## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(bdots)

## ---- include=FALSE-----------------------------------------------------------
# Make smaller for cran
cohort_unrelated$Subject <- as.numeric(cohort_unrelated$Subject)
cohort_unrelated <- as.data.table(cohort_unrelated)
cohort_unrelated <- cohort_unrelated[Subject < 10, ]

## -----------------------------------------------------------------------------
head(cohort_unrelated)

## -----------------------------------------------------------------------------
fit <- bdotsFit(data = cohort_unrelated,
                subject = "Subject",
                time = "Time",
                y = "Fixations",
                group = c("DB_cond", "LookType"),
                curveType = doubleGauss(concave = TRUE),
                cores = 2)

## -----------------------------------------------------------------------------
head(coef(fit))

head(coef(fit[DB_cond == 50, ]))

## ---- fig.align='center', fig.width = 8, fig.height=6-------------------------
plot(fit[1:4, ])

## ---- eval = FALSE------------------------------------------------------------
#  ## Quickly auto-refit (not run)
#  refit <- bdotsRefit(fit, fitCode = 1L, quickRefit = TRUE)
#  
#  ## Manual refit (not run)
#  refit <- bdotsRefit(fit, fitCode = 1L)

## -----------------------------------------------------------------------------
table(fit$fitCode)

## Remove all failed curve fits
refit <- bdRemove(fit, fitCode = 6L)

table(refit$fitCode)

## ---- eval = FALSE------------------------------------------------------------
#  ## Only one grouping variable in dataset, take bootstrapped difference
#  Outcome ~ Group1(value1, value2)
#  
#  ## More than one grouping variable in difference, must specify unique value
#  Outcome ~ Group1(value1, value2) + Group2(value3)

## ---- eval = FALSE------------------------------------------------------------
#  ## Must add LookType(Cohort) to specify
#  Fixations ~ DB_cond(50, 65) + LookType(Cohort)

## ---- eval = FALSE------------------------------------------------------------
#  ## Difference of difference. Here, outer difference is Group1, inner is Group2
#  diffs(Outcome, Group2(value3, value4)) ~ Group1(value1, value2)
#  
#  ## Same as above if three or more grouping variables
#  diffs(Outcome, Group2(value3, value4)) ~ Group1(value1, value2) + Group3(value5)

## ---- eval = FALSE------------------------------------------------------------
#  diffs(Fixations, DB_cond(50, 65)) ~ LookType(Cohort, Unrelated_Cohort)

## -----------------------------------------------------------------------------
boot1 <- bdotsBoot(formula = Fixation ~ DB_cond(50, 65) + LookType(Cohort),
                   bdObj = refit,
                   Niter = 1000,
                   alpha = 0.05,
                   padj = "oleson",
                   cores = 2)

boot2 <- bdotsBoot(formula = diffs(Fixation, LookType(Cohort, Unrelated_Cohort)) ~ DB_cond(50, 65),
                   bdObj = refit,
                   Niter = 1000,
                   alpha = 0.05,
                   padj = "oleson",
                   cores = 2)

## ---- fig.align='center', fig.width = 8, fig.height=6-------------------------
summary(boot1)

plot(boot1)