Read data from a text or csv file and recalculate the
exposure profile depending on the type of experiment (acute oral, acute contact, chronic oral).
dataGUTS(
file_location = NULL,
test_type = NULL,
bee_species = "Honey_Bee",
NA_string = getOption("datatable.na.strings", "NA"),
...
)An object of class beeSurvData, which is a list with the following information:
Number of files passed to the function
A table containing the survival data as entered by the user in the input file
A data frame containing the survival data in long format for model purposes
A table containing the concentration data as entered by the user in the input file
A data frame containing concentration data in long format
A character vector containing the units of the data as entered in the line Concentration unit
of the input file
A character vector containing the type of experiment
A character vector containing the type bee
A data frame containing the concentration data as recalculated by the model
A data frame containing the concentration data as recalculated by the model in a long format
Each element of the list is itself a list to account for multiple files that can be passed as input.
List of Locations of text files containing each two datasets, one for the survival data, and one for the concentration data. Both datasets must be included in the same file and contain the same number of column in the same order. The following columns must be included in the survival dataset:
Survival time \[d\]: a vector of time in days
Control A vector of number of survivors for the control
T1 - Tn A vector of number of survivors for the treatments
T1 to Tn, one column per treatment.
A line containing the Concentration unit must be included directly after the end of
the last row of the survival data.
The following columns must be included in the concentration dataset
Concentration time \[d\]: a vector of time in days.
Control A vector of concentrations for the control
T1 - Tn A vector of concentration for the treatments
T1 to Tn, one column per treatment.
For the Acute_Oral and Acute_Contact, only the initial
exposure concentration at time 0 is required.
See detail section for example
list of test types amongst "Acute_Oral", "Acute_Contact", and "Chronic_Oral" this list must have the same length of the list of file locations
the bee type among "Honey_Bee", "Bumble_Bee", "Osmia_bicornis", and "User_Bee". If "User_Bee" is selected, optional arguments to be passed to the concentration reconstruction need to be defined.
a character vector of strings which are to be interpreted as NA values
Optional arguments to be passed to the concentration reconstruction (e.g.
k_sr = for the stomach release rate (d-1), default is 0.625 for Honey bee,
k_ca = contact availability rate (d-1), default is 0.4 for Honey bee), or
cTime = the duration of exposure in days for the acute oral tests, default is 0.25 d
cstConcCal = logical, recalculate concentration in the Chronic_Oral test from mg a.s./kg feed to Xg/bee (default is TRUE)
f_rate = numerical vector, feeding rate used in the concentration recalculation in the Chronic_Oral (default is 25 mg/bee/day for honey bee)
targConc = numerical scalar, target concentration unit in the recalculation in the Chronic_Oral, 1 for µg/bee, 2 for ng/bee, 3 for mg/bee (default is 1).
binning = binning of the time vector of the exposure for acute tests (Acute_Oral and Acute_Contact), default 0.5 d
The filename must begin with name of the chemical substance being tested and each word of the filename should be separated via an underscore '_'.
#' Example of formatting of the input file for a chronic oral study
| Survival time [d] | Control | T1 | T2 | T3 | T4 | T5 |
| 0 | 120 | 120 | 120 | 120 | 120 | 120 |
| 1 | 120 | 118 | 117 | 112 | 115 | 94 |
| 2 | 120 | 118 | 115 | 112 | 98 | 88 |
| 3 | 120 | 118 | 114 | 106 | 83 | 27 |
| 4 | 119 | 118 | 113 | 103 | 67 | 9 |
| 5 | 119 | 118 | 112 | 100 | 43 | 3 |
| Concentration unit: ug/bee/day | ||||||
| Concentration time [d] | Control | T1 | T2 | T3 | T4 | T5 |
| 0 | 0 | 3 | 7 | 12 | 41 | 68 |
| 5 | 0 | 3 | 7 | 12 | 41 | 68 |
# \donttest{
file_location <- system.file("extdata", "betacyfluthrin_chronic_ug.txt", package = "BeeGUTS")
lsData <- dataGUTS(file_location = c(file_location),
test_type = c('Chronic_Oral'),
bee_species = "Honey_Bee",
cstConcCal = FALSE)
# }
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