Description Usage Arguments Details Value Examples

Networkeco for data series

1 2 3 4 5 6 | ```
NetworkEcoSeries(ecotonefinder, threshold = 0.8, method = c("cmeans",
"vegclust"), plot.type = c("percentage", "heatmap", "corrplot",
"network"), plot = c("species", "community"), no.plot = FALSE,
order.sp = NULL, dist.method = "inner_product", dist = c("count",
"relative", "raw"), network.group = c("site", "cluster"),
method.corr = "number", ...)
``` |

`ecotonefinder` |
A list containing elements named in the same way than EcotoneFinderSeries function outcomes. Must contain cmeans results or vegclust results. |

`threshold` |
If dist = "count", the membership grade threshold used to sort the species in the different clusters. |

`method` |
The membership computation method to be used. Must be present in the ecotonefinder list. |

`plot.type` |
Which graphical representation to be plotted. Among "percentage", "corrplot", "heatmap","network" |

`plot` |
If plot = "species", the distances are computed between the species in the data. If plot = "community", the distances are computed between the cluster centroids. |

`no.plot` |
Logical. Should the plot be displayed?. Set to TRUE to gain computation time with large community matrix. |

`order.sp` |
Vector providing the order in which to arrange the species. If NULL, the column order will be kept. |

`dist.method` |
Distance method for the computation of a distance matrix, when dist = "raw" or dist = "percent". |

`dist` |
The type of data on which distance calculations are made from. If dist = "raw", the distance matrix is computed from the membership matrix directly. if dist = "relative", the distance matrix is computed from the relative memberships grades of each species in the clusters (between 0 and 1). If dist = "count", the species are assigned to clusters according to the threshold and the distance matrix is computed from the number of common species between the different clusters. See details. |

`network.group` |
If network.group = "site" the nodes of the networks will be colored according to the different times or sites of the series. If network.group = "cluster" the nodes of the network will be colored according to the different fuzzy clusters. Can be user defined (see qgraph documentation for details) but must be a factor of the same lenght as the nodes of the graph. |

`method.corr` |
If plot.type = "corrplot", the method to be used for the corrplot. Must be one of "circle", "square", "ellipse", "number", "shade", "color", "pie". Default to "number". |

`...` |
Additional arguments to be passed to the plotting functions, see details. |

NetworkEcoSeries is a generalisation of the NetworkEco function to analyses space/time series. The ... argument may be used to pass additional arguments to the plotting functions (for graphical purposes).

A list containing the percentage matrix, the distance matrix and the network object (depending of the arguments passed to the function)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | ```
SyntheticTrialSeries <- SyntheticDataSeries(CommunityPool = 40,
CommunityNum = 4, SpCo = NULL,
Length = 500, SeriesNum = 5,
Parameters = list(a=rep(60, 4),
b=c(0,200,350,500),
c=rep(0.03,4)),
pal = c("#008585", "#B8CDAE", "#E6C186", "#C7522B"),
replacement = TRUE,
Parameters.repl = TRUE)
EcoTimeSeriesTrial <- EcotoneFinderSeries(data = SyntheticTrialSeries,
dist = "Distance",
method = c("cmeans","vegclust"),
series = "Time", groups = 4,
standardize = "hellinger", na.rm=TRUE)
#### Network from the common number of species above membership threshold between clusters:
SyntheticNetworkSeries <- NetworkEcoSeries(EcoTimeSeriesTrial, threshold = .2,
method = "cmeans", plot.type = "network",
plot = "community", dist = "count",
network.group = "cluster",
dist.method = "inner_product",
no.plot = FALSE, layout = "spring",
shape = "ellipse",
palette = "colorblind")
#### Network of relations between species from their raw membership values in each cluster:
SyntheticNetworkSeries <- NetworkEcoSeries(EcoTimeSeriesTrial, threshold = .2,
method = "cmeans", plot.type = "network",
plot = "species", dist = "raw",
dist.method = "inner_product",
no.plot = FALSE, layout = "spring",
shape = "ellipse",
palette = "colorblind")
``` |

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