Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", echo = FALSE)
## ----preare_base_PAM, eval=FALSE, echo=TRUE-----------------------------------
# # Data
# data("species_data", package = "biosurvey")
#
# # Create base_pam
# b_pam <- prepare_base_PAM(data = species_data, master_matrix = m_matrix,
# cell_size = 50)
# #> Preparing spatial grid
# #> Preprocessing 'data'
# #> |======================================================================| 100%
# #> Preparing PAM from information
# #> Calculating PAM indices
#
# summary(b_pam)
# #>
# #> Summary of a base_PAM object
# #> ---------------------------------------------------------------------------
# #>
# #> Presence-absence matrix:
# #> Number of cells: 1020
# #> Number of species: 25
# #>
# #> Spatial object representing the PAM:
# #> class : SpatialPolygonsDataFrame
# #> features : 1020
# #> extent : -118.4298, -86.51483, 14.28854, 32.77954 (xmin, xmax, ymin, ymax)
# #> crs : +proj=longlat +datum=WGS84 +no_defs
# #> variables : 28
# #> names : ID, Longitude, Latitude, Species_1, Species_2, Species_3, Species_4, Species_5, Species_6, Species_7, Species_8, Species_9, Species_10, Species_11, Species_12, ...
# #> min values : 471, -118.184325012541, 14.5140353096983, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...
# #> max values : 3602, -86.760325012541, 32.5540353096983, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ...
#
## ----PAM_indices, eval=FALSE, echo=TRUE---------------------------------------
# # Calculating indices
# b_pam <- PAM_indices(PAM = b_pam)
#
# # for a brief view of all indices use
# #print(b_pam)
## ----m_selection, eval=FALSE, echo=TRUE---------------------------------------
# # Data
# data("m_selection", package = "biosurvey")
## ----subset_PAM, eval=FALSE, echo=TRUE----------------------------------------
# # Subset of base PAM according to selections
# ## using all selections the time
# sub_pam_all <- subset_PAM(b_pam, m_selection, selection_type = "all")
## ----selected_sites_SAC, eval=FALSE, echo=TRUE--------------------------------
# # species accumulation curves for all selected sites based on PAM
# SACs <- selected_sites_SAC(PAM_subset = sub_pam_all, selection_type = "all")
## ----plot_SAC, eval=FALSE, echo=TRUE------------------------------------------
# ## all sets at the time
# plot_SAC(SAC_selected_sites = SACs)
#
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f1.png")
## ----compare_SAC, eval=FALSE, echo=TRUE---------------------------------------
# # random vs uniform in E
# compare_SAC(SAC_selected_sites = SACs, element_1 = 1, element_2 = 2)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f2.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # random vs uniform in G
# compare_SAC(SAC_selected_sites = SACs, element_1 = 1, element_2 = 3)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f3.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # uniform in E vs uniform in G
# compare_SAC(SAC_selected_sites = SACs, element_1 = 2, element_2 = 3)
#
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f4.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # calculating dissimilarities
# DI_sel <- selected_sites_DI(PAM_subset = sub_pam_all, selection_type = "all", method = "jaccard")
#
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # plots derived from dissimilarity calculations (matrix-like)
# plot_DI(DI_sel)
#
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f5.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # plots derived from dissimilarity calculations (dendrogram)
# DI_dendrogram(DI_sel)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f6.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # matrix-like plot derived from dissimilarity calculations for uniform in G selection
# plot_DI(DI_sel, selection_type = "G")
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f7.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # dendrogram plot derived from dissimilarity calculations for uniform in E selection
# DI_dendrogram(DI_sel, selection_type = "E")
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f8.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # random selection
# plot_PAM_geo(b_pam, master_selection = m_selection, selection_type = "random")
#
# # adding a legend for better interpretations
# ## this color palette is the same used by default in plots (purplow)
# colpal <- purplow(7)
# labs <- range(b_pam$PAM_indices$Richness)
#
# legend_bar("bottomleft", col = colpal, title = "Richness", labels = labs)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f9.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # G selection
# plot_PAM_geo(b_pam, master_selection = m_selection, selection_type = "G")
#
# # adding the legend
# legend_bar("bottomleft", col = colpal, title = "Richness", labels = labs)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f10.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # E selection
# plot_PAM_geo(b_pam, master_selection = m_selection, selection_type = "E")
#
# # adding the legend
# legend_bar("bottomleft", col = colpal, title = "Richness", labels = labs)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f11.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # random selection (using another palette)
# plot_PAM_geo(b_pam, index = "MCC", master_selection = m_selection,
# selection_type = "random", col_pal = greeple)
#
# # adding the appropriate legend
# colpal1 <- greeple(10)
# labs1 <- range(b_pam$PAM_indices$Mean_composition_covariance)
#
# legend_bar("bottomleft", col = colpal1, title = "Mean comp-covar",
# labels = labs1, digits = 2)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f12.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # G selection
# plot_PAM_geo(b_pam, index = "MCC", master_selection = m_selection,
# selection_type = "G", col_pal = greeple)
#
# # adding the legend
# legend_bar("bottomleft", col = colpal1, title = "Mean comp-covar",
# labels = labs1, digits = 2)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f13.png")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# # E selection
# plot_PAM_geo(b_pam, index = "MCC", master_selection = m_selection,
# selection_type = "E", col_pal = greeple)
#
# # adding the legend
# legend_bar("bottomleft", col = colpal1, title = "Mean comp-covar",
# labels = labs1, digits = 2)
## ---- fig.height=6, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V4_f14.png")
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