## ----echo = FALSE------------------------------------------------------------- rm(list = ls()) library(EMC2) ## ----results = "hide"--------------------------------------------------------- rm(list = ls()) library(EMC2) ## ----echo=TRUE, message=FALSE, warning=FALSE, results='hide'------------------ matchfun <- function(d) d$S == d$lR design_LBA <- design(factors=list(subjects=1,S=c("left", "right")), Rlevels = c("left", "right"), matchfun = matchfun, formula =list(v~lM,B~1, t0~1, sv~1, A~1), constants=c(sv=log(1)), model = LBA) prior_LBA <- prior(design_LBA, type = "single", pmean = c(1.3, .7, log(.8), log(.2), log(.3)), psd = c(.2, .1, .1, .05, .05)) ## ----fig.alt = "Prior for LBA non-hierarchical model", fig.height = 5--------- plot_prior(prior_LBA, design_LBA) ## ----eval=FALSE--------------------------------------------------------------- # SBC_LBA_single <- run_sbc(design_LBA, prior_LBA, replicates = 500, trials = 100, plot_data = FALSE, # iter = 1000, n_post = 1000, fileName = "SBC_data/SBC_LBA_single.RData", # cores_per_chain = 30) ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_LBA_single.RData") ## ----fig.height = 6, fig.alt = "Histogram SBC LBA single"--------------------- plot_sbc_hist(SBC_LBA_single, bins = 10) ## ----fig.height = 6, fig.alt = "ecdf LBA single"------------------------------ plot_sbc_ecdf(SBC_LBA_single) ## ----echo=TRUE, message=FALSE, warning=FALSE, results='hide', eval = FALSE---- # #?DDM # design_DDM <- design(factors=list(subjects=1,S=c("left", "right")), # Rlevels = c("left", "right"), # formula =list(v~1,a~1, t0~1, s~1, Z~1, sv~1, SZ~1, st0 ~ 1), # constants=c(s=log(1)), # model = DDM) # # # prior_DDM <- prior(design_DDM, type = "single", # pmean = c(1, log(.8), log(.3), qnorm(.5), log(.1), qnorm(.05), log(.05)), # psd = c(.15, .15, .1, .05, .15, .15, .15)) # # SBC_DDM_single <- run_sbc(design_DDM, prior_DDM, replicates = 500, trials = 100, # fileName = "SBC_data/SBC_DDM_single.RData", cores_per_chain = 30) # ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_DDM_single.RData") ## ----fig.height = 6, fig.alt = "ecdf DDM single", fig.width= 10--------------- plot_sbc_ecdf(SBC_DDM_single) ## ----echo=TRUE, message=FALSE, warning=FALSE, results='hide'------------------ n_subjects <- 30 # matchfun <- function(d) d$S == d$lR design_LBA <- design(factors=list(subjects=1:n_subjects,S=c("left", "right")), Rlevels = c("left", "right"), matchfun = matchfun, formula =list(v~lM,B~1, t0~1, sv~1, A~1), constants=c(sv=log(1)), model = LBA) prior_LBA <- prior(design_LBA, type = "diagonal-gamma", mu_mean = c(1.3, .7, log(.8), log(.2), log(.3)), mu_sd = c(.2, .1, .1, .05, .05), shape = 10, rate = c(.2, .2, .2, .1, .1)) ## ----fig.alt = "Prior for LBA hierarchical model", fig.height = 5------------- plot_prior(prior_LBA, design_LBA, selection = "alpha") ## ----eval=FALSE--------------------------------------------------------------- # SBC_LBA <- run_sbc(design_LBA, prior_LBA, replicates = 500, trials = 100, # n_subjects = n_subjects, fileName = "SBC_data/SBC_LBA.RData", cores_per_chain = 30) ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_LBA.RData") ## ----fig.height = 6, fig.alt = "ECDF SBC LBA"--------------------------------- plot_sbc_ecdf(SBC_LBA) ## ----echo=TRUE, message=FALSE, warning=FALSE, results='hide'------------------ n_subjects <- 30 design_DDM <- design(factors=list(subjects=1:n_subjects,S=c("left", "right")), Rlevels = c("left", "right"), formula =list(v~1,a~1, t0~1, s~1, Z~1, sv~1, SZ~1, st0 ~ 1), constants=c(s=log(1)), model = DDM) prior_DDM <- prior(design_DDM, type = "diagonal-gamma", pmean = c(1.2, log(.8), log(.3), qnorm(.5), log(.1), qnorm(.05), log(.05)), psd = c(.15, .15, .1, .05, .1, .1, .15), shape = 10, rate = c(.2, .2, .2, .1, .1, .1, .1)) ## ----eval=FALSE--------------------------------------------------------------- # SBC_DDM <- run_sbc(design_DDM, prior_DDM, replicates = 250, trials = 200, # n_subjects = n_subjects, fileName = "SBC_data/SBC_DDM.RData", cores_per_chain = 30) ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_DDM.RData") ## ----fig.height = 7, fig.alt = "ECDF SBC DDM"--------------------------------- plot_sbc_ecdf(SBC_DDM) ## ----echo=TRUE, eval = FALSE-------------------------------------------------- # n_subjects <- 30 # # matchfun <- function(d) d$S == d$lR # # # design_RDM <- design(factors=list(subjects=1:n_subjects,S=c("left", "right")), # Rlevels = c("left", "right"), # matchfun = matchfun, # formula =list(v~lM,B~1, t0~1, A~1, s ~ 1), # constants=c(s=log(1)), # model = RDM) # # prior_RDM <- prior(design_RDM, type = "diagonal-gamma", # mu_mean = c(1.4, .3, log(1.5), log(.2), log(.3)), # mu_sd = c(.05, .1, .1, .05, .05), # shape = 10, # rate = c(.1, .2, .2, .2, .1)) # # SBC_RDM <- run_sbc(design_RDM, prior_RDM, replicates = 500, trials = 100, # n_subjects = n_subjects, fileName = "SBC_RDM.RData", cores_per_chain = 30) # ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_RDM.RData") ## ----fig.height = 6, fig.alt = "ECDF SBC RDM"--------------------------------- plot_sbc_ecdf(SBC_RDM) ## ----echo=TRUE, eval = FALSE-------------------------------------------------- # n_subjects <- 30 # # matchfun <- function(d) d$S == d$lR # # design_LNR <- design(factors=list(subjects=1:n_subjects,S=c("left", "right")), # Rlevels = c("left", "right"), # matchfun = matchfun, # formula =list(m~lM,s~1, t0~1), # model = LNR) # # prior_LNR <- prior(design_LNR, type = "diagonal-gamma", # mu_mean = c(-.7, -.5, log(1), log(.2)), # mu_sd = c(.2, .1, .1, .05), # shape = 10, # rate = c(.2, .2, .2, .1)) # # SBC_LNR <- run_sbc(design_LNR, prior_LNR, replicates = 500, trials = 100, # n_subjects = n_subjects, fileName = "SBC_LNR.RData", cores_per_chain = 30) # ## ----include=FALSE------------------------------------------------------------ load("SBC_data/SBC_LNR.RData") ## ----fig.height = 6, fig.alt = "ECDF SBC RDM"--------------------------------- plot_sbc_ecdf(SBC_LNR, layout = c(2,2))