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nbaR

Source: vignettes/nbaR.Rmd
nbaR.Rmd

This Vignette is to help users become familiar with the NBA package and get the most use out of its functions.

This package was create to help create the figures, plots, tables, and maps for the NBA. The functions are split into those used to make plots, those used to makes tables, and those used to make maps.

The plot functions consist of one main plot funcion called NBA_plot that will create either a bar or donut plot and colour the graph by matching the category words (such as endangered, well protected, natural etc) with their set colours. There is then a complimentary function called NBA_comp which is used if you want to plot two plots together using gg_arrange as the underlying code, and NBA_theme that is a ggplot theme with all the NBA presets that can be applied to any ggplot object to ensure the graph maintains the NBA ‘look’.

The table functions consist of NBA_tbl which makes a basic table for a quarto document outputting to an html, NBA_bl_colr which makes a basic table with a purple heading bar and colours the category names by their preset colours. There is also a complimentary NBA_tbl_theme function that styles any gt table with the NBA’s preset styling.

The map functions currently only consist of one function NBA_map, made using ggplot 2 and recreates the maps in the marine technical report 2018.

There are then five example datasets that can be accessed to test the functions and see the required format of the data to use the functions, which are: NBA_example_thr_data, NBA_example_pro_data, NBA_example_comb_data, NBA_example_RLI_data, and NBA_example_map_data. There is also a list of the category names (NBA_categories) that are recognised by the function so that you can make sure you are using the correct naming convention. The functions are case sensitive so you must be careful when naming your categories.

Plot functions

Load the example data and use the variouse functions to create NBA plots.

1. bar plot

NBA_example_thr_data <- NBA_example_thr_data


bar_plot <- nba_plot(NBA_example_thr_data,
                  `OVERALL types`,
                  2:5,
                 CHRT = "bar",
                 NUM = TRUE,
                 LAB = "Percentage of ecosystem types",
                SAVE = NULL)

bar_plot

2. donut plot

NBA_example_pro_data <- NBA_example_pro_data


donut_plot <- nba_plot(NBA_example_pro_data,
                  `OVERALL types`,
                  2:5,
                 CHRT = "donut",
                 NUM = TRUE,
                 LAB = "Percentage of ecosystem types",
                 GRP = F,
                SAVE = NULL)

donut_plot

3. Combined plot

NBA_example_pro_data <- NBA_example_pro_data
NBA_example_thr_data <- NBA_example_thr_data
NBA_example_comb_data <- NBA_example_comb_data


bar_plot_comb <- nba_plot_comb(
               NBA_example_comb_data,
                GROUPS= `OVERALL types`,
                METRIC_COL = metric,
               METRICS = c("protection_level", "threat_status"),
                COLS = 3:10,
                CHRT = "bar",
                NUM = FALSE,
               LAB = "Percentage of ecosystem",
                SAVE=NULL)

bar_plot_comb

4. RLI plot

NBA_example_RLI_data <- NBA_example_RLI_data


RLI_plot <- nba_plot_RLI(NBA_example_RLI_data,
                 Years, 
                 RLI, 
                 min, 
                 max)

RLI_plot

5. NBA bubble plot

NBA_example_bubble_data <- NBA_example_bubble_data


 bubble_plot <- nba_plot_bubble(DF = NBA_example_bubble_data,
                        GROUP = taxon_group,
                       CAT = pressure,
                       SUB_CAT = sub_pressure,
                        VALUE = perc_concern_under_press,
                          SAVE = NULL)
                         
 bubble_plot

6. NBA ggplot theme

library(ggplot2)
NBA_example_pro_data <- NBA_example_pro_data


gg_plot <- ggplot(NBA_example_pro_data, aes(x = `OVERALL types`, y = `Well Protected`))+
  ggplot2::geom_point()+
  nba_plot_theme()

gg_plot

Table functions

Please note that these are designed to render on html outputs and so may not appear correct in the vignette examples.

7. Basic table


tbl <- nba_tbl(NBA_example_pro_data)

tbl
OVERALL types Well Protected Moderately Protected Poorly Protected Not Protected
subAntarctic 15 14 1 4
Coastal 65 28 52 41
Estuarine 4 8 7 3
Marine 47 62 22 19
Wetland 8 4 41 82
River 29 33 66 94
Inland Aquatic 37 37 107 176
Terrestrial 118 59 166 115

8. Coloured table


library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(tidyr)

tbl <- NBA_example_pro_data %>% 
  pivot_longer(2:5, names_to = "protection_level") %>% 
  nba_tbl_colr(COL = protection_level)
#> Warning: Since gt v0.9.0, the `colors` argument has been deprecated.
#> • Please use the `fn` argument instead.
#> This warning is displayed once every 8 hours.

tbl
OVERALL types protection_level value
subAntarctic Well Protected 15
subAntarctic Moderately Protected 14
subAntarctic Poorly Protected 1
subAntarctic Not Protected 4
Coastal Well Protected 65
Coastal Moderately Protected 28
Coastal Poorly Protected 52
Coastal Not Protected 41
Estuarine Well Protected 4
Estuarine Moderately Protected 8
Estuarine Poorly Protected 7
Estuarine Not Protected 3
Marine Well Protected 47
Marine Moderately Protected 62
Marine Poorly Protected 22
Marine Not Protected 19
Wetland Well Protected 8
Wetland Moderately Protected 4
Wetland Poorly Protected 41
Wetland Not Protected 82
River Well Protected 29
River Moderately Protected 33
River Poorly Protected 66
River Not Protected 94
Inland Aquatic Well Protected 37
Inland Aquatic Moderately Protected 37
Inland Aquatic Poorly Protected 107
Inland Aquatic Not Protected 176
Terrestrial Well Protected 118
Terrestrial Moderately Protected 59
Terrestrial Poorly Protected 166
Terrestrial Not Protected 115

9. gt table theme

library(gt)
library(dplyr)


gt_tbl <- NBA_example_thr_data %>% 
  gt() %>% 
  nba_tbl_theme()

gt_tbl
OVERALL types Critically Endangered Endangered Vulnerable Least Concern TOT
Sub-Antarctic 0 1 5 28 34
Coastal 21 37 54 74 186
Estuarine 2 10 7 3 22
Marine 2 22 51 75 150
Wetland 83 12 12 28 135
River 95 42 5 80 222
Inland Aquatic 178 54 17 108 357
Terrestrial 35 39 29 355 458

10. Threatened ecosystems protection level table

thr_pro_tbl <- NBA_example_map_data |>
nba_tbl_comb(GROUP = P_EcosysType,
THR = threat_status,
PRO = protection_level, 
FILE = "spatial")

thr_pro_tbl
Not Protected Poorly Protected Moderately Protected Well Protected Total
Critically Endangered 0 1 1 1 3
Endangered 0 1 0 1 2
Vulnerable 1 0 1 1 3
Near Threatened 0 0 1 1 2
Least Concern 0 1 1 1 3
Total (n) 1 3 4 5 13

Map functions

11. Basic map

Please note this was modeled after the maps in the marine technical report 2018.


map <- nba_map(DF = NBA_example_map_data,
               GEOM = geometry, 
               CAP = "Figure 1. A map of the protection level of marine pelagic ecosystem types in South Africa", 
               FILL = protection_level)

map