plot_PAM_CS {biosurvey} | R Documentation |

Graphic representations of results from
`prepare_PAM_CS`

. Plots present the new range-diversity diagram
and geographic views of results. Geographic representations are only possible
when significant analyses were performed.

```
plot_PAM_CS(PAM_CS, add_significant = FALSE,
add_random_values = FALSE, col_all = "#CACACA",
col_significant_low = "#6D6D6D",
col_significant_high = "#000000",
col_random_values = "#D2D2D2", pch_all = 1,
pch_significant_low = 16, pch_significant_high = 16,
pch_random_values = 1, main = NULL,
xlab = NULL, ylab = NULL, xlim = NULL, ylim = NULL,
ylim_expansion = 0.25, las = 1, add_legend = TRUE)
plot_PAM_CS_geo(PAM_CS, xy_coordinates = NULL, col_all = "#CACACA",
col_significant_low = "#6D6D6D",
col_significant_high = "#000000", border = NULL,
pch_all = 16, pch_significant_low = 16,
pch_significant_high = 16, xlim = NULL, ylim = NULL)
```

`PAM_CS` |
object of class PAM_CS or a base_PAM object containing
a PAM_CS object as part of PAM_indices. These objects can be obtained using
the function |

`add_significant` |
(logical) whether to add statistically significant
values using a different symbol. Default = FALSE. If TRUE and values
indicating significance are not in |

`add_random_values` |
(logical) whether to add values resulted from
the randomization process done when preparing |

`col_all` |
color code or name for all values or those that are not statistically significant. Default = "#CACACA". |

`col_significant_low` |
color code or name for significant values below confidence limits of random expectations. Default = "#000000". |

`col_significant_high` |
color code or name for significant values above confidence limits of random expectations. Default = "#000000". |

`col_random_values` |
color code or name for randomized values. Default = "D2D2D2". |

`pch_all` |
point symbol to be used for all values. Defaults = 1 or 16. |

`pch_significant_low` |
point symbol to be used for significant values below confidence limits of random expectations. Default = 16. |

`pch_significant_high` |
point symbol to be used for significant values above confidence limits of random expectations. Default = 16. |

`pch_random_values` |
point symbol to be used for randomized values. Default = 1. |

`main` |
main title for the plot. Default = NULL. |

`xlab` |
label for the x-axis. Default = NULL. |

`ylab` |
label for the y-axis. Default = NULL. |

`xlim` |
x limits of the plot (x1, x2). For |

`ylim` |
y limits of the plot. For |

`ylim_expansion` |
value used or expanding the |

`las` |
the style of axis labels; default = 1.
See |

`add_legend` |
(logical) whether to add a legend describing information relevant for interpreting the diagram. Default = TRUE. |

`xy_coordinates` |
Only required if |

`border` |
color for cell borders of the PAM grid. The default, NULL, does not plot any border. |

For `plot_PAM_CS`

:

A range-diversity plot with values of normalized richness in the x-axis, and normalized values of the dispersion field index divided by number of species in the y-axis.

For `plot_PAM_CS_geo`

:

A geographic view of the PAM representing the areas or points identified as non statistically significant, significant above random expectations, and significant below random expectations.

```
# Data
data("b_pam", package = "biosurvey")
# Preparing data for CS diagram
pcs <- prepare_PAM_CS(PAM = b_pam)
# Plot
plot_PAM_CS(pcs)
```

[Package *biosurvey* version 0.1.1 Index]