diff --git a/README.Rmd b/README.Rmd index 4528e48e8..f2ac4ae08 100644 --- a/README.Rmd +++ b/README.Rmd @@ -84,7 +84,6 @@ spatial and spatiotemporal random fields. bioRxiv A list of (known) publications that use sdmTMB can be found [here](https://github.com/pbs-assess/sdmTMB/wiki/Publications-using-sdmTMB). Please use the above citation so we can track publications. - ## Related software sdmTMB is heavily inspired by the [VAST](https://github.com/James-Thorson-NOAA/VAST) R package: @@ -167,12 +166,14 @@ Run some basic sanity checks on our model: sanity(fit) ``` -Use the [ggeffects](https://github.com/strengejacke/ggeffects) package (**the GitHub version until the next ggeffects CRAN update**) to plot the smoother effect: +Use the [ggeffects](https://github.com/strengejacke/ggeffects) package to plot the smoother effect: ```{r plot-ggpredict-link, warning=FALSE, message=FALSE} ggeffects::ggpredict(fit, "depth [50:400, by=2]") |> plot() ``` +If the depth effect was parametric and not a penalized smoother, we could have alternatively used `ggeffects::ggeffect()` for a fast marginal effect plot. + Predict on new data: ```{r} diff --git a/README.md b/README.md index 7ac76d611..0503ab326 100644 --- a/README.md +++ b/README.md @@ -321,8 +321,7 @@ sanity(fit) ``` Use the [ggeffects](https://github.com/strengejacke/ggeffects) package -(**the GitHub version until the next ggeffects CRAN update**) to plot -the smoother effect: +to plot the smoother effect: ``` r ggeffects::ggpredict(fit, "depth [50:400, by=2]") |> plot() @@ -330,6 +329,10 @@ ggeffects::ggpredict(fit, "depth [50:400, by=2]") |> plot() +If the depth effect was parametric and not a penalized smoother, we +could have alternatively used `ggeffects::ggeffect()` for a fast +marginal effect plot. + Predict on new data: ``` r