Brextract: Extract a simulation from the output of emaxsim

In clinDR: Simulation and Analysis Tools for Clinical Dose Response Modeling

Extract a simulation from the output of emaxsim

Description

Extract a simulated data set from the output of emaxsim. Data are re-created using the stored random number seed.

Usage

## S3 method for class 'emaxsim'
x[i, ...]

Arguments

x	Output object from emaxsim
i	Simulation replication to extract
...	Parameters passed to other functions (none currently)

Details

Re-creates the ith simulated data set for subsequent analyses. Also returns all analyses done for the ith data set in emaxsim

Value

A list is returned with class(emaxsimobj) containing:

y	Response vector
dose	Doses corresponding to y
pop	Population parameters; type of parameter depends on constructor function generating study data.
popSD	Vector containing the population SD used to generate continuous data. NULL for binary data.
init	Starting Emax parameters
est4	4-parmameter Emax fit (ed50,lambda,emax,e0). NA if failed to converge or 3-parameter model requested.
est3	3-parmameter Emax fit (ed50,emax,e0). NA if failed to converge or 4-parameter model successfully fit.
estA	Alternative parameter estimates. NA if Emax model fit successfully
vc	The variance-covariance matrix of the model parameters for the selected model.
residSD	The residual SD based on the selected model.
bigC	bigC= TRUE if the primary fit (from modType) yielded an ED50 > ED50 upper limit.
negC	negC= TRUE if the primary fit (from modType) yielded a negative ED50 estimate< ED50 lower limit
modType	When modType=4, the fitting begins with the 4 parameter model. If estimation fails or modType=3, the 3-parameter estimation is applied. If it fails, a best-fitting model linear in its parameters is selected.
fit	Output of model determined by fitType
fitType	Character vector with "4", "3", "L", "LL", or "E" for 4-Emax, 3-Emax, linear, log-linear, or exponential when an alternative model is selected.
ed50cutoff	Upper allowed limit for ED50 estimates.
ed50lowcutoff	Lower allowed limit for the ED50 estimates.
switchMod	If switchMod is TRUE, the algorithm substitutes a simpler model if (1) convergence is not achieved, (2) the information matrix is not positive definite at the converged values, (3) the ED50 estimates are outside the cutoff bounds. If switchMod is F, only conditions (1) or (2) cause a simpler model to be used.
PL	T if the 'plinear' algorithm in nls converged
predpop	Population means for each dose group
dm	Vector containing dose group means
dsd	Vector containing dose group SDs
fitpred	Dose groups means estimated from the model
sepred	SEs for estimates in fitpred
sedif	SEs for model-based estimates of difference with placebo
pVal, selContrast	P-value and contrast selected from MCP-MOD test
idmax	Index of default dose group for comparison to placebo

Note

Extraction from a simulation object requires re-creation of the simulated data set. If the extracted object is to be used more than once, it is more efficient to save the extracted object than reuse [].

Author(s)

Neal Thomas

See Also

emaxsim, print.emaxsimobj, plot.emaxsimobj, update.emaxsimobj

Examples

## Not run: 
## code change random number seed

nsim<-50
idmax<-5
doselev<-c(0,5,25,50,100)
n<-c(78,81,81,81,77)

### population parameters for simulation
e0<-2.465375 
ed50<-67.481113 

dtarget<-100
diftarget<-9.032497
emax<-solveEmax(diftarget,dtarget,log(ed50),1,e0)

sdy<-7.967897
pop<-c(log(ed50),emax,e0)    
meanlev<-emaxfun(doselev,pop)  

###FixedMean is specialized constructor function for emaxsim
gen.parm<-FixedMean(n,doselev,meanlev,sdy)  

D1 <- emaxsim(nsim,gen.parm,modType=3)
e49<-D1[49]                  #### extract 49th simulation


## End(Not run)

clinDR documentation built on Aug. 9, 2023, 9:08 a.m.