Nothing
## ----set-options, echo=FALSE, cache=FALSE---------------------------------------------------------
options(width = 100)
## -------------------------------------------------------------------------------------------------
library("joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("simjointmeta", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
exampledat1 <- simjointmeta(k = 5, n = rep(500, 5), sepassoc = FALSE,
ntms = 5,longmeasuretimes = c(0, 1, 2, 3, 4),
beta1 = c(1, 2, 3), beta2 = 1,
rand_ind = "intslope", rand_stud = NULL,
gamma_ind = 1,
sigb_ind = matrix(c(1, 0.5, 0.5, 1.5),nrow = 2),
vare = 0.01, theta0 = -3, theta1 = 1,
censoring = TRUE, censlam = exp(-3),
truncation = FALSE,
trunctime = max(longmeasuretimes))
## ---- eval=FALSE----------------------------------------------------------------------------------
# exampledat1$percentevent
## -------------------------------------------------------------------------------------------------
str(exampledat1$longitudinal)
## -------------------------------------------------------------------------------------------------
str(exampledat1$survival)
## -------------------------------------------------------------------------------------------------
exampledat2 <- simjointmeta(k = 5, n = rep(500, 5), sepassoc = TRUE, ntms = 5,
longmeasuretimes = c(0, 1, 2, 3, 4), beta1 = c(1, 2, 3),
beta2 = 1, rand_ind = "intslope", rand_stud = "inttreat",
gamma_ind = c(0.5, 1), gamma_stud = c(0.5, 1),
sigb_ind = matrix(c(1, 0.5, 0.5, 1.5), nrow = 2),
sigb_stud = matrix(c(1, 0.5, 0.5, 1.5), nrow = 2),
vare = 0.01, theta0 = -3, theta1 = 1, censoring = TRUE,
censlam = exp(-3), truncation = FALSE,
trunctime = max(longmeasuretimes))
## -------------------------------------------------------------------------------------------------
gamma_ind_set <- list(c(0.5, 1), c(0.4, 0.9), c(0.6, 1.1), c(0.5, 0.9), c(0.4, 1.1))
gamma_stud_set <- list(c(0.6, 1.1), c(0.5, 1), c(0.5, 0.9), c(0.4, 1.1), c(0.4, 0.9))
censlamset <- c(exp(-3), exp(-2.9), exp(-3.1), exp(-3), exp(-3.05))
theta0set <- c(-3, -2.9, -3, -2.9, -3.1)
theta1set <- c(1, 0.9, 1.1, 1, 0.9)
exampledat2 <- simjointmeta(k = 5, n = rep(500, 5), sepassoc = TRUE, ntms = 5,
longmeasuretimes = c(0, 1, 2, 3, 4), beta1 = c(1, 2, 3),
beta2 = 1, rand_ind = "intslope", rand_stud = "inttreat",
gamma_ind = gamma_ind_set, gamma_stud = gamma_stud_set,
sigb_ind = matrix(c(1, 0.5, 0.5, 1.5), nrow = 2),
sigb_stud = matrix(c(1, 0.5, 0.5, 1.5), nrow = 2),
vare = 0.01, theta0 = theta0set, theta1 = theta1set,
censoring = TRUE, censlam = censlamset, truncation = FALSE,
trunctime = max(longmeasuretimes))
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("simdat2", package = "joineRmeta")
# help("simdat3", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# data("simdat2")
# str(simdat2)
## -------------------------------------------------------------------------------------------------
jointdat<-tojointdata(longitudinal = simdat2$longitudinal,
survival = simdat2$survival, id = "id", longoutcome = "Y",
timevarying = c("time","ltime"), survtime = "survtime", cens = "cens",
time = "time")
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("tojointdata", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
str(jointdat)
## -------------------------------------------------------------------------------------------------
jointdat$baseline$study <- as.factor(jointdat$baseline$study)
jointdat$baseline$treat <- as.factor(jointdat$baseline$treat)
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("removeafter", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# str(simdat3)
## -------------------------------------------------------------------------------------------------
jointdat3<-tojointdata(longitudinal = simdat3$longitudinal,
survival = simdat3$survival, id = "id", longoutcome = "Y",
timevarying = c("time","ltime"), survtime = "survtime", cens = "cens",
time = "time")
## ---- results = "hide"----------------------------------------------------------------------------
jointdat3.1<-removeafter(data = jointdat3, longitudinal = "Y",
survival = "survtime", id = "id", time = "time")
## -------------------------------------------------------------------------------------------------
str(jointdat3)
str(jointdat3.1)
## -------------------------------------------------------------------------------------------------
sepplots <- jointmetaplot(dataset = jointdat, study = "study", longoutcome = "Y",
longtime = "time", survtime = "survtime", cens = "cens",
id = "id", smoother = TRUE,
studynames = c("Study 1", "Study 2", "Study 3"), type = "Both")
## ---- fig.show='hold', fig.keep='high'------------------------------------------------------------
sepplots$longplots$`studyplot.Study 3`
sepplots$eventplots[[1]]
## -------------------------------------------------------------------------------------------------
sepplots2 <- jointmetaplot(dataset = jointdat, study = "study", longoutcome = "Y",
longtime = "time", survtime = "survtime", cens = "cens",
id = "id", smoother = TRUE,
studynames = c("Study 1", "Study 2", "Study 3"),
type = "Both", eventby = "treat")
sepplots3 <- jointmetaplot(dataset = jointdat, study = "study", longoutcome = "Y",
longtime = "time", survtime = "survtime", cens = "cens",
id = "id", smoother = TRUE,
studynames = c("Study 1", "Study 2", "Study 3"),
type = "Event", eventconfint = TRUE)
sepplots2$eventplots$`studyplot.Study 3`
sepplots3$eventplots[[2]]
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmetaplot", package = "joineRmeta")
## ---- fig.show='hide'-----------------------------------------------------------------------------
allplot2 <- suppressWarnings(jointmetaplotall(plotlist = sepplots2, ncol = 2,
top = "All studies",
type = "Both"))
## ---- eval=FALSE----------------------------------------------------------------------------------
# allplot2$longall
# allplot2$eventsall
## ---- fig.height=10, fig.width=5------------------------------------------------------------------
allplot2$longall
allplot2$eventsall
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmetaplotall", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("joineRfits", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
joineRmodels <- joineRfits[c("joineRfit1", "joineRfit2", "joineRfit3")]
joineRmodelsSE <- joineRfits[c("joineRfit1SE", "joineRfit2SE", "joineRfit3SE")]
## -------------------------------------------------------------------------------------------------
summary(joineRmodels[[1]])
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("joineRfits2", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
joineRmodels2 <- joineRfits2[c("joineRfit6", "joineRfit7", "joineRfit8")]
joineRmodels2SE <- joineRfits2[c("joineRfit6SE", "joineRfit7SE", "joineRfit8SE")]
## -------------------------------------------------------------------------------------------------
summary(joineRmodels2[[1]])
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("JMfits", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
summary(JMfits[[1]])
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("JMfits2", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
summary(JMfits2[[1]])
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmeta2", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
MAjoineRfits <- jointmeta2(fits = joineRmodels, SE = joineRmodelsSE,
longpar = c("time", "treat1"),
survpar = "treat1", assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3"))
## -------------------------------------------------------------------------------------------------
names(MAjoineRfits$longMA)
## ---- fig.height=4, fig.width=9, warning = FALSE, message = FALSE---------------------------------
library(meta)
forest(MAjoineRfits$longMA$treat1)
## ---- error = TRUE--------------------------------------------------------------------------------
MAjoineRfits2 <- jointmeta2(fits = c(joineRmodels[1:3], joineRmodels2[1:2]),
SE = c(joineRmodelsSE[1:3],joineRmodels2SE[1:2]),
longpar = c("time", "treat1"), survpar = "treat1",
assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3",
"Study 4", "Study 5"))
## -------------------------------------------------------------------------------------------------
MAJMfits <- jointmeta2(fits = JMfits, longpar = c("time", "treat1"),
survpar = "treat1", assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3"))
## -------------------------------------------------------------------------------------------------
MAJMfits2 <- jointmeta2(fits = JMfits2, longpar = c("time", "treat1"),
survpar = "treat1", assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3"))
## ---- error = TRUE--------------------------------------------------------------------------------
MAtest <- jointmeta2(fits = c(JMfits2[1:3], JMfits[1:2]),
longpar = c("time", "treat1"),
survpar = "treat1", assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3",
"Study 4", "Study 5"))
## ---- error = TRUE--------------------------------------------------------------------------------
MAtest <- jointmeta2(fits = c(JMfits2[1:3], joineRfits[1:2]),
longpar = c("time", "treat1"),
survpar = "treat1", assoc = TRUE,
studynames = c("Study 1","Study 2", "Study 3",
"Study 4", "Study 5"))
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmeta1", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("onestage1", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit0 <- jointmeta1(data = jointdat,
# long.formula = Y ~ 1 + time + treat,
# long.rand.ind = c("int", "time"),
# sharingstrct = "randprop",
# surv.formula = Surv(survtime, cens) ~ treat,
# study.name = "study", strat = F)
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit1 <- jointmeta1(data = jointdat,
# long.formula = Y ~ 1 + time + treat*study,
# long.rand.ind = c("int", "time"),
# sharingstrct = "randprop",
# surv.formula = Surv(survtime, cens) ~ treat*study,
# study.name = "study", strat = F)
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmeta1.object", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit1SE <- jointmetaSE(fitted = onestagefit1, n.boot = 200,
# overalleffects = list(long = list(c("treat1", "treat1:study2"),
# c("treat1", "treat1:study3")),
# surv = list(c("treat1", "treat1:study2"),
# c("treat1", "treat1:study3"))))
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("jointmeta1SE.object", package = "joineRmeta")
## -------------------------------------------------------------------------------------------------
#extract the saved model fit and bootstrap results
onestagefit1 <- onestage1$onestagefit1
onestagefit1SE <- onestage1$onestagefit1SE
## -------------------------------------------------------------------------------------------------
summary(onestagefit1)
## -------------------------------------------------------------------------------------------------
print(onestagefit1)
## -------------------------------------------------------------------------------------------------
fixef(onestagefit1, type = "Longitudinal")
## -------------------------------------------------------------------------------------------------
fixef(onestagefit1, type = "Survival")
## -------------------------------------------------------------------------------------------------
fixef(onestagefit1, type = "Latent")
## ---- eval=FALSE----------------------------------------------------------------------------------
# ranef(onestagefit1, type = "individual")
## -------------------------------------------------------------------------------------------------
rancov(onestagefit1, type = "individual")
## -------------------------------------------------------------------------------------------------
formula(onestagefit1, type = "Longitudinal")
## -------------------------------------------------------------------------------------------------
formula(onestagefit1, type = "Survival")
## -------------------------------------------------------------------------------------------------
formula(onestagefit1, type = "Rand_ind")
## -------------------------------------------------------------------------------------------------
print(onestagefit1SE)
## -------------------------------------------------------------------------------------------------
confint(onestagefit1SE)
## ---- eval=FALSE----------------------------------------------------------------------------------
# vcov(onestagefit1SE)
## ---- eval=FALSE----------------------------------------------------------------------------------
# help("onestage2", package = "joineRmeta")
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit2 <- jointmeta1(data = jointdat,
# long.formula = Y ~ 1 + time + treat,
# long.rand.ind = c("int", "time"),
# long.rand.stud = c("study", "treat"),
# sharingstrct = "randprop",
# surv.formula = Surv(survtime, cens) ~ treat,
# study.name = "study", strat = F)
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit2SE<-jointmetaSE(fitted = onestagefit2, n.boot = 200)
## -------------------------------------------------------------------------------------------------
#extract the saved model fit and bootstrap results
onestagefit2<-onestage2$onestagefit2
onestagefit2SE<-onestage2$onestagefit2SE
## ---- eval=FALSE----------------------------------------------------------------------------------
# ranef(onestagefit2, type = "study")
## -------------------------------------------------------------------------------------------------
rancov(onestagefit2, type = "study")
## -------------------------------------------------------------------------------------------------
formula(onestagefit2, type = "Rand_stud")
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit3 <- jointmeta1(data = jointdat,
# long.formula = Y ~ 1 + time + treat*study,
# long.rand.ind = c("int", "time"),
# sharingstrct = "randprop",
# surv.formula = Surv(survtime, cens) ~ treat,
# study.name = "study", strat = TRUE)
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit3SE <- jointmetaSE(fitted = onestagefit3, n.boot = 200,
# overalleffects = list(long = list(c("treat1", "treat1:study2"),
# c("treat1", "treat1:study3"))))
## -------------------------------------------------------------------------------------------------
#extract the saved model fit and bootstrap results
onestagefit3<-onestage3$onestagefit3
onestagefit3SE<-onestage3$onestagefit3SE
## -------------------------------------------------------------------------------------------------
summary(onestagefit3)
## -------------------------------------------------------------------------------------------------
rancov(fitted = onestagefit3, type = "individual")
## ---- error = TRUE--------------------------------------------------------------------------------
rancov(fitted = onestagefit3, type = "study")
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit4 <- jointmeta1(data = jointdat, long.formula = Y ~ 1 + time + treat + study,
# long.rand.ind = c("int", "time"), long.rand.stud = c("treat"),
# sharingstrct = "randprop", surv.formula = Surv(survtime, cens) ~ treat,
# study.name = "study", strat = TRUE)
## ---- eval=FALSE----------------------------------------------------------------------------------
# onestagefit4SE <- jointmetaSE(fitted = onestagefit4, n.boot = 200)
## -------------------------------------------------------------------------------------------------
#extract the saved model fit and bootstrap results
onestagefit4 <- onestage4$onestagefit4
onestagefit4SE <- onestage4$onestagefit4SE
## -------------------------------------------------------------------------------------------------
summary(onestagefit4)
## -------------------------------------------------------------------------------------------------
rancov(fitted = onestagefit4, type = "individual")
## -------------------------------------------------------------------------------------------------
rancov(fitted = onestagefit4, type = "study")
## ---- eval=FALSE----------------------------------------------------------------------------------
# ###CODE NOT RUN
# #to extract the results from a separate longitudinal model
# modelfit$sepests$longests$modelfit
#
# #to extract the results from a separate survival model
# modelfit$sepests$survests$modelfit
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