### tests
library(testthat)
library(jagshelper)
# library(jagsUI)

test_that("skeleton", {
  expect_output(skeleton("a"))
})

test_that("jags_df", {
  out_df <- jags_df(asdf_jags_out)
  expect_true(inherits(out_df, "data.frame"))
  expect_equal(dim(out_df), c(1500,8))
  expect_equal(sum(out_df), 259036, tolerance = 0.1)
  expect_error(jags_df(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("pull_post", {
  out_df <- jags_df(asdf_jags_out)
  a <- pull_post(out_df, "a")
  expect_true(inherits(a, "data.frame"))
  expect_equal(dim(a), c(1500,3))
  expect_equal(dim(pull_post(out_df)), c(1500,8))
  expect_equal(sum(a), 108.1291, tolerance = 0.1)
  expect_error(pull_post(asdf_jags_out), "Input must be a data.frame")
})

test_that("jags_plist", {
  out_plist <- jags_plist(asdf_jags_out)
  expect_equal(length(out_plist),8)
  dims <- lapply(out_plist, dim)
  expect_true(all(sapply(dims,"[",1)==500))
  expect_true(all(sapply(dims,"[",2)==3))
})

test_that("trace_jags", {
  out_df <- jags_df(asdf_jags_out)
  expect_silent(trace_jags(asdf_jags_out))
  expect_silent(trace_jags(asdf_jags_out, p="a", parmfrow=c(2,2)))
  expect_error(trace_jags(asdf_jags_out, p="steve"), "No parameters with matching names")
  expect_error(trace_jags(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("chaindens_jags", {
  out_df <- jags_df(asdf_jags_out)
  expect_silent(chaindens_jags(asdf_jags_out))
  expect_silent(chaindens_jags(asdf_jags_out, p="a", parmfrow=c(2,2)))
  expect_error(chaindens_jags(asdf_jags_out, p="steve"), "No parameters with matching names")
  expect_error(chaindens_jags(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("tracedens_jags", {
  out_df <- jags_df(asdf_jags_out)
  expect_silent(tracedens_jags(asdf_jags_out))
  expect_silent(tracedens_jags(asdf_jags_out, p="a", parmfrow=c(2,2)))
  expect_error(tracedens_jags(asdf_jags_out, p="steve"), "No parameters with matching names")
  expect_error(tracedens_jags(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("nparam", {
  out_df <- jags_df(asdf_jags_out)
  expect_equal(nparam(asdf_jags_out),8)
  expect_equal(nparam(SS_out), 334)
  expect_error(nparam(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("nbyname", {
  out_df <- jags_df(asdf_jags_out)
  expect_true(inherits(nbyname(asdf_jags_out),"list"))
  expect_equal(sum(unlist(nbyname(asdf_jags_out))), 8)
  expect_equal(nbyname(asdf_jags_out)$a, 3)
  expect_equal(nbyname(SS_out)$cycle_s, c(41,2))
  expect_error(nbyname(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("check_Rhat", {
  out_df <- jags_df(asdf_jags_out)
  expect_equal(length(check_Rhat(SS_out)),12)
  expect_equal(sum(unlist(check_Rhat(asdf_jags_out))), 6)
  expect_equal(sum(unlist(check_Rhat(SS_out))), 10.5863,tolerance=0.0001)
  expect_equal(unname(check_Rhat(SS_out)[9]), 0.5121951, tolerance=0.0001)
  expect_equal(names(check_Rhat(SS_out)[9]), "cycle_s")
  expect_error(check_Rhat(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("check_neff", {
  out_df <- jags_df(asdf_jags_out)
  expect_equal(length(check_neff(SS_out)),12)
  expect_equal(sum(unlist(check_neff(asdf_jags_out))), 5)
  expect_equal(sum(unlist(check_neff(SS_out))), 1.012195,tolerance=0.0001)
  expect_equal(unname(check_neff(SS_out)[9]), 0.03658537, tolerance=0.0001)
  expect_equal(names(check_neff(SS_out)[9]), "cycle_s")
  expect_error(check_neff(out_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("logit", {
  expect_equal(logit(0.5),0)
})

test_that("expit", {
  expect_equal(expit(0),0.5)
})

test_that("trace_line", {
  expect_silent(trace_line(1:30, nline=3))
  out_df <- jags_df(asdf_jags_out)
  b1 <- pull_post(out_df, "b1")
  a <- pull_post(out_df, "a")
  expect_silent(trace_line(b1, nline=3))
})

test_that("chaindens_line", {
  expect_silent(chaindens_line(1:30, nline=3))
  out_df <- jags_df(asdf_jags_out)
  b1 <- pull_post(out_df, "b1")
  a <- pull_post(out_df, "a")
  expect_silent(chaindens_line(b1, nline=3))
})

test_that("trace_df", {
  out_df <- jags_df(asdf_jags_out)
  expect_silent(trace_df(out_df, nline=3))
  expect_silent(trace_df(as.matrix(out_df), nline=3))
  expect_silent(trace_df(out_df, nline=3, parmfrow=c(2,2)))
  expect_error(trace_df(asdf_jags_out), "Input must be a data.frame")
})

test_that("chaindens_df", {
  out_df <- jags_df(asdf_jags_out)
  expect_silent(chaindens_df(out_df, nline=3))
  expect_silent(chaindens_df(as.matrix(out_df), nline=3))
  expect_silent(chaindens_df(out_df, nline=3, parmfrow=c(2,2)))
  expect_error(chaindens_df(asdf_jags_out), "Input must be a data.frame")
})

test_that("envelope", {
  SS_df <- jags_df(SS_out)
  trend <- pull_post(SS_df, "trend")
  expect_silent(envelope(trend, x=SS_data$x))
  expect_silent(envelope(trend, x=SS_data$x ,ci=.5))
  expect_silent(envelope(trend, x=SS_data$x ,ci=c(.1,.5,.9)))
  expect_silent(envelope(SS_out, p="trend"))
  expect_silent(envelope(SS_out, p="cycle_s", column=1))
  expect_silent(envelope(SS_out, p="cycle_s", column=1, main="cycle_s"))
  expect_silent(envelope(SS_out, p="cycle_s", column=2, col=2, add=TRUE))

  expect_error(envelope(SS_out, p=c("trend","rate")), "Need single parameter name in p= argument")
  expect_error(envelope(SS_out), "Need single parameter name in p= argument")
  expect_error(envelope(SS_out, p="steve"), "No parameters with matching names")
})

test_that("overlayenvelope", {
  expect_silent(overlayenvelope(df=list(SS_out$sims.list$cycle_s[,,1],SS_out$sims.list$cycle_s[,,2])))
  expect_silent(overlayenvelope(df=SS_out$sims.list$cycle_s))
  expect_silent(overlayenvelope(df=SS_out, p="cycle_s"))
  expect_silent(overlayenvelope(df=SS_out, p=c("trend","rate")))
  expect_silent(overlayenvelope(df=SS_out, p=c("trend","cycle_s"), column=2))
  expect_silent(overlayenvelope(df=SS_out, p=c("trend","rate"), legendnames=c("bob","larry")))
  expect_error(overlayenvelope(df=SS_out))
})

test_that("caterpillar", {
  SS_df <- jags_df(SS_out)
  trend <- pull_post(SS_df, "trend")
  expect_silent(caterpillar(trend, x=SS_data$x))
  expect_silent(caterpillar(trend, x=SS_data$x ,ci=.5))
  expect_silent(caterpillar(trend, x=SS_data$x ,ci=c(.1,.5,.9)))
  expect_silent(caterpillar(SS_out, p="trend"))
  expect_silent(caterpillar(SS_out, p="trend", ylim=c(-10, 10)))
  expect_silent(caterpillar(SS_out, p="cycle_s", column=1))
  expect_silent(caterpillar(SS_out, p="cycle_s", column=1, main="cycle_s"))
  expect_silent(caterpillar(SS_out, p="cycle_s", column=2, col=2, add=TRUE))

  expect_error(caterpillar(SS_out, p=c("trend","rate")), "Need single parameter name in p= argument")
  expect_error(caterpillar(SS_out), "Need single parameter name in p= argument")
  expect_error(caterpillar(SS_out, p="steve"), "No parameters with matching names")
})

test_that("traceworstRhat", {
  expect_silent(traceworstRhat(SS_out, parmfrow=c(3,2)))
  expect_silent(traceworstRhat(SS_out, parmfrow=c(3,2), n.eff=TRUE))
  expect_silent(traceworstRhat(x=SS_out, p="cycle_s", margin=2, parmfrow=c(2,2)))
  expect_silent(traceworstRhat(x=SS_out, p="cycle_s", margin=2, parmfrow=c(2,2), n.eff=TRUE))

  SS_df <- jags_df(SS_out)
  expect_error(traceworstRhat(SS_df), "Input must be an output object returned from jagsUI::jags().")
})

test_that("rcolors", {
  expect_equal(length(rcolors(10)),10)
})

test_that("plotRhats", {
  expect_silent(plotRhats(SS_out))
  expect_silent(plotRhats(SS_out, n.eff=TRUE))
  expect_silent(plotRhats(SS_out))
  expect_silent(plotRhats(SS_out, splitarr=TRUE, n.eff=TRUE))
  expect_silent(plotRhats(SS_out, splitarr=TRUE, margin=2))
  expect_silent(plotRhats(SS_out, p=c("trend", "cycle"), splitarr=TRUE, plotsequence=TRUE))
  SS_df <- jags_df(SS_out)
  expect_error(plotRhats(SS_df), "Input must be an output object returned from jagsUI::jags().")
  expect_error(plotRhats(SS_out, p="steve"), "No parameters with matching names")
})

test_that("comparedens", {
  expect_silent(comparedens(x1=asdf_jags_out, x2=asdf_jags_out, p=c("a","b","sig")))
  out_df <- jags_df(asdf_jags_out)
  expect_silent(comparedens(x1=out_df, x2=asdf_jags_out, p=c("a","b","sig")))
  expect_silent(comparedens(x1=out_df, x2=asdf_jags_out, p=c("a","b","sig"), ylim=c(-10,10)))
  expect_silent(comparedens(x1=out_df, x2=asdf_jags_out, p=c("a","b","sig"), col=2:3))
  expect_silent(comparedens(x2=out_df, x1=asdf_jags_out, p=c("a","b","sig")))
  expect_error(comparedens(x2=1:10, x1=asdf_jags_out, p=c("a","b","sig")),"Inputs must be data.frames or output objects returned from jagsUI::jags().")
})

test_that("comparecat", {
  expect_silent(comparecat(x=list(asdf_jags_out, asdf_jags_out, asdf_jags_out),p=c("a","b","sig")))
  expect_silent(comparecat(x=list(asdf_jags_out, asdf_jags_out, asdf_jags_out),p=c("a","b","sig"), col=1:3))
  expect_error(comparecat(x=list(1:10, asdf_jags_out, asdf_jags_out),p=c("a","b","sig")))
  expect_error(comparecat(x=asdf_jags_out))
})

test_that("pairstrace_jags", {
  expect_silent(pairstrace_jags(SS_out, p="sig", parmfrow=c(2,3), lwd=2))
  expect_silent(pairstrace_jags(SS_out, p="sig", parmfrow=c(2,3), points=TRUE))
  expect_silent(pairstrace_jags(SS_out, p="sig", parmfrow=c(2,3), contour=TRUE))
  expect_silent(pairstrace_jags(asdf_jags_out, parmfrow=c(3,3)))
  expect_silent(pairstrace_jags(asdf_jags_out, parmfrow=c(3,3), points=TRUE))
  expect_silent(pairstrace_jags(asdf_jags_out, parmfrow=c(3,3), contour=TRUE))
  out_df <- jags_df(asdf_jags_out)
  expect_error(pairstrace_jags(out_df),"Input must be an output object returned from jagsUI::jags().")
})

test_that("cor_jags", {
  expect_equal(sum(cor_jags(asdf_jags_out)), 8.291098, tolerance=0.0001)
  expect_equal(dim(cor_jags(asdf_jags_out)), c(8,8))
  expect_equal(dim(cor_jags(asdf_jags_out, p=c("a","b"))), c(5,5))
})

test_that("plotcor_jags", {
  expect_silent(plotcor_jags(asdf_jags_out))
  expect_silent(plotcor_jags(asdf_jags_out, p=c("a","b")))
  expect_silent(plotcor_jags(asdf_jags_out, legend=F, mincor=0.1, maxn=1))
})

test_that("plotdens", {
  expect_silent(plotdens(asdf_jags_out, p="b1"))
  expect_silent(plotdens(asdf_jags_out, p="b1", add=T, shade=F, lwd=F))
  expect_silent(plotdens(asdf_jags_out, p="a", minCI=.95, col=2:4))
  expect_silent(plotdens(asdf_jags_out, p=c("a[1]","a[2]","a[3]"), legend=F))
  expect_silent(plotdens(jags_df(asdf_jags_out, p="a"),legendnames=c("albert","betty","chuck")))
  expect_silent(plotdens(list(asdf_jags_out,asdf_jags_out,asdf_jags_out), p="b1"))
  expect_error(plotdens(list(asdf_jags_out,asdf_jags_out,asdf_jags_out), p="a"),"No parameter names are an exact match to p= argument.")
  expect_silent(plotdens(list(asdf_jags_out,asdf_jags_out,asdf_jags_out), p=c("a[1]","a[2]","a[3]")))
})

test_that("qq_postpred", {
  expect_silent(qq_postpred(ypp=SS_out, p="ypp", y=SS_data$y))
  expect_silent(qq_postpred(ypp=SS_out$sims.list$ypp, y=SS_data$y))
  expect_silent(qq_postpred(ypp=jags_df(x=SS_out, p="ypp"), y=SS_data$y))
  expect_silent(qq_postpred(ypp=SS_out, p="ypp", y=SS_data$y, add=T, pch="+", col=4))
  expect_error(qq_postpred(ypp=SS_out, p="ypp", y=SS_data$y[1]))
  expect_error(qq_postpred(ypp=SS_out, p="ypp", y=SS_data$y[1:2]), "Posterior matrix ypp must have the same number of columns as length of data matrix y")
  expect_error(qq_postpred(ypp=SS_out, y=SS_data$y), "Parameter name must be supplied to p= argument if jagsUI object is used in argument ypp")
})

test_that("ts_postpred", {
  expect_silent(ts_postpred(ypp=SS_out, p="ypp", y=SS_data$y))
  expect_silent(ts_postpred(ypp=SS_out, x=SS_data$x, p="ypp", y=SS_data$y))
  expect_silent(ts_postpred(ypp=SS_out$sims.list$ypp, y=SS_data$y))
  expect_silent(ts_postpred(ypp=jags_df(x=SS_out, p="ypp"), y=SS_data$y))
  expect_silent(ts_postpred(ypp=SS_out, p="ypp", y=SS_data$y, add=T, col=3))
  expect_error(ts_postpred(ypp=SS_out, p="ypp", y=SS_data$y[1]))
  expect_error(ts_postpred(ypp=SS_out, p="ypp", y=SS_data$y[1:2]), "Posterior matrix ypp must have the same number of columns as length of data matrix y")
  expect_error(ts_postpred(ypp=SS_out, y=SS_data$y), "Parameter name must be supplied to p= argument if jagsUI object is used in argument ypp")
})

test_that("comparepriors", {
  expect_silent(comparepriors(x=asdf_prior_jags_out))
  expect_silent(comparepriors(x=asdf_prior_jags_out, parmfrow=c(3,2)))
  expect_silent(comparepriors(x=asdf_prior_jags_out, parmfrow=c(3,2), col=3:2, minCI=0.7, legendpos="bottomleft"))
  expect_warning(comparepriors(x=asdf_jags_out), 'No parameter names ending in "_prior"')
})