README.md

In Acanthiza/envEcosystems: Create Ecosystem Definitions

output: rmarkdown::github_document

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

library("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 |

Acanthiza/envEcosystems documentation built on May 21, 2024, 6:20 p.m.