 0.5902015
2 Test II FALSE FALSE 0 0.4134320 0.5978339 0.4134320 0.5978339
3 Test III FALSE FALSE 0 0.4397406 0.5695813 0.4397406 0.5695813
meanEC50 sdEC50 ci90EC50.lo ci90EC50.up ci95EC50.lo ci95EC50.up meanEC50.orig
1 NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA
ci90EC50.orig.lo ci90EC50.orig.up ci95EC50.orig.lo ci95EC50.orig.up
1 NA NA NA NA
2 NA NA NA NA
3 NA NA NA NA
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