22# '
33# ' A \emph{raster} dataset defining the grid cells of the Tasmanian study region for the
44# ' Thylacine example vignette.
5- # '
6- # ' @examples
5+ # '
6+ # ' @examples
77# ' data(tasmania_raster)
88# ' tasmania_region <- Region$new(
99# ' template_raster = tasmania_raster
2727# ' A \emph{raster} dataset (11 timesteps) defining the intensity land-use cover for each
2828# ' grid-cell in the Tasmania study region. NB. This dataset is projected and will not natively overlay
2929# ' the other \emph{raster} datasets contained in \emph{poems}.
30- # '
31- # ' @examples
30+ # '
31+ # ' @examples
3232# ' data(tasmania_raster)
3333# ' data(tasmania_modifier)
3434# ' tasmania_region <- Region$new(
5454# ' A dataset describing the nine Interim Bioregionalisation of Australia (IBRA)
5555# ' bioregions for the Tasmanian study region of the Thylacine example vignette.
5656# '
57- # ' @examples
57+ # ' @examples
5858# ' data(tasmania_ibra_data)
5959# ' data(tasmania_ibra_raster)
60- # ' raster::values(tasmania_ibra_raster)[!is.na(raster::values(tasmania_ibra_raster))] |>
61- # ' table() |> as.data.frame() |>
62- # ' merge(tasmania_ibra_data, by.x = "Var1", by.y = "index")
63- # '
60+ # ' raster::values(tasmania_ibra_raster)[!is.na(raster::values(tasmania_ibra_raster))] |>
61+ # ' table() |>
62+ # ' as.data.frame() |>
63+ # ' merge(tasmania_ibra_data, by.x = "Var1", by.y = "index")
64+ # '
6465# ' @format A data frame with 9 rows and 4 variables:
6566# ' \describe{
6667# ' \item{index}{Cross-reference index for each bioregion}
7778# ' A \emph{raster} dataset defining the grid cells of the nine Interim
7879# ' Bioregionalisation of Australia (IBRA) bioregions for the Tasmanian study region of
7980# ' the Thylacine example vignette.
80- # '
81- # ' @examples
81+ # '
82+ # ' @examples
8283# ' data(tasmania_ibra_raster)
8384# ' data(tasmania_raster)
8485# ' tasmania_region <- Region$new(
@@ -104,10 +105,10 @@ NULL
104105# ' A \emph{raster} dataset defining estimated habitat suitability values for each grid
105106# ' cells of the Tasmanian study region of the Thylacine example vignette.
106107# '
107- # ' @examples
108+ # ' @examples
108109# ' data(thylacine_hs_raster)
109110# ' raster::plot(thylacine_hs_raster, colNA = "blue")
110- # '
111+ # '
111112# ' @format A \emph{raster::RasterLayer} object:
112113# ' \describe{
113114# ' \item{dimensions}{32 rows by 40 columns grid}
@@ -125,15 +126,17 @@ NULL
125126# ' A dataset containing the historical record of the Thylacine bounty numbers submitted
126127# ' across the Tasmanian study region, and for each of the nine Interim Bioregionalisation
127128# ' of Australia (IBRA) bioregions for Thylacine example vignette.
128- # '
129- # ' @examples
129+ # '
130+ # ' @examples
130131# ' data(thylacine_bounty_record)
131132# ' summary(thylacine_bounty_record)
132133# ' # Assuming your data frame is named thylacine_bounty_record
133- # ' plot(thylacine_bounty_record$Year, thylacine_bounty_record$Total, type="l",
134- # ' main="Change in Total Bounties Over Time",
135- # ' xlab="Year",
136- # ' ylab="Total Bounties")
134+ # ' plot(thylacine_bounty_record$Year, thylacine_bounty_record$Total,
135+ # ' type = "l",
136+ # ' main = "Change in Total Bounties Over Time",
137+ # ' xlab = "Year",
138+ # ' ylab = "Total Bounties"
139+ # ' )
137140# '
138141# ' @format A data frame with 22 rows and 11 variables:
139142# ' \describe{
@@ -159,12 +162,12 @@ NULL
159162# ' example vignette in demonstration mode. The values were obtained by running the
160163# ' vignette code for 20,000 model simulations with \code{DEMONSTRATION = FALSE}.
161164# '
162- # ' @examples
165+ # ' @examples
163166# ' data(thylacine_example_metrics)
164167# ' hist(thylacine_example_metrics$bounty_slope_error)
165168# ' hist(thylacine_example_metrics$ibra_extirpation_error)
166169# ' hist(thylacine_example_metrics$total_extinction)
167- # '
170+ # '
168171# ' @format A data frame with 20,000 rows and 4 variables:
169172# ' \describe{
170173# ' \item{index}{Example simulation number from 1 to 20,000}
@@ -183,13 +186,13 @@ NULL
183186# ' the vignette code for 20,000 model simulations with \code{DEMONSTRATION = FALSE}.
184187# ' Note that some matrices were only stored for the selected 'best' 200 models.
185188# '
186- # ' @examples
189+ # ' @examples
187190# ' data(thylacine_example_matrices)
188191# ' data(tasmania_raster)
189192# ' region <- Region$new(template_raster = tasmania_raster)
190- # ' region$raster_from_values(thylacine_example_matrices$extirpation[1,]) |>
191- # ' raster::plot(colNA = "blue")
192- # '
193+ # ' region$raster_from_values(thylacine_example_matrices$extirpation[1, ]) |>
194+ # ' raster::plot(colNA = "blue")
195+ # '
193196# ' @format A list containing the following matrices:
194197# ' \describe{
195198# ' \item{extirpation}{200 row by 795 column matrix of cell extirpation dates for the 'best' 200 models}
208211# ' Thylacine example vignette in demonstration mode. The values were obtained by running
209212# ' the vignette code for 10 replicate re-runs of the selected 'best' 200 model
210213# ' simulations with \code{DEMONSTRATION = FALSE}.
211- # '
212- # ' @examples
214+ # '
215+ # ' @examples
213216# ' data(thylacine_example_metrics_rerun)
214217# ' hist(thylacine_example_metrics_rerun$bounty_slope_error)
215218# ' hist(thylacine_example_metrics_rerun$ibra_extirpation_error)
232235# ' Thylacine example vignette in demonstration mode. The values were obtained by running
233236# ' the vignette code for 10 replicate re-runs of the selected 'best' 200 model
234237# ' simulations with \code{DEMONSTRATION = FALSE}.
235- # '
236- # ' @examples
238+ # '
239+ # ' @examples
237240# ' data(thylacine_example_matrices_rerun)
238241# ' rowMeans(thylacine_example_matrices_rerun$bounty_slope)
239242# ' rowMeans(thylacine_example_matrices_rerun$ibra_extirpation)
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