R/analyze.R
In jservadio/TrialistNof1: Bayesian N-of-1 calculations
analyze <- function(Y, Outcome, Treat, score.range = c(30, 4, 5, 4, 4, 4,30), Covs, slopeprior, nChains = 3, conv.limit = 1.05,
niters = 50000, nruns = 5000, setsize = 4000, alphaprior, beta.norm.prior, beta.ord.prior, c1prior, dcprior, varprior,
varprior.params, path = "", mod.id)
{
nobs = length(Y)
stopifnot(length(varprior)==2)
stopifnot(length(alphaprior)==3, length(beta.norm.prior)==3, length(beta.ord.prior)==3)
stopifnot(length(dcprior) == 3, length(c1prior) == 3, length(varprior.params)==2)
varprior = as.list(varprior)
alphaprior = as.list(alphaprior)
beta.norm.prior = as.list(beta.norm.prior)
beta.ord.prior = as.list(beta.ord.prior)
dcprior = as.list(dcprior)
outnames = c("Pain", "Fatigue", "Drowsy", "Sleep", "Thinking", "Constipation", "Neuropathic Pain")
names(score.range) = outnames
if (Outcome == "Pain") { index = 1
} else if (Outcome == "Fatigue") { index = 2
} else if (Outcome == "Drowsy") { index = 3
} else if (Outcome == "Sleep") { index = 4
} else if (Outcome == "Thinking") { index = 5
} else if (Outcome == "Constipation") { index = 6
} else if (Outcome == "Neuropain") { index = 7
}
if (mod.id %in% c(1, 2, 3, 5.1, 5.2, 5.3)) {
cat("\n \n \n", Outcome, mod.id, "\n \n \n")
if (index == 1) {
Pain.out = tryCatch({run.norm(Y, Treat, Covs, "normal", "hom", nChains, conv.limit, niters, nruns, setsize,
slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
} else if (index == 2) {
Fatigue.out = tryCatch({run.ord(Y, Treat, Covs, score.range[2]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 3) {
Drowsy.out = tryCatch({run.ord(Y, Treat, Covs, score.range[3]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 4) {
Sleep.out = tryCatch({run.ord(Y, Treat, Covs, score.range[4]+1, "cumlogit", nChains, conv.limit, niters, nruns,
setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 5) {
Thinking.out = tryCatch({run.ord(Y, Treat, Covs, score.range[5]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 6) {
Constipation.out = tryCatch({run.ord(Y, Treat, Covs, score.range[6]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 7) {
Neuropain.out = tryCatch({run.norm(Y, Treat, Covs, "normal", "hom", nChains, conv.limit, niters, nruns,
setsize, slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
}
} else if (mod.id %in% c(4, 4.1, 4.2, 5.4, 5.41, 5.42)) {
cat("\n \n \n", Outcome, mod.id, "\n \n \n")
if (index == 1) {
Pain.out = tryCatch({run.norm(Y, Treat, Covs[ , -c(2:7)], "normal", "hom", nChains, conv.limit, niters, nruns, setsize,
slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
} else if (index == 2) {
Fatigue.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1, 3:7)], score.range[2]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 3) {
Drowsy.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:2, 4:7)], score.range[3]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 4) {
Sleep.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:3, 5:7)], score.range[4]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 5) {
Thinking.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:4, 6:7)], score.range[5]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 6) {
Constipation.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:5, 7)], score.range[6]+1, "cumlogit", nChains, conv.limit,
niters, nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 7) {
Neuropain.out = tryCatch({run.norm(Y, Treat, Covs[ , -c(1:6)], "normal", "hom", nChains, conv.limit, niters, nruns,
setsize, slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
}
}
out = list()
if (index == 1) {
if (length(Pain.out) > 1) {Pain.treat.diff = Pain.out[["beta"]]}
if (length(Pain.out) > 1) {
Pain.treat.diff.change = treat.diff.change(Pain.treat.diff, score.range[1])
Pain.urun = FALSE
} else {
Pain.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Pain.urun = TRUE
}
change.interval = round(Pain.treat.diff.change[[1]], 3)
change.probs = round(Pain.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Pain.urun, Pain.treat.diff.change, Pain.out$alpha, Pain.out$beta, Pain.out$Sd, Pain.out$Slope, Pain.out$DIC, Pain.out$Dev)
names(out) = c("pain", "Outcome", "mod.id", "Pain.urun", "Pain.treat.diff.change", "alpha", "beta", "Sd", "Slope", "DIC", "Dev")
} else if (index == 2) {
if (length(Fatigue.out) > 1) {Fatigue.treat.diff = treat.diffs(Fatigue.out[["p"]], Treat)}
if (length(Fatigue.out) > 1) {
Fatigue.treat.diff.change = treat.diff.change(Fatigue.treat.diff,score.range[2])
Fatigue.urun = FALSE
} else{
Fatigue.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Fatigue.urun = TRUE
}
change.interval = round(Fatigue.treat.diff.change[[1]], 3)
change.probs = round(Fatigue.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Fatigue.urun, Fatigue.treat.diff.change, Fatigue.out$beta, Fatigue.out$c, Fatigue.out$p, Fatigue.out$Slopes,
Fatigue.out$DIC)
names(out) = c("fatigue", "Outcome", "mod.id", "Fatigue.urun", "Fatigue.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 3) {
if (length(Drowsy.out) > 1) {Drowsy.treat.diff = treat.diffs(Drowsy.out[["p"]], Treat)}
if (length(Drowsy.out) > 1) {
Drowsy.treat.diff.change = treat.diff.change(Drowsy.treat.diff,score.range[3])
Drowsy.urun = FALSE
} else{
Drowsy.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Drowsy.urun = TRUE
}
change.interval = round(Drowsy.treat.diff.change[[1]], 3)
change.probs = round(Drowsy.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Drowsy.urun, Drowsy.treat.diff.change, Drowsy.out$beta, Drowsy.out$c, Drowsy.out$p, Drowsy.out$Slopes,
Drowsy.out$DIC)
names(out) = c("drowsy", "Outcome", "mod.id", "Drowsy.urun", "Drowsy.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 4) {
if (length(Sleep.out) > 1) {Sleep.treat.diff = treat.diffs(Sleep.out[["p"]], Treat)}
if (length(Sleep.out) > 1) {
Sleep.treat.diff.change = treat.diff.change(Sleep.treat.diff,score.range[4])
Sleep.urun = FALSE
} else{
Sleep.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Sleep.urun = TRUE
}
change.interval = round(Sleep.treat.diff.change[[1]], 3)
change.probs = round(Sleep.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Sleep.urun, Sleep.treat.diff.change, Sleep.out$beta, Sleep.out$c, Sleep.out$p, Sleep.out$Slopes, Sleep.out$DIC)
names(out) = c("sleep", "Outcome", "mod.id", "Sleep.urun", "Sleep.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 5) {
if (length(Thinking.out) > 1) {Thinking.treat.diff = treat.diffs(Thinking.out[["p"]], Treat)}
if (length(Thinking.out) > 1) {
Thinking.treat.diff.change = treat.diff.change(Thinking.treat.diff,score.range[5])
Thinking.urun = FALSE
} else{
Thinking.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Thinking.urun = TRUE
}
change.interval = round(Thinking.treat.diff.change[[1]], 3)
change.probs = round(Thinking.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Thinking.urun, Thinking.treat.diff.change, Thinking.out$beta, Thinking.out$c, Thinking.out$p,
Thinking.out$Slopes, Thinking.out$DIC)
names(out) = c("thinking", "Outcome", "mod.id", "Thinking.urun", "Thinking.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 6) {
if (length(Constipation.out) > 1) {Constipation.treat.diff = treat.diffs(Constipation.out[["p"]], Treat)}
if (length(Constipation.out) > 1) {
Constipation.treat.diff.change = treat.diff.change(Constipation.treat.diff,score.range[6])
Constipation.urun = FALSE
} else{
Constipation.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Constipation.urun = TRUE
}
change.interval = round(Constipation.treat.diff.change[[1]], 3)
change.probs = round(Constipation.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Constipation.urun, Constipation.treat.diff.change, Constipation.out$beta, Constipation.out$c,
Constipation.out$p, Constipation.out$Slopes, Constipation.out$DIC)
names(out) = c("constipation", "Outcome", "mod.id", "Constipation.urun", "Constipation.treat.diff.change", "beta", "c", "p", "Slope",
"DIC")
} else if (index == 7) {
if (length(Neuropain.out) > 1) {Neuropain.treat.diff = Neuropain.out[["beta"]]}
if (length(Neuropain.out) > 1) {
Neuropain.treat.diff.change = treat.diff.change(Neuropain.treat.diff, score.range[1])
Neuropain.urun = FALSE
} else{
Neuropain.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Neuropain.urun = TRUE
}
change.interval = round(Neuropain.treat.diff.change[[1]], 3)
change.probs = round(Neuropain.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Neuropain.urun, Neuropain.treat.diff.change, Neuropain.out$alpha, Neuropain.out$beta, Neuropain.out$Sd,
Neuropain.out$Slopes, Neuropain.out$DIC, Neuropain.out$Dev)
names(out) = c("neuropain", "Outcome", "mod.id", "Neuropain.urun", "Neuropain.treat.diff.change", "alpha", "beta", "Sd", "Slope", "DIC", "Dev")
}
if (index == 1) {
out[[length(out) + 1]] = Pain.out$Y.samp
names(out)[length(out)] = "Y.samp"
if (mod.id %in% c(2, 4.1, 5.2, 5.41)) {
out[[length(out) + 1]] = Pain.out$Time.samp
names(out)[length(out)] = "Time.samp"
}
} else if (index == 2) {
out[[length(out) + 1]] = Fatigue.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 3) {
out[[length(out) + 1]] = Drowsy.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 4) {
out[[length(out) + 1]] = Sleep.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 5) {
out[[length(out) + 1]] = Thinking.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 6) {
out[[length(out) + 1]] = Constipation.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 7) {
out[[length(out) + 1]] = Neuropain.out$Y.samp
names(out)[length(out)] = "Y.samp"
if (mod.id %in% c(2, 4.1, 5.2, 5.41)) {
out[[length(out) + 1]] = Neuropain.out$Time.samp
names(out)[length(out)] = "Time.samp"
}
}
return(out)
}
jservadio/TrialistNof1 documentation built on May 20, 2019, 2:08 a.m.
R Package Documentation
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analyze <- function(Y, Outcome, Treat, score.range = c(30, 4, 5, 4, 4, 4,30), Covs, slopeprior, nChains = 3, conv.limit = 1.05,
niters = 50000, nruns = 5000, setsize = 4000, alphaprior, beta.norm.prior, beta.ord.prior, c1prior, dcprior, varprior,
varprior.params, path = "", mod.id)
{
nobs = length(Y)
stopifnot(length(varprior)==2)
stopifnot(length(alphaprior)==3, length(beta.norm.prior)==3, length(beta.ord.prior)==3)
stopifnot(length(dcprior) == 3, length(c1prior) == 3, length(varprior.params)==2)
varprior = as.list(varprior)
alphaprior = as.list(alphaprior)
beta.norm.prior = as.list(beta.norm.prior)
beta.ord.prior = as.list(beta.ord.prior)
dcprior = as.list(dcprior)
outnames = c("Pain", "Fatigue", "Drowsy", "Sleep", "Thinking", "Constipation", "Neuropathic Pain")
names(score.range) = outnames
if (Outcome == "Pain") { index = 1
} else if (Outcome == "Fatigue") { index = 2
} else if (Outcome == "Drowsy") { index = 3
} else if (Outcome == "Sleep") { index = 4
} else if (Outcome == "Thinking") { index = 5
} else if (Outcome == "Constipation") { index = 6
} else if (Outcome == "Neuropain") { index = 7
}
if (mod.id %in% c(1, 2, 3, 5.1, 5.2, 5.3)) {
cat("\n \n \n", Outcome, mod.id, "\n \n \n")
if (index == 1) {
Pain.out = tryCatch({run.norm(Y, Treat, Covs, "normal", "hom", nChains, conv.limit, niters, nruns, setsize,
slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
} else if (index == 2) {
Fatigue.out = tryCatch({run.ord(Y, Treat, Covs, score.range[2]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 3) {
Drowsy.out = tryCatch({run.ord(Y, Treat, Covs, score.range[3]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 4) {
Sleep.out = tryCatch({run.ord(Y, Treat, Covs, score.range[4]+1, "cumlogit", nChains, conv.limit, niters, nruns,
setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 5) {
Thinking.out = tryCatch({run.ord(Y, Treat, Covs, score.range[5]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 6) {
Constipation.out = tryCatch({run.ord(Y, Treat, Covs, score.range[6]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 7) {
Neuropain.out = tryCatch({run.norm(Y, Treat, Covs, "normal", "hom", nChains, conv.limit, niters, nruns,
setsize, slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
}
} else if (mod.id %in% c(4, 4.1, 4.2, 5.4, 5.41, 5.42)) {
cat("\n \n \n", Outcome, mod.id, "\n \n \n")
if (index == 1) {
Pain.out = tryCatch({run.norm(Y, Treat, Covs[ , -c(2:7)], "normal", "hom", nChains, conv.limit, niters, nruns, setsize,
slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
} else if (index == 2) {
Fatigue.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1, 3:7)], score.range[2]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 3) {
Drowsy.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:2, 4:7)], score.range[3]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 4) {
Sleep.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:3, 5:7)], score.range[4]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 5) {
Thinking.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:4, 6:7)], score.range[5]+1, "cumlogit", nChains, conv.limit, niters,
nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 6) {
Constipation.out = tryCatch({run.ord(Y, Treat, Covs[ , -c(1:5, 7)], score.range[6]+1, "cumlogit", nChains, conv.limit,
niters, nruns, setsize, beta.ord.prior, dcprior, c1prior, path, mod.id)}, error=function(cond){caught <- list("DIC" = 1000)})
} else if (index == 7) {
Neuropain.out = tryCatch({run.norm(Y, Treat, Covs[ , -c(1:6)], "normal", "hom", nChains, conv.limit, niters, nruns,
setsize, slopeprior, alphaprior, beta.norm.prior, varprior,varprior.params, path = "", mod.id)}, error=function(cond){
caught <- list("DIC" = 1000)})
}
}
out = list()
if (index == 1) {
if (length(Pain.out) > 1) {Pain.treat.diff = Pain.out[["beta"]]}
if (length(Pain.out) > 1) {
Pain.treat.diff.change = treat.diff.change(Pain.treat.diff, score.range[1])
Pain.urun = FALSE
} else {
Pain.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Pain.urun = TRUE
}
change.interval = round(Pain.treat.diff.change[[1]], 3)
change.probs = round(Pain.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Pain.urun, Pain.treat.diff.change, Pain.out$alpha, Pain.out$beta, Pain.out$Sd, Pain.out$Slope, Pain.out$DIC, Pain.out$Dev)
names(out) = c("pain", "Outcome", "mod.id", "Pain.urun", "Pain.treat.diff.change", "alpha", "beta", "Sd", "Slope", "DIC", "Dev")
} else if (index == 2) {
if (length(Fatigue.out) > 1) {Fatigue.treat.diff = treat.diffs(Fatigue.out[["p"]], Treat)}
if (length(Fatigue.out) > 1) {
Fatigue.treat.diff.change = treat.diff.change(Fatigue.treat.diff,score.range[2])
Fatigue.urun = FALSE
} else{
Fatigue.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Fatigue.urun = TRUE
}
change.interval = round(Fatigue.treat.diff.change[[1]], 3)
change.probs = round(Fatigue.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Fatigue.urun, Fatigue.treat.diff.change, Fatigue.out$beta, Fatigue.out$c, Fatigue.out$p, Fatigue.out$Slopes,
Fatigue.out$DIC)
names(out) = c("fatigue", "Outcome", "mod.id", "Fatigue.urun", "Fatigue.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 3) {
if (length(Drowsy.out) > 1) {Drowsy.treat.diff = treat.diffs(Drowsy.out[["p"]], Treat)}
if (length(Drowsy.out) > 1) {
Drowsy.treat.diff.change = treat.diff.change(Drowsy.treat.diff,score.range[3])
Drowsy.urun = FALSE
} else{
Drowsy.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Drowsy.urun = TRUE
}
change.interval = round(Drowsy.treat.diff.change[[1]], 3)
change.probs = round(Drowsy.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Drowsy.urun, Drowsy.treat.diff.change, Drowsy.out$beta, Drowsy.out$c, Drowsy.out$p, Drowsy.out$Slopes,
Drowsy.out$DIC)
names(out) = c("drowsy", "Outcome", "mod.id", "Drowsy.urun", "Drowsy.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 4) {
if (length(Sleep.out) > 1) {Sleep.treat.diff = treat.diffs(Sleep.out[["p"]], Treat)}
if (length(Sleep.out) > 1) {
Sleep.treat.diff.change = treat.diff.change(Sleep.treat.diff,score.range[4])
Sleep.urun = FALSE
} else{
Sleep.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Sleep.urun = TRUE
}
change.interval = round(Sleep.treat.diff.change[[1]], 3)
change.probs = round(Sleep.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Sleep.urun, Sleep.treat.diff.change, Sleep.out$beta, Sleep.out$c, Sleep.out$p, Sleep.out$Slopes, Sleep.out$DIC)
names(out) = c("sleep", "Outcome", "mod.id", "Sleep.urun", "Sleep.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 5) {
if (length(Thinking.out) > 1) {Thinking.treat.diff = treat.diffs(Thinking.out[["p"]], Treat)}
if (length(Thinking.out) > 1) {
Thinking.treat.diff.change = treat.diff.change(Thinking.treat.diff,score.range[5])
Thinking.urun = FALSE
} else{
Thinking.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Thinking.urun = TRUE
}
change.interval = round(Thinking.treat.diff.change[[1]], 3)
change.probs = round(Thinking.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Thinking.urun, Thinking.treat.diff.change, Thinking.out$beta, Thinking.out$c, Thinking.out$p,
Thinking.out$Slopes, Thinking.out$DIC)
names(out) = c("thinking", "Outcome", "mod.id", "Thinking.urun", "Thinking.treat.diff.change", "beta", "c", "p", "Slope", "DIC")
} else if (index == 6) {
if (length(Constipation.out) > 1) {Constipation.treat.diff = treat.diffs(Constipation.out[["p"]], Treat)}
if (length(Constipation.out) > 1) {
Constipation.treat.diff.change = treat.diff.change(Constipation.treat.diff,score.range[6])
Constipation.urun = FALSE
} else{
Constipation.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Constipation.urun = TRUE
}
change.interval = round(Constipation.treat.diff.change[[1]], 3)
change.probs = round(Constipation.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Constipation.urun, Constipation.treat.diff.change, Constipation.out$beta, Constipation.out$c,
Constipation.out$p, Constipation.out$Slopes, Constipation.out$DIC)
names(out) = c("constipation", "Outcome", "mod.id", "Constipation.urun", "Constipation.treat.diff.change", "beta", "c", "p", "Slope",
"DIC")
} else if (index == 7) {
if (length(Neuropain.out) > 1) {Neuropain.treat.diff = Neuropain.out[["beta"]]}
if (length(Neuropain.out) > 1) {
Neuropain.treat.diff.change = treat.diff.change(Neuropain.treat.diff, score.range[1])
Neuropain.urun = FALSE
} else{
Neuropain.treat.diff.change = list(c(-1, 0, 1), c(0, 0.2, 0.2, 0.2, 0.2, 0.2, 0))
Neuropain.urun = TRUE
}
change.interval = round(Neuropain.treat.diff.change[[1]], 3)
change.probs = round(Neuropain.treat.diff.change[[2]], 3)
out = list(list(
"interval" = structure(as.list(change.interval), names=c("P025", "Median", "P975")),
"probs" = structure(as.list(change.probs), names=c("P(< -0.2)", "P(-0.2 - -0.1)", "P(-0.1 - -0.05)", "P(-0.05 - 0.05)", "P(0.05 - 0.1)", "P(0.1 - 0.2)", "P(> 0.2)"))
), Outcome, mod.id, Neuropain.urun, Neuropain.treat.diff.change, Neuropain.out$alpha, Neuropain.out$beta, Neuropain.out$Sd,
Neuropain.out$Slopes, Neuropain.out$DIC, Neuropain.out$Dev)
names(out) = c("neuropain", "Outcome", "mod.id", "Neuropain.urun", "Neuropain.treat.diff.change", "alpha", "beta", "Sd", "Slope", "DIC", "Dev")
}
if (index == 1) {
out[[length(out) + 1]] = Pain.out$Y.samp
names(out)[length(out)] = "Y.samp"
if (mod.id %in% c(2, 4.1, 5.2, 5.41)) {
out[[length(out) + 1]] = Pain.out$Time.samp
names(out)[length(out)] = "Time.samp"
}
} else if (index == 2) {
out[[length(out) + 1]] = Fatigue.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 3) {
out[[length(out) + 1]] = Drowsy.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 4) {
out[[length(out) + 1]] = Sleep.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 5) {
out[[length(out) + 1]] = Thinking.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 6) {
out[[length(out) + 1]] = Constipation.out$Y.samp
names(out)[length(out)] = "Y.samp"
} else if (index == 7) {
out[[length(out) + 1]] = Neuropain.out$Y.samp
names(out)[length(out)] = "Y.samp"
if (mod.id %in% c(2, 4.1, 5.2, 5.41)) {
out[[length(out) + 1]] = Neuropain.out$Time.samp
names(out)[length(out)] = "Time.samp"
}
}
return(out)
}
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