Description Usage Arguments Value Examples
Calculates the latitudinal diversity of taxa (species, genera, ...) and creates a plot of the paleogeographical continental masses with the fossil occurrences and the latitudinal diversity.
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data |
data.frame. Fossil occurrence data. |
method |
character. The method of diversity measure, method = "shannon" or method = "richness". Must be defined by the user. |
rank |
character. The taxonomic rank of interest. "species", "genus", "family", "order", "class" or "phylum". By default rank = "genus". |
res |
numeric. The spatial resolution. By default res = 1. |
map |
(list of) SpatialPolygonDataFrame(s). Containing map(s) which can be created with the function mapast::getmap(ma, model). |
model |
character. The model the map should be created with. "SETON2012" (default), "MULLER2016", "GOLONKA", "PALEOMAP" or "MATTHEWS2016". |
colland |
character. The color of the land masses. By default colland = "#66666660". |
colsea |
character. The color of the sea. By default colsea = "#00509010". |
colpoints |
character. The color of the fossil occurrence-points. By default colpoints = "#65432190". |
rich.col |
character. The color of the richness curve. By default rich.col = "#654321". |
pch |
numeric. Point symbol for plotting the occurences. By default pch = 21. |
do.plot |
logical. If a plot is created or not. By default do.plot = TRUE. |
save.as |
character. The format the plots should be saved. "tiff", "pdf", "jpeg" or "png". |
... |
Graphical parameters. Any argument that can be passed to image.plot and to plot, such as main = "my own title" or main.col = "red". |
data.frame
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 | ## Not run:
library(mapast)
#get data and preprocess it
data <- base::data.frame(paleobioDB::pbdb_occurrences(base_name = "Canis",
min_ma = 0, max_ma = 10,
show = c("coords", "phylo"),
vocab = "pbdb", limit = 100))
df <- formatdata(data = data)
df_auto <- paleocoords(data = df, time = "automatic")
#create a plot with fossils on the paleogeographical map
latrich <- latdivgrad(data = df_auto, method = "richness", rank = "species", res = 1,
model = "SETON2012")
latdiv <- latdivgrad(data = df_auto, method = "shannon", rank = "species", res = 1,
model = "SETON2012")
#save the maps before so the function does not need to load them
maps <- getmap(ma = 2.5, model = "SETON2012", do.plot = FALSE)
latdivgrad(data = df_auto, method = "richness", rank = "species", res = 1, map = maps,
model = "SETON2012")
latdivgrad(data = df_auto, method = "shannon", rank = "species", res = 1, map = maps,
model = "SETON2012")
#save maps with latitudinal diversity as pdf
latdivgrad(data = df_auto, method = "richness", rank = "species", res = 1, map = maps,
model = "SETON2012", save.as = "pdf")
latdivgrad(data = df_auto, method = "shannon", rank = "species", res = 1, map = maps,
model = "SETON2012", save.as = "pdf")
## End(Not run)
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