This function creates a survData object from experimental data
provided as a data.frame. The resulting object
can then be used for plotting and model fitting. It can also be used
to generate individual-time estimates.
The survDataCheck function can be used to check if an object
containing survival data is formatted according to the expectations of the
survData function.
survData(x)survDataCheck(data, diagnosis.plot = FALSE)
A dataframe of class survData and column replicate as factor.
The function returns a dataframe of class msgTable and data.frame with two columns: id and msg of
character strings. When no error is detected the object is empty.
Here is the list of possible error ids with their meaning:
dataframeExpected | an object of class data.frame is expected |
missingColumn | at least one expected column heading is missing |
firstTime0 | the first time point for some (concentration, replicate) couples is not 0 |
concNumeric | column conc contains a value of class other than numeric |
timeNumeric | column time contains a value of class other than numeric |
NsurvInteger | column Nsurv contains a value of class other than integer |
tablePositive | some data are negative |
Nsurv0T0 | Nsurv is 0 at time 0 for some (concentration, replicate) |
duplicateID | there are two identical (replicate, time) couples |
NsurvIncrease | Nsurv increases at some time point of some (concentration, replicate) |
maxTimeDiffer | maximum time for concentration is lower than maximum time for survival |
a data.frame containing the following four columns:
replicate: a vector of any class numeric, character or factor for replicate
identification. A given replicate value should identify the same group of
individuals followed in time
conc: a vector of class numeric with tested concentrations
(positive values, may contain NAs)
time: a vector of class integer with time points, minimal value must be 0
Nsurv: a vector of class integer providing the number of
alive individuals at each time point for each concentration and each replicate
(may contain NAs)
any object
if TRUE, the function may produce diagnosis plots
Survival data sets can be under either constant or time-variable exposure profile. The
resulting object, in addition to its survData class, inherits the
class survDataCstExp or survDataVarExp respectively.
The x argument describes experimental results from a survival
toxicity test. Each line of the data.frame
corresponds to one experimental measurement, that is a number of alive
individuals at a given concentration at a given time point and in a given replicate.
Note that either the concentration
or the number of alive individuals may be missing. The data set is inferred
to be under constant exposure if the concentration is constant for each
replicate and systematically available. The function survData fails if
x does not meet the
expected requirements. Please run survDataCheck to ensure
x is well-formed.
survDataCheck
survData