In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

```{asis, echo = {{xfer_mess_knit}}, eval = {{xfer_mess_knit}}, include = {{xfer_mess_knit}}} Generate a MESS map for the transferring variables given the variables used for modelling

```r}, include = {{xfer_mess_knit}}}
# R code to generate MESS raster
xferMess_{{spAbr}} <- xfer_mess(
  occs = occs_{{spAbr}},
  bg = bgEnvsVals_{{spAbr}} ,
  bgMsk =  bgMask_{{spAbr}},
  xferExtRas =  xferExt_{{spAbr}})

# Generate MESS map
rasVals_{{spAbr}} <-  getRasterVals(xferMess_{{spAbr}})

  # define colorRamp for mess
  if (max(rasVals_{{spAbr}}) > 0 & min(rasVals_{{spAbr}}) < 0) {
    rc1 <- colorRampPalette(colors = rev(RColorBrewer::brewer.pal(n = 3, name = 'Reds')),
                            space = "Lab")(abs(min(rasVals_{{spAbr}})))
    rc2 <- colorRampPalette(colors = RColorBrewer::brewer.pal(n = 3, name = 'Blues'),
                            space = "Lab")(max(rasVals_{{spAbr}}))
    rasCols_{{spAbr}} <- c(rc1, rc2)
  } else if (max(rasVals_{{spAbr}}) < 0 & min(rasVals_{{spAbr}}) < 0) {
    rasCols_{{spAbr}} <- colorRampPalette(colors = rev(RColorBrewer::brewer.pal(n = 3, name = 'Reds')),
                                space = "Lab")(abs(min(rasVals)))
  } else if (max(rasVals_{{spAbr}}) > 0 & min(rasVals_{{spAbr}}) > 0) {
    rasCols{{spAbr}} <- colorRampPalette(colors = RColorBrewer::brewer.pal(n = 3, name = 'Blues'),
                                space = "Lab")(max(rasVals_{{spAbr}}))
  }
  legendPal_{{spAbr}} <- colorNumeric(rev(rasCols_{{spAbr}}), rasVals_{{spAbr}}, na.color='transparent')
  rasPal_{{spAbr}} <- colorNumeric(rasCols_{{spAbr}}, rasVals_{{spAbr}}, na.color='transparent')
  #Create map
  m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap) 
m  %>%
    leaflet::addLegend("bottomright", pal = legendPal_{{spAbr}}, title = "MESS Values",
              values = rasVals_{{spAbr}}, layerId = 'xfer',
              labFormat = reverseLabel(2, reverse_order=TRUE)) %>%
  # map model prediction raster and transferring polygon
 clearMarkers() %>% clearShapes() %>% removeImage('xferRas') %>%
    addRasterImage(xferMess_{{spAbr}}, colors =   rasPal_{{spAbr}} , opacity = 0.9,
                   layerId = 'xferRas', group = 'xfer', method = "ngb") %>%
  ##add transferring polygon: this we need to fix for now please replace bgExt_{{spAbr}} for the name of your transferring polygon.
  addPolygons(data = bgExt_{{spAbr}}, fill = FALSE,
              weight = 4, color = "blue", group = 'xfer')

wallace documentation built on Sept. 11, 2024, 9:16 p.m.