X-Git-Url: https://code.communitydata.science/ml_measurement_error_public.git/blobdiff_plain/47e9367ed5c61b721bdc17cddd76bced4f8ed621..979dc14b6861ae31f00d56392fd5b8cf69f17333:/simulations/irr_dv_simulation_base.R

diff --git a/simulations/irr_dv_simulation_base.R b/simulations/irr_dv_simulation_base.R
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+++ b/simulations/irr_dv_simulation_base.R
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+library(matrixStats) # for numerically stable logsumexps
+
+options(amelia.parallel="no",
+        amelia.ncpus=1)
+library(Amelia)
+
+source("measerr_methods.R") ## for my more generic function.
+
+run_simulation_depvar <- function(df, result, outcome_formula = y ~ x + z, rater_formula = y.obs ~ x, proxy_formula = w_pred ~ y){
+
+    accuracy <- df[,mean(w_pred==y)]
+    result <- append(result, list(accuracy=accuracy))
+
+    (model.true <- glm(y ~ x + z, data=df, family=binomial(link='logit')))
+    true.ci.Bxy <- confint(model.true)['x',]
+    true.ci.Bzy <- confint(model.true)['z',]
+
+    result <- append(result, list(Bxy.est.true=coef(model.true)['x'],
+                                  Bzy.est.true=coef(model.true)['z'],
+                                  Bxy.ci.upper.true = true.ci.Bxy[2],
+                                  Bxy.ci.lower.true = true.ci.Bxy[1],
+                                  Bzy.ci.upper.true = true.ci.Bzy[2],
+                                  Bzy.ci.lower.true = true.ci.Bzy[1]))
+
+
+
+    loa0.feasible <- glm(y.obs.0 ~ x + z, data = df[!(is.na(y.obs.0))], family=binomial(link='logit'))
+
+    loa0.ci.Bxy <- confint(loa0.feasible)['x',]
+    loa0.ci.Bzy <- confint(loa0.feasible)['z',]
+
+    result <- append(result, list(Bxy.est.loa0.feasible=coef(loa0.feasible)['x'],
+                                  Bzy.est.loa0.feasible=coef(loa0.feasible)['z'],
+                                  Bxy.ci.upper.loa0.feasible = loa0.ci.Bxy[2],
+                                  Bxy.ci.lower.loa0.feasible = loa0.ci.Bxy[1],
+                                  Bzy.ci.upper.loa0.feasible = loa0.ci.Bzy[2],
+                                  Bzy.ci.lower.loa0.feasible = loa0.ci.Bzy[1]))
+
+
+    df.loa0.mle <- copy(df)
+    df.loa0.mle[,y:=y.obs.0]
+    loa0.mle <- measerr_mle_dv(df.loa0.mle, outcome_formula=outcome_formula, proxy_formula=proxy_formula)
+    fisher.info <- solve(loa0.mle$hessian)
+    coef <- loa0.mle$par
+    ci.upper <- coef + sqrt(diag(fisher.info)) * 1.96
+    ci.lower <- coef - sqrt(diag(fisher.info)) * 1.96
+
+    result <- append(result, list(Bxy.est.loa0.mle=coef['x'],
+                                  Bzy.est.loa0.mle=coef['z'],
+                                  Bxy.ci.upper.loa0.mle = ci.upper['x'],
+                                  Bxy.ci.lower.loa0.mle = ci.lower['x'],
+                                  Bzy.ci.upper.loa0.mle = ci.upper['z'],
+                                  Bzy.ci.lower.loa0.mle = ci.upper['z']))
+
+    loco.feasible <- glm(y.obs.0 ~ x + z, data = df[(!is.na(y.obs.0)) & (y.obs.1 == y.obs.0)], family=binomial(link='logit'))
+
+    loco.feasible.ci.Bxy <- confint(loco.feasible)['x',]
+    loco.feasible.ci.Bzy <- confint(loco.feasible)['z',]
+
+    result <- append(result, list(Bxy.est.loco.feasible=coef(loco.feasible)['x'],
+                                  Bzy.est.loco.feasible=coef(loco.feasible)['z'],
+                                  Bxy.ci.upper.loco.feasible = loco.feasible.ci.Bxy[2],
+                                  Bxy.ci.lower.loco.feasible = loco.feasible.ci.Bxy[1],
+                                  Bzy.ci.upper.loco.feasible = loco.feasible.ci.Bzy[2],
+                                  Bzy.ci.lower.loco.feasible = loco.feasible.ci.Bzy[1]))
+
+
+    df.loco.mle <- copy(df)
+    df.loco.mle[,y.obs:=NA]
+    df.loco.mle[(y.obs.0)==(y.obs.1),y.obs:=y.obs.0]
+    df.loco.mle[,y.true:=y]
+    df.loco.mle[,y:=y.obs]
+    print(df.loco.mle[!is.na(y.obs.1),mean(y.true==y,na.rm=TRUE)])
+    loco.mle <- measerr_mle_dv(df.loco.mle, outcome_formula=outcome_formula, proxy_formula=proxy_formula)
+    fisher.info <- solve(loco.mle$hessian)
+    coef <- loco.mle$par
+    ci.upper <- coef + sqrt(diag(fisher.info)) * 1.96
+    ci.lower <- coef - sqrt(diag(fisher.info)) * 1.96
+
+    result <- append(result, list(Bxy.est.loco.mle=coef['x'],
+                                  Bzy.est.loco.mle=coef['z'],
+                                  Bxy.ci.upper.loco.mle = ci.upper['x'],
+                                  Bxy.ci.lower.loco.mle = ci.lower['x'],
+                                  Bzy.ci.upper.loco.mle = ci.upper['z'],
+                                  Bzy.ci.lower.loco.mle = ci.upper['z']))
+
+    print(rater_formula)
+    print(proxy_formula)
+
+    ## mle.irr <- measerr_irr_mle( df, outcome_formula = outcome_formula, rater_formula = rater_formula, proxy_formula=proxy_formula, truth_formula=truth_formula)
+
+    ## fisher.info <- solve(mle.irr$hessian)
+    ## coef <- mle.irr$par
+    ## ci.upper <- coef + sqrt(diag(fisher.info)) * 1.96
+    ## ci.lower <- coef - sqrt(diag(fisher.info)) * 1.96
+    
+    ## result <- append(result,
+    ##                  list(Bxy.est.mle = coef['x'],
+    ##                       Bxy.ci.upper.mle = ci.upper['x'],
+    ##                       Bxy.ci.lower.mle = ci.lower['x'],
+    ##                       Bzy.est.mle = coef['z'],
+    ##                       Bzy.ci.upper.mle = ci.upper['z'],
+    ##                       Bzy.ci.lower.mle = ci.lower['z']))
+
+    return(result)
+
+}