diff --git a/vignettes/vignette-06-diagnostics.Rmd b/vignettes/vignette-06-diagnostics.Rmd index 24c0684..ccc7814 100644 --- a/vignettes/vignette-06-diagnostics.Rmd +++ b/vignettes/vignette-06-diagnostics.Rmd @@ -136,6 +136,7 @@ modelX <- function(Ne_A, Ne_B, Ne_C, Ne_D, T_1, T_2, T_3, gf) { return(list(model, samples)) } + modelY <- function(Ne_A, Ne_B, Ne_C, Ne_D, T_1, T_2, T_3, gf) { popA <- population("popA", time = 1, N = Ne_A) popB <- population("popB", time = T_1, N = Ne_B, parent = popA) @@ -211,10 +212,12 @@ compute_diversity <- function(ts) { samples <- ts_names(ts, split = "pop") ts_diversity(ts, sample_sets = samples) } + compute_divergence <- function(ts) { samples <- ts_names(ts, split = "pop") ts_divergence(ts, sample_sets = samples) } + compute_f4 <- function(ts) { samples <- ts_names(ts, split = "pop") A <- samples["popA"]; B <- samples["popB"] @@ -295,12 +298,6 @@ seconds <- round(tdelta - hours * 3600 - minutes * 60) **The total runtime for the ABC simulations was `r paste(hours, "hours", minutes, "minutes", seconds, "seconds")` parallelized across `r ncores` CPUs.** -```{r, eval=!abc_exists, echo=FALSE} -abcX <- readRDS(abcX_path) -abcY <- readRDS(abcY_path) -abcZ <- readRDS(abcZ_path) -``` - ```{r, eval=!abc_exists, results="hide"} abcX <- run_abc(dataX, engine = "abc", tol = 0.01, method = "neuralnet") abcY <- run_abc(dataY, engine = "abc", tol = 0.01, method = "neuralnet") @@ -313,7 +310,7 @@ saveRDS(abcY, abcY_path) saveRDS(abcZ, abcZ_path) ``` -```{r, eval=abc_exists, echo=FALSE} +```{r, eval=!abc_exists, echo=FALSE} abcX <- readRDS(abcX_path) abcY <- readRDS(abcY_path) abcZ <- readRDS(abcZ_path)