diff --git a/vignettes/graph1-1.png b/vignettes/graph1-1.png index 1cfebf6..4f88e09 100644 Binary files a/vignettes/graph1-1.png and b/vignettes/graph1-1.png differ diff --git a/vignettes/graph1_df2-1.png b/vignettes/graph1_df2-1.png index 169f260..a9b67af 100644 Binary files a/vignettes/graph1_df2-1.png and b/vignettes/graph1_df2-1.png differ diff --git a/vignettes/graph1_no_cov-1.png b/vignettes/graph1_no_cov-1.png deleted file mode 100644 index 11e53d2..0000000 Binary files a/vignettes/graph1_no_cov-1.png and /dev/null differ diff --git a/vignettes/modelbpp.Rmd b/vignettes/modelbpp.Rmd index f073c10..f32c0f1 100644 --- a/vignettes/modelbpp.Rmd +++ b/vignettes/modelbpp.Rmd @@ -138,7 +138,12 @@ out1_bpp_2 <- sort(out1_bpp, decreasing = TRUE)[2] ``` The total number of models examined, -including the original model, is 9. +including the original model, is `r length(out1$models)`. + +(Note: The total number of models +was 9 in previous version. Please +refer to the Note in the printout for +the changes.) The BIC posterior probabilities (BPPs) suggest that @@ -186,17 +191,17 @@ equally probable before having data prior probabilities). A researcher fits the original model because - - its - prior probability is higher than other - models, at least other neighboring - models (otherwise, it is not worthy - of collecting data assess thi original - model), but +- its + prior probability is higher than other + models, at least other neighboring + models (otherwise, it is not worthy + of collecting data assess thi original + model), but - - the prior probability - is not so high to eliminate the need - for collecting data to see how much it is - supported by data. +- the prior probability + is not so high to eliminate the need + for collecting data to see how much it is + supported by data. Suppose we decide that the prior probability of the original model is .50: probable, but @@ -258,7 +263,7 @@ out1_df2 <- model_set(fit1, ``` This is the printout. By default, when there -are more than 10 models, only the top 10 +are more than 20 models, only the top 20 models on BPP will be printed: ```{r} @@ -266,7 +271,7 @@ out1_df2 ``` The number of models examined, including -the original model, is 18. +the original model, is `r length(out1_df2$models)`. This is the output of `model_graph()`: @@ -289,32 +294,32 @@ specify parameters that must be excluded from the list to be added (`must_not_add`), or must not be dropped (`must_not_drop`). -For example, it may not make sense To -add the error covariance between `m1` -and `y` (`m1~~y`). We can exclude it +For example, suppose it is well +established that `m1~x` exists and should +not be dropped, we can exclude it when calling `model_set()` ```{r results = FALSE} -out1_no_cov <- model_set(fit1, - must_not_add = "m1~~y") +out1_no_m1_x <- model_set(fit1, + must_not_drop = "m1~x") ``` This is the output: ```{r} -out1_no_cov +out1_no_m1_x ``` -The number of models reduced to 8. +The number of models reduced to `r length(out1_df2$models)`. This is the plot: -```{r graph1_no_cov, ig.height = 8, fig.width = 8, eval = FALSE} -graph1_no_cov <- model_graph(out1_no_cov) -plot(graph1_no_cov) +```{r out1_no_m1_x, ig.height = 8, fig.width = 8, eval = FALSE} +out1_no_m1_x <- model_graph(out1_no_m1_x) +plot(out1_no_m1_x) ``` -![](graph1_no_cov-1.png) +![](out1_no_m1_x-1.png) ## Models With Constraints diff --git a/vignettes/out1_no_m1_x-1.png b/vignettes/out1_no_m1_x-1.png new file mode 100644 index 0000000..6457c86 Binary files /dev/null and b/vignettes/out1_no_m1_x-1.png differ diff --git a/vignettes/out1_prior-1.png b/vignettes/out1_prior-1.png index e8a4806..7cd6127 100644 Binary files a/vignettes/out1_prior-1.png and b/vignettes/out1_prior-1.png differ