library(formula.tools)
library(matrixStats)
-
+library(bbmle)
## df: dataframe to model
## outcome_formula: formula for y | x, z
## outcome_family: family for y | x, z
## outcome_formula <- y ~ x + z; proxy_formula <- w_pred ~ y + x + z + x:z + x:y + z:y
-measerr_mle_dv <- function(df, outcome_formula, outcome_family=binomial(link='logit'), proxy_formula, proxy_family=binomial(link='logit')){
+measerr_mle_dv <- function(df, outcome_formula, outcome_family=binomial(link='logit'), proxy_formula, proxy_family=binomial(link='logit'),method='optim'){
nll <- function(params){
df.obs <- model.frame(outcome_formula, df)
start <- rep(0.1,length(params))
names(start) <- params
- fit <- optim(start, fn = nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+ if(method=='optim'){
+ fit <- optim(start, fn = nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+ } else {
+ quoted.names <- gsub("[\\(\\)]",'',names(start))
+ print(quoted.names)
+ text <- paste("function(", paste0(quoted.names,'=',start,collapse=','),"){params<-c(",paste0(quoted.names,collapse=','),");return(nll(params))}")
+
+ measerr_mle_nll <- eval(parse(text=text))
+ names(start) <- quoted.names
+ names(lower) <- quoted.names
+ fit <- mle2(minuslogl=measerr_mle_nll, start=start, lower=lower, parnames=params,control=list(maxit=1e6),method='L-BFGS-B')
+ }
return(fit)
}
## Experimental, and not necessary if errors are independent.
-measerr_irr_mle <- function(df, outcome_formula, outcome_family=gaussian(), rater_formula, proxy_formula, proxy_family=binomial(link='logit'), truth_formula, truth_family=binomial(link='logit')){
+measerr_irr_mle <- function(df, outcome_formula, outcome_family=gaussian(), rater_formula, proxy_formula, proxy_family=binomial(link='logit'), truth_formula, truth_family=binomial(link='logit'),method='optim'){
### in this scenario, the ground truth also has measurement error, but we have repeated measures for it.
start <- rep(0.1,length(params))
names(start) <- params
- fit <- optim(start, fn = nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+
+ if(method=='optim'){
+ fit <- optim(start, fn = nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+ } else {
+
+ quoted.names <- gsub("[\\(\\)]",'',names(start))
+ print(quoted.names)
+ text <- paste("function(", paste0(quoted.names,'=',start,collapse=','),"){params<-c(",paste0(quoted.names,collapse=','),");return(nll(params))}")
+
+ measerr_mle_nll <- eval(parse(text=text))
+ names(start) <- quoted.names
+ names(lower) <- quoted.names
+ fit <- mle2(minuslogl=measerr_mle_nll, start=start, lower=lower, parnames=params,control=list(maxit=1e6),method='L-BFGS-B')
+ }
+
return(fit)
}
-measerr_mle <- function(df, outcome_formula, outcome_family=gaussian(), proxy_formula, proxy_family=binomial(link='logit'), truth_formula, truth_family=binomial(link='logit')){
+measerr_mle <- function(df, outcome_formula, outcome_family=gaussian(), proxy_formula, proxy_family=binomial(link='logit'), truth_formula, truth_family=binomial(link='logit'),method='optim'){
- measrr_mle_nll <- function(params){
+ measerr_mle_nll <- function(params){
df.obs <- model.frame(outcome_formula, df)
proxy.variable <- all.vars(proxy_formula)[1]
proxy.model.matrix <- model.matrix(proxy_formula, df)
lower <- c(lower, rep(-Inf, length(truth.params)))
start <- rep(0.1,length(params))
names(start) <- params
-
- fit <- optim(start, fn = measrr_mle_nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+
+ if(method=='optim'){
+ fit <- optim(start, fn = measerr_mle_nll, lower=lower, method='L-BFGS-B', hessian=TRUE, control=list(maxit=1e6))
+ } else { # method='mle2'
+
+ quoted.names <- gsub("[\\(\\)]",'',names(start))
+
+ text <- paste("function(", paste0(quoted.names,'=',start,collapse=','),"){params<-c(",paste0(quoted.names,collapse=','),");return(measerr_mle_nll(params))}")
+
+ measerr_mle_nll_mle <- eval(parse(text=text))
+ names(start) <- quoted.names
+ names(lower) <- quoted.names
+ fit <- mle2(minuslogl=measerr_mle_nll_mle, start=start, lower=lower, parnames=params,control=list(maxit=1e6),method='L-BFGS-B')
+ }
return(fit)
}
+