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In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions
```{asis, echo = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, eval = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}, include = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user drawn area
```r}, include = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}}
# First must generate the transfer area according to the drawn polygon in the GUI
xfer_draw_{{spAbr}} <-xfer_draw(
polyXfXY = matrix({{polyXfXY_rmd}},ncol=2,byrow=FALSE),
polyXfID = {{polyXfID_rmd}},
drawXfBuf = {{BgBuf_rmd}})
# Create object of transfer variables
xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}}
# Generate a transfer of the model to the desired area
xfer_area_{{spAbr}} <- xfer_area(
evalOut = model_{{spAbr}},
curModel = "{{curModel_rmd}}",
envs = xferAreaEnvs_{{spAbr}} ,
outputType = "{{outputType_rmd}}",
alg = "{{alg_rmd}}",
clamp = {{clamp_rmd}},
xfExt = xfer_draw_{{spAbr}})
# store the cropped transfer variables
xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt
#map result
###Make map of transfer
bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox
bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2],
bb_{{spAbr}}[2, 2], fraction = 0.05)
mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}}$xferArea,"{{outputType_rmd}}")
rasCols_{{spAbr}} <- c("#2c7bb6", "#abd9e9", "#ffffbf", "#fdae61", "#d7191c")
# if no threshold specified
legendPal <- colorNumeric(rev(rasCols_{{spAbr}}), mapXferVals_{{spAbr}}, na.color = 'transparent')
rasPal_{{spAbr}} <- colorNumeric(rasCols_{{spAbr}}, mapXferVals_{{spAbr}}, na.color = 'transparent')
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>%
leaflet::addLegend("bottomright", pal = legendPal,
title = "Predicted Suitability<br>(Transferred)",
values = mapXferVals_{{spAbr}}, layerId = 'xfer',
labFormat = reverseLabel(2, reverse_order = TRUE)) %>%
# map model prediction raster and transfer polygon
clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
addRasterImage(xfer_area_{{spAbr}}$xferArea, colors = rasPal_{{spAbr}}, opacity = 0.7,
layerId = 'xferRas', group = 'xfer', method = "ngb") %>%
##add transfer polygon (user drawn area)
addPolygons(data = xfer_draw_{{spAbr}}, fill = FALSE,
weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, eval = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, include = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user drawn area using a "{{xfer_thresholdRule_rmd}}" threshold of {{xfer_threshold_rmd}}.
```r}, include = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}}
# First must generate the transfer area according to the drawn polygon in the GUI
xfer_draw_{{spAbr}} <-xfer_draw(
polyXfXY = matrix({{polyXfXY_rmd}},ncol=2,byrow=FALSE),
polyXfID = {{polyXfID_rmd}},
drawXfBuf = {{BgBuf_rmd}})
# Create object of transfer variables
xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}}
# Generate a transfer of the model to the desired area
xfer_area_{{spAbr}} <- xfer_area(
evalOut = model_{{spAbr}},
curModel = "{{curModel_rmd}}",
envs = xferAreaEnvs_{{spAbr}} ,
outputType = "{{outputType_rmd}}",
alg = "{{alg_rmd}}",
clamp = {{clamp_rmd}},
xfExt = xfer_draw_{{spAbr}})
#store the cropped transfer variables
xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt
# extract the suitability values for all occurrences
occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')]
# determine the threshold based on the current prediction
occPredVals_{{spAbr}} <- raster::extract(predSel_{{spAbr}}, occs_xy_{{spAbr}})
# Define probability of quantile based on selected threshold
xfer_thresProb_{{spAbr}} <- switch("{{xfer_thresholdRule_rmd}}",
"mtp" = 0, "p10" = 0.1, "qtp" = {{xfer_probQuantile_rmd}})
# Define threshold value
xfer_thres_{{spAbr}} <- stats::quantile(occPredVals_{{spAbr}},
probs = xfer_thresProb_{{spAbr}})
# Add threshold if specified
xfer_area_{{spAbr}} <- xfer_area_{{spAbr}}$xferArea > xfer_thres_{{spAbr}}
##Make map
###Make map of transfer
bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox
bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2],
bb_{{spAbr}}[2, 2], fraction = 0.05)
mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}},"{{outputType_rmd}}")
# if threshold specified
rasPal_{{spAbr}} <- c('gray', 'red')
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>%
leaflet::addLegend("bottomright", colors = c('gray', 'red'),
title = "Thresholded Suitability<br>(Transferred)",
labels = c("predicted absence", "predicted presence"),
opacity = 1, layerId = 'xfer')%>%
# map model prediction raster and transfer polygon
clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
addRasterImage(xfer_area_{{spAbr}}, colors = rasPal_{{spAbr}}, opacity = 0.7,
layerId = 'xferRas', group = 'xfer', method = "ngb") %>%
##add transfer polygon (user drawn area)
addPolygons(data = xfer_draw_{{spAbr}}, fill = FALSE,
weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & xfer_area_extent_knit}} , eval = {{xfer_area_knit & xfer_area_extent_knit }}, include = {{xfer_area_knit & xfer_area_extent_knit}}}
Transfer model
Transfering the model to a new user provided area
```r}, include = {{xfer_area_knit & xfer_area_extent_knit}}}
# First must generate the transfer area based on user provided files
##User must input the path to shapefile or csv file and the file name
xfer_userExt_{{spAbr}} <- xfer_userExtent(
bgShp_path = "Input path here",
bgShp_name = "Input file name here",
userBgBuf = {{BgBuf_rmd}})
# Create object of transfer variables
xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}}
# Generate a transfer of the model to the desired area
xfer_area_{{spAbr}} <- xfer_area(
evalOut = model_{{spAbr}},
curModel = "{{curModel_rmd}}",
envs = xferAreaEnvs_{{spAbr}} ,
outputType = "{{outputType_rmd}}",
alg = "{{alg_rmd}}",
clamp = {{clamp_rmd}},
xfExt = xfer_userExt_{{spAbr}})
#store the cropped transfer variables
xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt
###Make map of transfer
bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox
bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2],
bb_{{spAbr}}[2, 2], fraction = 0.05)
mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}}$xferArea,"{{outputType_rmd}}")
rasCols_{{spAbr}} <- c("#2c7bb6", "#abd9e9", "#ffffbf", "#fdae61", "#d7191c")
# if no threshold specified
legendPal <- colorNumeric(rev(rasCols_{{spAbr}}), mapXferVals_{{spAbr}}, na.color = 'transparent')
rasPal_{{spAbr}} <- colorNumeric(rasCols_{{spAbr}}, mapXferVals_{{spAbr}}, na.color = 'transparent')
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>%
leaflet::addLegend("bottomright", pal = legendPal,
title = "Predicted Suitability<br>(Transferred)",
values = mapXferVals_{{spAbr}}, layerId = 'xfer',
labFormat = reverseLabel(2, reverse_order = TRUE)) %>%
# map model prediction raster and transfer polygon
clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
addRasterImage(xfer_area_{{spAbr}}$xferArea, colors = rasPal_{{spAbr}}, opacity = 0.7,
layerId = 'xferRas', group = 'xfer', method = "ngb") %>%
##add transfer polygon (user provided area)
addPolygons(data = xfer_userExt_{{spAbr}}, fill = FALSE,
weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}} , eval = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}, include = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user provided area using a "{{xfer_thresholdRule_rmd}}" threshold of {{xfer_threshold_rmd}}.
```r}, include = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}}
# First must generate the transfer area based on user provided files
##User must input the path to shapefile or csv file and the file name
xfer_userExt_{{spAbr}} <- xfer_userExtent(
bgShp_path = "Input path here",
bgShp_name = "Input file name here",
userBgBuf = {{BgBuf_rmd}})
# Create object of transfer variables
xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}}
# Generate a transfer of the model to the desired area
xfer_area_{{spAbr}} <- xfer_area(
evalOut = model_{{spAbr}},
curModel = "{{curModel_rmd}}",
envs = xferAreaEnvs_{{spAbr}} ,
outputType = "{{outputType_rmd}}",
alg = "{{alg_rmd}}",
clamp = {{clamp_rmd}},
xfExt = xfer_userExt_{{spAbr}})
# store the cropped transfer variables
xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt
# extract the suitability values for all occurrences
occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')]
# determine the threshold based on the current prediction
occPredVals_{{spAbr}} <- raster::extract(predSel_{{spAbr}}, occs_xy_{{spAbr}})
# Define probability of quantile based on selected threshold
xfer_thresProb_{{spAbr}} <- switch("{{xfer_thresholdRule_rmd}}",
"mtp" = 0, "p10" = 0.1, "qtp" = {{xfer_probQuantile_rmd}})
# Define threshold value
xfer_thres_{{spAbr}} <- stats::quantile(occPredVals_{{spAbr}},
probs = xfer_thresProb_{{spAbr}})
# Add threshold if specified
xfer_area_{{spAbr}} <- xfer_area_{{spAbr}}$xferArea > xfer_thresProb_{{spAbr}}
##Make map
###Make map of transfer
bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox
bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2],
bb_{{spAbr}}[2, 2], fraction = 0.05)
mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}},"{{outputType_rmd}}")
# if threshold specified
rasPal_{{spAbr}} <- c('gray', 'red')
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>%
leaflet::addLegend("bottomright", colors = c('gray', 'red'),
title = "Thresholded Suitability<br>(Transferred)",
labels = c("predicted absence", "predicted presence"),
opacity = 1, layerId = 'xfer')%>%
# map model prediction raster and transfer polygon
clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
addRasterImage(xfer_area_{{spAbr}}, colors = rasPal_{{spAbr}}, opacity = 0.7,
layerId = 'xferRas', group = 'xfer', method = "ngb") %>%
##add transfer polygon (user provided area)
addPolygons(data = xfer_userExt_{{spAbr}}, fill = FALSE,
weight = 4, color = "blue", group = 'xfer')
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```{asis, echo = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, eval = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}, include = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user drawn area
```r}, include = {{xfer_area_knit & !xfer_area_extent_knit & !xfer_area_threshold_knit}}} # First must generate the transfer area according to the drawn polygon in the GUI xfer_draw_{{spAbr}} <-xfer_draw( polyXfXY = matrix({{polyXfXY_rmd}},ncol=2,byrow=FALSE), polyXfID = {{polyXfID_rmd}}, drawXfBuf = {{BgBuf_rmd}}) # Create object of transfer variables xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}} # Generate a transfer of the model to the desired area xfer_area_{{spAbr}} <- xfer_area( evalOut = model_{{spAbr}}, curModel = "{{curModel_rmd}}", envs = xferAreaEnvs_{{spAbr}} , outputType = "{{outputType_rmd}}", alg = "{{alg_rmd}}", clamp = {{clamp_rmd}}, xfExt = xfer_draw_{{spAbr}}) # store the cropped transfer variables xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt #map result ###Make map of transfer bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2], bb_{{spAbr}}[2, 2], fraction = 0.05) mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}}$xferArea,"{{outputType_rmd}}") rasCols_{{spAbr}} <- c("#2c7bb6", "#abd9e9", "#ffffbf", "#fdae61", "#d7191c") # if no threshold specified legendPal <- colorNumeric(rev(rasCols_{{spAbr}}), mapXferVals_{{spAbr}}, na.color = 'transparent') rasPal_{{spAbr}} <- colorNumeric(rasCols_{{spAbr}}, mapXferVals_{{spAbr}}, na.color = 'transparent') m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap) m %>% fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>% leaflet::addLegend("bottomright", pal = legendPal, title = "Predicted Suitability<br>(Transferred)", values = mapXferVals_{{spAbr}}, layerId = 'xfer', labFormat = reverseLabel(2, reverse_order = TRUE)) %>% # map model prediction raster and transfer polygon clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>% addRasterImage(xfer_area_{{spAbr}}$xferArea, colors = rasPal_{{spAbr}}, opacity = 0.7, layerId = 'xferRas', group = 'xfer', method = "ngb") %>% ##add transfer polygon (user drawn area) addPolygons(data = xfer_draw_{{spAbr}}, fill = FALSE, weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, eval = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}, include = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user drawn area using a "{{xfer_thresholdRule_rmd}}" threshold of {{xfer_threshold_rmd}}.
```r}, include = {{xfer_area_knit & !xfer_area_extent_knit & xfer_area_threshold_knit}}} # First must generate the transfer area according to the drawn polygon in the GUI xfer_draw_{{spAbr}} <-xfer_draw( polyXfXY = matrix({{polyXfXY_rmd}},ncol=2,byrow=FALSE), polyXfID = {{polyXfID_rmd}}, drawXfBuf = {{BgBuf_rmd}}) # Create object of transfer variables xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}} # Generate a transfer of the model to the desired area xfer_area_{{spAbr}} <- xfer_area( evalOut = model_{{spAbr}}, curModel = "{{curModel_rmd}}", envs = xferAreaEnvs_{{spAbr}} , outputType = "{{outputType_rmd}}", alg = "{{alg_rmd}}", clamp = {{clamp_rmd}}, xfExt = xfer_draw_{{spAbr}}) #store the cropped transfer variables xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt # extract the suitability values for all occurrences occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')] # determine the threshold based on the current prediction occPredVals_{{spAbr}} <- raster::extract(predSel_{{spAbr}}, occs_xy_{{spAbr}}) # Define probability of quantile based on selected threshold xfer_thresProb_{{spAbr}} <- switch("{{xfer_thresholdRule_rmd}}", "mtp" = 0, "p10" = 0.1, "qtp" = {{xfer_probQuantile_rmd}}) # Define threshold value xfer_thres_{{spAbr}} <- stats::quantile(occPredVals_{{spAbr}}, probs = xfer_thresProb_{{spAbr}}) # Add threshold if specified xfer_area_{{spAbr}} <- xfer_area_{{spAbr}}$xferArea > xfer_thres_{{spAbr}} ##Make map ###Make map of transfer bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2], bb_{{spAbr}}[2, 2], fraction = 0.05) mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}},"{{outputType_rmd}}") # if threshold specified rasPal_{{spAbr}} <- c('gray', 'red') m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap) m %>% fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>% leaflet::addLegend("bottomright", colors = c('gray', 'red'), title = "Thresholded Suitability<br>(Transferred)", labels = c("predicted absence", "predicted presence"), opacity = 1, layerId = 'xfer')%>% # map model prediction raster and transfer polygon clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>% addRasterImage(xfer_area_{{spAbr}}, colors = rasPal_{{spAbr}}, opacity = 0.7, layerId = 'xferRas', group = 'xfer', method = "ngb") %>% ##add transfer polygon (user drawn area) addPolygons(data = xfer_draw_{{spAbr}}, fill = FALSE, weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & xfer_area_extent_knit}} , eval = {{xfer_area_knit & xfer_area_extent_knit }}, include = {{xfer_area_knit & xfer_area_extent_knit}}}
Transfer model
Transfering the model to a new user provided area
```r}, include = {{xfer_area_knit & xfer_area_extent_knit}}} # First must generate the transfer area based on user provided files ##User must input the path to shapefile or csv file and the file name xfer_userExt_{{spAbr}} <- xfer_userExtent( bgShp_path = "Input path here", bgShp_name = "Input file name here", userBgBuf = {{BgBuf_rmd}}) # Create object of transfer variables xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}} # Generate a transfer of the model to the desired area xfer_area_{{spAbr}} <- xfer_area( evalOut = model_{{spAbr}}, curModel = "{{curModel_rmd}}", envs = xferAreaEnvs_{{spAbr}} , outputType = "{{outputType_rmd}}", alg = "{{alg_rmd}}", clamp = {{clamp_rmd}}, xfExt = xfer_userExt_{{spAbr}}) #store the cropped transfer variables xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt ###Make map of transfer bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2], bb_{{spAbr}}[2, 2], fraction = 0.05) mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}}$xferArea,"{{outputType_rmd}}") rasCols_{{spAbr}} <- c("#2c7bb6", "#abd9e9", "#ffffbf", "#fdae61", "#d7191c") # if no threshold specified legendPal <- colorNumeric(rev(rasCols_{{spAbr}}), mapXferVals_{{spAbr}}, na.color = 'transparent') rasPal_{{spAbr}} <- colorNumeric(rasCols_{{spAbr}}, mapXferVals_{{spAbr}}, na.color = 'transparent') m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap) m %>% fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>% leaflet::addLegend("bottomright", pal = legendPal, title = "Predicted Suitability<br>(Transferred)", values = mapXferVals_{{spAbr}}, layerId = 'xfer', labFormat = reverseLabel(2, reverse_order = TRUE)) %>% # map model prediction raster and transfer polygon clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>% addRasterImage(xfer_area_{{spAbr}}$xferArea, colors = rasPal_{{spAbr}}, opacity = 0.7, layerId = 'xferRas', group = 'xfer', method = "ngb") %>% ##add transfer polygon (user provided area) addPolygons(data = xfer_userExt_{{spAbr}}, fill = FALSE, weight = 4, color = "blue", group = 'xfer')
```{asis, echo = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}} , eval = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}, include = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}}
Transfer model
Transfering the model to a new user provided area using a "{{xfer_thresholdRule_rmd}}" threshold of {{xfer_threshold_rmd}}.
```r}, include = {{xfer_area_knit & xfer_area_extent_knit & xfer_area_threshold_knit}}} # First must generate the transfer area based on user provided files ##User must input the path to shapefile or csv file and the file name xfer_userExt_{{spAbr}} <- xfer_userExtent( bgShp_path = "Input path here", bgShp_name = "Input file name here", userBgBuf = {{BgBuf_rmd}}) # Create object of transfer variables xferAreaEnvs_{{spAbr}} <- envs_{{spAbr}} # Generate a transfer of the model to the desired area xfer_area_{{spAbr}} <- xfer_area( evalOut = model_{{spAbr}}, curModel = "{{curModel_rmd}}", envs = xferAreaEnvs_{{spAbr}} , outputType = "{{outputType_rmd}}", alg = "{{alg_rmd}}", clamp = {{clamp_rmd}}, xfExt = xfer_userExt_{{spAbr}}) # store the cropped transfer variables xferExt_{{spAbr}} <- xfer_area_{{spAbr}}$xferExt # extract the suitability values for all occurrences occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')] # determine the threshold based on the current prediction occPredVals_{{spAbr}} <- raster::extract(predSel_{{spAbr}}, occs_xy_{{spAbr}}) # Define probability of quantile based on selected threshold xfer_thresProb_{{spAbr}} <- switch("{{xfer_thresholdRule_rmd}}", "mtp" = 0, "p10" = 0.1, "qtp" = {{xfer_probQuantile_rmd}}) # Define threshold value xfer_thres_{{spAbr}} <- stats::quantile(occPredVals_{{spAbr}}, probs = xfer_thresProb_{{spAbr}}) # Add threshold if specified xfer_area_{{spAbr}} <- xfer_area_{{spAbr}}$xferArea > xfer_thresProb_{{spAbr}} ##Make map ###Make map of transfer bb_{{spAbr}} <- bgExt_{{spAbr}}@bbox bbZoom <- polyZoom(bb_{{spAbr}}[1, 1], bb_{{spAbr}}[2, 1], bb_{{spAbr}}[1, 2], bb_{{spAbr}}[2, 2], fraction = 0.05) mapXferVals_{{spAbr}} <- getRasterVals(xfer_area_{{spAbr}},"{{outputType_rmd}}") # if threshold specified rasPal_{{spAbr}} <- c('gray', 'red') m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap) m %>% fitBounds(bbZoom[1], bbZoom[2], bbZoom[3], bbZoom[4]) %>% leaflet::addLegend("bottomright", colors = c('gray', 'red'), title = "Thresholded Suitability<br>(Transferred)", labels = c("predicted absence", "predicted presence"), opacity = 1, layerId = 'xfer')%>% # map model prediction raster and transfer polygon clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>% addRasterImage(xfer_area_{{spAbr}}, colors = rasPal_{{spAbr}}, opacity = 0.7, layerId = 'xferRas', group = 'xfer', method = "ngb") %>% ##add transfer polygon (user provided area) addPolygons(data = xfer_userExt_{{spAbr}}, fill = FALSE, weight = 4, color = "blue", group = 'xfer')
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