diff --git a/_pkgdown.yml b/_pkgdown.yml index 176129a..00fd59f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -32,4 +32,5 @@ reference: - model_param_ex - title: Misc contents: - - TelemetrySpace-package \ No newline at end of file + - TelemetrySpace-package + diff --git a/vignettes/stancode.Rmd b/vignettes/stancode.Rmd new file mode 100644 index 0000000..d1b96fd --- /dev/null +++ b/vignettes/stancode.Rmd @@ -0,0 +1,74 @@ +--- +title: "Full Stan code" +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{stancode} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +In the course of developing TelemetrySpace, we realized that we were reusing a ton of Stan code. To make this easier on ourselves, we decided to split out the chunks we use most-often utilizing [Stan's Includes framework](https://mc-stan.org/docs/reference-manual/includes.html). This is a dream for development, but makes it kind of tough to work step-by-step through the code: before you only had to go through the file line-by-line, whereas now you have to do this while _also_ flipping between different files. + +The following vignette serves to make things easier on you (and us!) by listing, in their completed form, the Stan code of the programs that TelemetrySpace uses. + +```{r setup} +library(TelemetrySpace) +``` + +The Stan models used in TelemetrySpace are stored in a non-exported list [created by `rstantools`](https://mc-stan.org/rstantools/reference/use_rstan.html#using-the-pre-compiled-stan-programs-in-your-package), `stanmodels`. Each element of the list contains the knitted-together Stan code we're looking for. We can access the code like so: +```{r eval=-2} +stanmodels <- TelemetrySpace:::stanmodels +stanmodels$COA_Standard_gaussian +``` + +This code will be hidden for the rest of the vignette, but feel free to poke around in the package yourself. + +## COA Standard + +### Gaussian transmitter signal decay +`COA_Standard(...)` or `COA_Standard(..., decay = "gaussian")`: +```{r echo=FALSE} +stanmodels$COA_Standard_gaussian +``` + +### Logistic transmitter signal decay +`COA_Standard(..., decay = "logistic")`: +```{r echo=FALSE} +stanmodels$COA_Standard_logistic +``` + +## COA Time Varying + +### Gaussian transmitter signal decay +`COA_TimeVarying(...)` or `COA_TimeVarying(..., decay = "gaussian")` +```{r echo=FALSE} +stanmodels$COA_TimeVarying_gaussian +``` + +### Logistic transmitter signal decay +`COA_TimeVarying(..., decay = "logistic")`: +```{r echo=FALSE} +stanmodels$COA_TimeVarying_logistic +``` + + +## COA Tag-Itegrated + +### Gaussian transmitter signal decay +`COA_TagInt(...)` or `COA_TagInt(..., decay = "gaussian")`: +```{r echo=FALSE} +stanmodels$COA_Tag_Integrated_gaussian +``` + +### Logistic transmitter signal decay +`COA_TagInt(..., decay = "logistic")`: +```{r echo=FALSE} +stanmodels$COA_Tag_Integrated_logistic +``` \ No newline at end of file