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.Rhistory
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load("F:/PHD/Projects/NMADAS/data/demodata1.rda")
source('F:/PHD/Projects/NMADAS/R/dataprep.R')
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
data("demodata1")
model <- model.nmadas(copula = "fgm", marginals = "beta")
fileConn<-file("model.txt")
writeLines(model, fileConn)
close(fileConn)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
fgm <- rstan::stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
data <- prepdata.nmadas(
data = data,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- rstan::stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/dataprep.R')
data("demodata1")
data <- prepdata.nmadas(
data = data,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- rstan::stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/dataprep.R')
data <- prepdata.nmadas(
data = demodata1,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- rstan::stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
library(rstan)
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
model <- model.nmadas(copula = "fgm", marginals = "beta")
fileConn<-file("model.txt")
writeLines(model, fileConn)
close(fileConn)
data <- prepdata.nmadas(
data = demodata1,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
stan(model_code = modelcode,
data = datalist,
chains = 1,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
model <- model.nmadas(copula = "fgm", marginals = "beta")
fileConn<-file("model.txt")
writeLines(model, fileConn)
close(fileConn)
data <- prepdata.nmadas(
data = demodata1,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
model <- model.nmadas(copula = "fgm", marginals = "beta")
fileConn<-file("model.txt")
writeLines(model, fileConn)
close(fileConn)
data <- prepdata.nmadas(
data = demodata1,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- model.nmadas(copula = "fgm", marginals = "beta")
fgm <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/tests.R')
source('F:/PHD/Projects/NMADAS/R/tests.R')
source('F:/PHD/Projects/NMADAS/R/tests.R')
source('F:/PHD/Projects/NMADAS/R/tests.R')
modelcode <- nmamodel.nmadas(copula = "frank", marginals = "beta")
frank <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
model <- nmamodel.nmadas(copula = "fgm", marginals = "beta")
fileConn<-file("model.txt")
writeLines(model, fileConn)
close(fileConn)
data(demodata)
data <- prepdata.nmadas(
data = demodata,
S.ID = 'study',
T.ID = 'Test',
tp = 'TP',
fn = 'FN',
tn = 'TN',
fp = 'FP')
N <- nrow(data)
Ns <- max(data$SID)
Nt <- max(data$TID)
datalist <- list(
N = N,
Ns = Ns,
Nt = Nt,
TP = data$TP,
Dis = data$Dis,
TN = data$TN,
NDis = data$NDis,
Test = data$TID,
Study = data$SID)
modelcode <- nmamodel.nmadas(copula = "c90", marginals = "beta")
c90 <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
source('F:/PHD/Projects/NMADAS/R/ModelCode.R')
modelcode <- nmamodel.nmadas(copula = "c90", marginals = "beta")
c90 <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
modelcode <- nmamodel.nmadas(copula = "c270", marginals = "beta")
c270 <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
modelcode <- nmamodel.nmadas(copula = "c270", marginals = "beta")
c270 <- stan(model_code = modelcode,
data = datalist,
chains = 3,
iter = 8000,
warmup = 2000,
thin = 10,
seed = 1,
cores=3,
verbose=FALSE)
View(demodata)
View(demodata)
ls()
load("F:/PHD/Projects/nmadas_support/output.RData")
ls()
?save
save(modelf, modelr, fgm, frank, c90, c270, file="F:/PHD/Projects/nmadas_support/NMADAS.RData")
library(devtools)
library(roxygen2)
session_info()
document()
load_all()
devtools::document()
devtools::build()
library(devtools)
library(roxygen2)
session_info()
document()
load_all()
devtools::document()
devtools::build()
library(devtools)
library(roxygen2)
session_info()
document()
load_all()
devtools::document()
devtools::build()
library(devtools)
library(roxygen2)
session_info()
document()
load_all()
devtools::document()
devtools::build()
head(demodata)
networkplot.nmadas(data=demodata,S.ID="study", T.ID="Test")
library(httr)
mylink <- GET(url="https://www.dropbox.com/s/wm1wzehrglmqog9/NMADAS.RData?dl=1")
load(rawConnection(mylink$content))
ls()
nmamodel(marginals = 'normal', fullcov = TRUE)
nmamodel.nmadas(marginals = 'normal', fullcov = TRUE)
library(NMADAS)
nmamodel.nmadas(marginals = 'normal', fullcov = TRUE)
#install.packages("NMADAS", dependencies = TRUE)
library(NMADAS)
data(demodata)
head(demodata)
networkplot.nmadas(data=demodata, S.ID="study", T.ID="Test")
traceplot(modelf)
traceplot.nmadas(modelf)
str(modelf)
data = demodata
S.ID = 'study'
T.ID = 'Test'
df <- prepdata.nmadas(demodata,S.ID = S.ID,
T.ID = T.ID)
df <- prepdata(demodata,S.ID = S.ID,
T.ID = T.ID)
library(devtools)
library(roxygen2)
session_info()
document()
load_all()
devtools::document()
document()
load_all()
devtools::document()
devtools::build()