Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", echo = FALSE)
## ----prepare_master_matrix, eval=FALSE, echo=TRUE-----------------------------
# # Data
# data("mx", package = "biosurvey")
# variables <- raster::stack(system.file("extdata/variables.tif",
# package = "biosurvey"))
# names(variables) <- c("Mean_temperature", "Max_temperature", "Min_temperature",
# "Annual_precipitation", "Prec_wettest_month",
# "Prec_driest_month" )
#
# # Create master matrix object
# m_matrix <- prepare_master_matrix(region = mx, variables = variables,
# do_pca = TRUE, center = TRUE, scale = TRUE)
# #> Processing raster layers, please wait...
# #> Performing PCA analysis
#
# summary(m_matrix)
# #>
# #> Summary of a master_matrix object
# #> ---------------------------------------------------------------------------
# #>
# #> Data matrix summary:
# #> Longitude Latitude Mean_temperature Max_temperature
# #> Min. :-116.92 Min. :14.58 Min. : 85.0 Min. :180
# #> 1st Qu.:-106.79 1st Qu.:19.92 1st Qu.:174.0 1st Qu.:309
# #> Median :-102.58 Median :24.25 Median :203.0 Median :335
# #> Mean :-102.52 Mean :23.95 Mean :203.6 Mean :330
# #> 3rd Qu.: -98.75 3rd Qu.:27.92 3rd Qu.:236.0 3rd Qu.:354
# #> Max. : -86.92 Max. :32.58 Max. :291.0 Max. :425
# #> Min_temperature Annual_precipitation Prec_wettest_month Prec_driest_month
# #> Min. :-60.00 Min. : 53.0 Min. : 9.0 Min. : 0.00
# #> 1st Qu.: 30.00 1st Qu.: 352.0 1st Qu.: 78.0 1st Qu.: 3.00
# #> Median : 60.00 Median : 619.0 Median :144.5 Median : 6.00
# #> Mean : 70.66 Mean : 768.8 Mean :164.7 Mean : 10.67
# #> 3rd Qu.:112.00 3rd Qu.:1046.2 3rd Qu.:224.0 3rd Qu.: 12.00
# #> Max. :213.00 Max. :4103.0 Max. :750.0 Max. :140.00
# #> PC1 PC2
# #> Min. :-2.5770 Min. :-5.9018
# #> 1st Qu.:-1.3957 1st Qu.:-0.7861
# #> Median :-0.6003 Median : 0.1946
# #> Mean : 0.0000 Mean : 0.0000
# #> 3rd Qu.: 1.0825 3rd Qu.: 0.9541
# #> Max. : 9.1506 Max. : 3.1070
# #>
# #>
# #> No preselected sites were defined
# #>
# #>
# #> Region of interest:
# #> class : SpatialPolygonsDataFrame
# #> features : 1
# #> extent : -118.4042, -86.7014, 14.55055, 32.71846 (xmin, xmax, ymin, ymax)
# #> crs : +proj=longlat +datum=WGS84 +no_defs
# #> variables : 11
# #> names : FIPS, ISO2, ISO3, UN, NAME, AREA, POP2005, REGION, SUBREGION, LON, LAT
# #> value : MX, MX, MEX, 484, Mexico, 190869, 104266392, 19, 13, -102.535, 23.951
#
## ----prepare_master_matrix1, eval=FALSE, echo=TRUE----------------------------
# # preselected site example
# data("preselected", package = "biosurvey")
#
# # Create master matrix object
# m_matrix_pre <- prepare_master_matrix(region = mx, variables = variables,
# preselected_sites = preselected,
# do_pca = TRUE, center = TRUE, scale = TRUE)
# #> Processing raster layers, please wait...
# #> Performing PCA analysis
#
# summary(m_matrix_pre)
# #>
# #> Summary of a master_matrix object
# #> ---------------------------------------------------------------------------
# #>
# #> Data matrix summary:
# #> Longitude Latitude Mean_temperature Max_temperature
# #> Min. :-116.92 Min. :14.58 Min. : 85.0 Min. :180
# #> 1st Qu.:-106.79 1st Qu.:19.92 1st Qu.:174.0 1st Qu.:309
# #> Median :-102.58 Median :24.25 Median :203.0 Median :335
# #> Mean :-102.52 Mean :23.95 Mean :203.6 Mean :330
# #> 3rd Qu.: -98.75 3rd Qu.:27.92 3rd Qu.:236.0 3rd Qu.:354
# #> Max. : -86.92 Max. :32.58 Max. :291.0 Max. :425
# #> Min_temperature Annual_precipitation Prec_wettest_month Prec_driest_month
# #> Min. :-60.00 Min. : 53.0 Min. : 9.0 Min. : 0.00
# #> 1st Qu.: 30.00 1st Qu.: 352.0 1st Qu.: 78.0 1st Qu.: 3.00
# #> Median : 60.00 Median : 619.0 Median :144.5 Median : 6.00
# #> Mean : 70.66 Mean : 768.8 Mean :164.7 Mean : 10.67
# #> 3rd Qu.:112.00 3rd Qu.:1046.2 3rd Qu.:224.0 3rd Qu.: 12.00
# #> Max. :213.00 Max. :4103.0 Max. :750.0 Max. :140.00
# #> PC1 PC2
# #> Min. :-2.5770 Min. :-5.9018
# #> 1st Qu.:-1.3957 1st Qu.:-0.7861
# #> Median :-0.6003 Median : 0.1946
# #> Mean : 0.0000 Mean : 0.0000
# #> 3rd Qu.: 1.0825 3rd Qu.: 0.9541
# #> Max. : 9.1506 Max. : 3.1070
# #>
# #>
# #> Sites preselected by user:
# #> Site Longitude Latitude
# #> 1 Chamela -105.04479 19.50090
# #> 2 Los Tuxtlas -95.07419 18.58489
# #> 3 Chajul -90.94067 16.17000
# #> 4 Parque de Tlalpan -99.19778 19.29139
# #> 5 Parque Chipinque -100.35940 25.61750
# #>
# #>
# #> Region of interest:
# #> class : SpatialPolygonsDataFrame
# #> features : 1
# #> extent : -118.4042, -86.7014, 14.55055, 32.71846 (xmin, xmax, ymin, ymax)
# #> crs : +proj=longlat +datum=WGS84 +no_defs
# #> variables : 11
# #> names : FIPS, ISO2, ISO3, UN, NAME, AREA, POP2005, REGION, SUBREGION, LON, LAT
# #> value : MX, MX, MEX, 484, Mexico, 190869, 104266392, 19, 13, -102.535, 23.951
#
## ----explore_data_EG, eval=FALSE, echo=TRUE-----------------------------------
# # Plot using environmental variables
# explore_data_EG(m_matrix, variable_1 = "Mean_temperature",
# variable_2 = "Annual_precipitation")
## ---- fig.height=4, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V1f1.png")
## ----explore_data_EG1, eval=FALSE, echo=TRUE----------------------------------
# # Plot using Principal Components resulted
# explore_data_EG(m_matrix, variable_1 = "PC1", variable_2 = "PC2")
## ---- fig.height=4, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V1f2.png")
## ----make_blocks, eval=FALSE, echo=TRUE---------------------------------------
# # Creating blocks
# m_blocks <- make_blocks(m_matrix, variable_1 = "PC1",
# variable_2 = "PC2", n_cols = 10, n_rows = 10,
# block_type = "equal_area")
# unique(m_blocks$data_matrix$Block)
# #> [1] 7 9 32 6 31 10 5 8 30 4 29 28 3 42 27 41 40 39 26
# #> [20] 43 38 52 25 51 37 36 53 50 62 61 73 71 72 63 49 59 60 48
# #> [39] 70 64 58 81 80 91 47 68 35 54 24 2 23 82 74 83 92 93 84
# #> [58] 69 102 103 94 104 114 113 65
#
## ----plot_blocks_EG, eval=FALSE, echo=TRUE------------------------------------
# # plotting all blocks
# plot_blocks_EG(master = m_blocks, block_ID = TRUE)
#
## ---- fig.height=4, fig.width=6-----------------------------------------------
knitr::include_graphics("vignette_img/V1f3.png")
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