Added vignettes to show demo

traitecoevo · Oct 9, 2023 · 0982b25 · 0982b25
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
 ^rmot\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
@@ -48,3 +48,6 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 
+inst/doc
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,3 +30,7 @@ LinkingTo:
     rstan (>= 2.18.1),
     StanHeaders (>= 2.18.0)
 SystemRequirements: GNU make
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
diff --git a/R/rmot_run.R b/R/rmot_run.R
@@ -7,8 +7,11 @@
 #' @export
 #'
 #' @examples
-#' mtcars
-#' rmot_lm(mtcars$mpg, mtcars$disp)
+#' rmot_model("linear") |>
+#'   rmot_assign_data(X = Loblolly$age,
+#'                  Y = Loblolly$height,
+#'                  N = nrow(Loblolly)) |>
+#'  rmot_run()
 rmot_run <- function(model_template, ...) {
 
   # Detect model

diff --git a/README.Rmd b/README.Rmd
@@ -33,5 +33,13 @@ remotes::install_github("traitecoevo/rmot")
 ## Demo
 
 ```{r example}
-
+rmot_model("linear") |>
+  rmot_assign_data(X = Loblolly$age,
+                   Y = Loblolly$height,
+                   N = nrow(Loblolly)) |>
+  rmot_run()
 ```
+
+## Found a bug? 
+
+Please lodge a GitHub Issue with details of the bug
diff --git a/README.md b/README.md
@@ -1,3 +1,4 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # rmot
@@ -18,3 +19,15 @@ remotes::install_github("traitecoevo/rmot")
 ```
 
 ## Demo
+
+``` r
+rmot_model("linear") |>
+  rmot_assign_data(X = Loblolly$age,
+                   Y = Loblolly$height,
+                   N = nrow(Loblolly)) |>
+  rmot_run()
+```
+
+## Found a bug?
+
+Please lodge a GitHub Issue with details of the bug
diff --git a/man/rmot_run.Rd b/man/rmot_run.Rd
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/rmot.Rmd b/vignettes/rmot.Rmd
@@ -0,0 +1,68 @@
+---
+title: "rmot"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{rmot}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+
+library(rmot)
+```
+
+## Goal of package
+
+## Installation
+
+'rmot' is under active development, you can install the development version of 'rmot' from [GitHub](https://github.com/) with:
+
+```{r, eval=FALSE}
+# install.packages("remotes")
+remotes::install_github("traitecoevo/rmot")
+
+library(rmot)
+```
+
+## {rmot} supported models
+
+### Linear model
+
+```{r example}
+rmot_model("linear") |>
+  rmot_assign_data(X = Loblolly$age,
+                   Y = Loblolly$height,
+                   N = nrow(Loblolly)) |>
+  rmot_run()
+```
+
+### Constant Growth - Single Species
+
+```{r}
+# Create data
+true <- c(seq(from=1, by=2.5, length.out=7),
+          seq(from=2, by=2, length.out=7))
+y <- true + true*rnorm(n=14, 0, 0.02) + rnorm(n=14, 0, 0.2)
+
+# Configure model template
+cgs_output <- rmot_model("constant_single") |>
+  rmot_assign_data(N_obs = length(y),
+                   N_ind = 2,
+                   S_obs = y,
+                   census = rep(seq(from=1, to=7, by=1), times=2), #vector length N_obs
+                   census_interval = rep(5, times=length(y)), #Vector length N_obs
+                   id_factor = c(rep(1, times=7), rep(2, times=7)), #Vector length N_obs
+                   S_0_obs = y[c(1, 8)] #vector length N_ind
+                   )  |>
+  rmot_run()
+
+# Look at output
+cgs_output
+```
+
+