Skip to content

Commit

Permalink
add line in vignettes to mention that only some models will return plots
Browse files Browse the repository at this point in the history
  • Loading branch information
svteichman committed Jan 17, 2025
1 parent 6d3c912 commit e387137
Show file tree
Hide file tree
Showing 2 changed files with 5 additions and 3 deletions.
4 changes: 2 additions & 2 deletions vignettes/breakaway.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ You should get some output to screen, including your estimate & s.e. You can als
plot(breakaway(frequencytablelist[[1]]))
```

Note that it is not a fit to the frequencies, it is a fit to the ratios of frequencies. You would never need to include this type of plot in one of your papers. It is solely for you to check for model misspecification. What's model misspecification? If the model fit (pink circles) don't remotely follow the pattern of the observed ratios (green triangles), that's model misspecification.
Note that it is not a fit to the frequencies, it is a fit to the ratios of frequencies. You would never need to include this type of plot in one of your papers. It is solely for you to check for model misspecification. What's model misspecification? If the model fit (pink circles) don't remotely follow the pattern of the observed ratios (green triangles), that's model misspecification.

Sometimes, breakaway's usual procedure doesn't work, that is, it gives a negative estimate, which is of course silly. In that case, breakaway returns a different model's result. It's called the WLRM. There isn't a picture. Here is an example of a case where breakaway returns the WLRM.
Sometimes, breakaway's usual procedure doesn't work, that is, it gives a negative estimate, which is of course silly. In that case, breakaway returns a different model's result. It's called the WLRM. There isn't a picture. Only some of the models will provide plots, and if the model chosen does not include a plot, the plot function will instead return `NULL`. Here is an example of a case where breakaway returns the WLRM.

```{r}
breakaway(frequencytablelist[[2]])
Expand Down
4 changes: 3 additions & 1 deletion vignettes/intro-diversity-estimation.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,9 @@ First, we need to find out what model was fit:
estimated_richness$model
```

Kemp models were originally described in the breakaway paper. They are based on fitting flexible non-linear models (that have a probabilistic interpretation!) to ratios of contiguous frequency counts. We can therefore investigate model specification by looking at the plot of fitted ratios:
Kemp models were originally described in the breakaway paper. They are based on fitting flexible non-linear models (that have a probabilistic interpretation!) to ratios of contiguous frequency counts. We can therefore investigate model specification by looking at the plot of fitted ratios.

Note that this plot will only be made for some of the models (including the Kemp model), and some of the other models will not include a plot and instead `plot(breakaway_results)` will return `NULL`.

```{r}
plot(estimated_richness)
Expand Down

0 comments on commit e387137

Please sign in to comment.