envEcosystems: an R package of objects and tools to create ecosystem descriptions

The goal of envEcosystems is to help create ecosystem descriptions based on outputs from other envPackages.

Installation

envEcosystems is not on CRAN.

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("Acanthiza/envEcosystems")

Load envEcosystems

Convert between cover value systems

lucover provides a lookup table from modified Braun-Blanquet cover codes to various numeric cover values.


  lucover
#> # A tibble: 7 × 12
#>   cover_code cover_description                           cover_desc cover_seq cover_1 cover_2 cover_3 cover_4    pa cover_mid cover_max cover_min
#>   <chr>      <chr>                                       <chr>          <int>   <int>   <dbl>   <dbl>   <dbl> <int>     <dbl>     <dbl>     <dbl>
#> 1 N          not many, 1-10 individuals                  1-10 indi…        13       1    0.02    0.01    0.01     1     0.01       0.01      0   
#> 2 T          sparsely or very sparsely present - cover … sparsely …        11       2    0.01    0.5     0.1      1     0.015      0.02      0.01
#> 3 1          plentiful but of small cover (less than 5%) <5%                9       3    0.03    1       1        1     0.025      0.05      0.02
#> 4 2          any number of individuals covering 5-25% o… 5-25%              7       4    0.05    2       2        1     0.15       0.25      0.05
#> 5 3          any no. of individuals covering 25-50% of … 25-50%             5       5    0.25    3       3        1     0.375      0.5       0.25
#> 6 4          any no. of individuals covering 50-75% of … 50-75%             3       6    0.5     4       4        1     0.625      0.75      0.5 
#> 7 5          covering more than 75% of the area          >75%               1       7    0.75    5       5        1     0.875      1         0.75

What else is in envEcosystems

The following functions and data sets are provided in envEcosystems. See https://acanthiza.github.io/envEcosystems/ for more examples.

object class description
[add_landcover_desc()] function Add ‘extra’ ecosystem descriptions
[cut_cov] tbl_df, tbl and data.frame Cover class threshold values
[cut_ht] tbl_df, tbl and data.frame Height class threshold values
[lucover] tbl_df, tbl and data.frame Lookup for cover codes
[lulandcover] tbl_df, tbl and data.frame Lookup for landcover classes and their associated colours
[lulifeform] tbl_df, tbl and data.frame Lookup for lifeform codes
[lulifespan] tbl_df, tbl and data.frame Lookup for lifespan classes
[make_eco_desc()] function Make a description for an ecosystem
[make_eco_env()] function Make a dataframe summarising environmental variables per cluster.
[make_eco_str_per()] function Create a dataframe of taxa percent cover for each cluster
[make_eco_taxa_per()] function Create a dataframe of taxa percent cover for each cluster
[sa_sf] tbl_df, tbl and data.frame Lookup for broad structural formations
[sa_vsf] tbl_df, tbl and data.frame Lookup for South Australian vegetation structural formations
[set_eco_col()] function Set colours for individual ecosystems, using gradations within ecotype
[taxa_samphire] character Vector of samphire taxa
[taxa_wetland] character Vector of wetland taxa