vignettes/Appendix_S2_Valcu_et_al_2012.R

In valcu/rangeMapper: A Platform for the Study of Macro-Ecology of Life History Traits

## ------------------------------------------------------------------------
td = tempdir()
require(rangeMapper)
dbcon = rangeMap.start(file = "wrens.sqlite", dir = td, overwrite = TRUE)

# Location of the vector(*.shp) breeding ranges on disk
branges = system.file(package = "rangeMapper", "extdata", "wrens", "vector_combined")

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global.bbox.save(con = dbcon, bbox = branges)

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gridSize.save(dbcon)

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canvas.save(dbcon)

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r = rgdal::readOGR(branges, "wrens", verbose = FALSE)
processRanges(spdf = r, con =  dbcon, ID = "sci_name", metadata = rangeTraits() )

## ------------------------------------------------------------------------
data(wrens)
bio.save(con = dbcon, loc = wrens, ID = "sci_name")

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P_richness = 0.75 # species richness probability
P_endemics = 0.35 # endemic species richness probability

## ------------------------------------------------------------------------
# 1) Save the species richness (SR) map
rangeMap.save(dbcon, tableName = "species_richness")

# 2) Fetch the SR map and find the SR value corresponding with the probability
 # previously defined by P_richness
sr = rangeMap.fetch(dbcon, "species_richness")
sr_threshold = quantile(sr$species_richness, probs = P_richness, na.rm = TRUE)

# 3) Save the SR hotspots map; only canvas cells with species_richness >= sr_threshold will be included
rangeMap.save(dbcon, tableName = "species_richness_hotspots",
    subset = list(MAP_species_richness =
        paste("species_richness >=", sr_threshold)) )

## ------------------------------------------------------------------------
# 1) Save endemics species richness map
es = dbGetQuery(dbcon, "select Area from metadata_ranges")
es_threshold = quantile(es$Area, probs = P_endemics, na.rm = TRUE)

rangeMap.save(dbcon, tableName = "endemics_spRichness",subset =
    list(metadata_ranges = paste("Area <= ", es_threshold) ) )

# 2) Save hotspots of endemics
er = rangeMap.fetch(dbcon, "endemics_spRichness")
er_threshold = quantile(er$endemics_spRichness, probs = P_richness, na.rm = TRUE)

rangeMap.save(dbcon, tableName = "endemics_hotspots", subset = list(
    MAP_endemics_spRichness = paste("endemics_spRichness >=", er_threshold) ) )

## ---- fig.width = 5, fig.height = 5--------------------------------------
#1) Save Coefficient of variation (CV_Mass) map using a function (FUN) defined
 # on the fly. The ... argument of the function will allow further arguments
 # in this case 'na.rm = TRUE' to be passed to FUN.

rangeMap.save(dbcon,
    FUN = function(x,...) (sd(log(x),...)/mean(log(x),...)),
    na.rm = TRUE, biotab = "wrens", biotrait = "body_mass",
    tableName = "CV_Mass")

# 2) Find the 'CV_Mass' threshold which corresponds with 'P_richness'
bmr = rangeMap.fetch(dbcon, "CV_Mass")
bmr_threshold = quantile(bmr$CV_Mass, probs = P_richness, na.rm = TRUE)

# 3) Save bodyMass richness hotspots map using the computed threshold
rangeMap.save(dbcon, tableName = "bodyMass_richness_hotspots",
    subset = list(MAP_CV_Mass =
        paste("body_mass >=", bmr_threshold) ) )

#  FETCH MAPS & PLOT
SRmaps = rangeMap.fetch(dbcon, c("species_richness", "species_richness_hotspots",
    "endemics_spRichness", "CV_Mass"), spatial = FALSE )
plot(SRmaps)

## ------------------------------------------------------------------------
sr = rangeMap.fetch(dbcon, "species_richness")
Q_richnes = quantile(sr$species_richness, probs = P_richness, na.rm = TRUE)

er = rangeMap.fetch(dbcon, "endemics_spRichness")
Q_endemics = quantile(er$endemics_spRichness, probs = P_richness, na.rm = TRUE)

bmr = rangeMap.fetch(dbcon, "CV_Mass")
Q_bodyMass = quantile(bmr$CV_Mass, probs = P_richness,na.rm = TRUE)

## ------------------------------------------------------------------------
rangeMap.save(dbcon, tableName = "cumul_congruence_hotspots",subset = list(
    MAP_CV_Mass             = paste("body_mass>=",Q_bodyMass),
    MAP_species_richness    = paste("species_richness>=",Q_richnes),
    MAP_endemics_spRichness = paste("endemics_spRichness>=",Q_endemics) ))

## ------------------------------------------------------------------------
rangeMap.save(dbcon, tableName = "SR_ER_congruence_hotspots",subset = list(
    MAP_species_richness    = paste("species_richness>=",Q_richnes),
    MAP_endemics_spRichness = paste("endemics_spRichness>=",Q_endemics) ))

## ------------------------------------------------------------------------
rangeMap.save(dbcon, tableName = "ER_BR_congruence_hotspots",
     subset = list(
     MAP_CV_Mass=paste("body_mass>=",Q_bodyMass),
     MAP_endemics_spRichness=paste("endemics_spRichness>=",Q_endemics) ))

## ------------------------------------------------------------------------
rangeMap.save(dbcon, tableName = "SR_BR_congruence_hotspots",
     subset = list(
     MAP_CV_Mass=paste("body_mass>=",Q_bodyMass),
     MAP_species_richness=paste("species_richness>=",Q_richnes) ))

## ------------------------------------------------------------------------
m = rangeMap.fetch(dbcon, c("species_richness_hotspots","endemics_hotspots",
    "bodyMass_richness_hotspots","cumul_congruence_hotspots",
    "SR_ER_congruence_hotspots","SR_BR_congruence_hotspots",
    "ER_BR_congruence_hotspots") )

## ------------------------------------------------------------------------
# The data slot of the map 'm' can be queried for presence/absence using the 'is.na' function.

sr = length( which(!is.na(m$species_richness_hotspots)))
er = length( which(!is.na(m$endemics_hotspots)))
br = length( which(!is.na(m$bodyMass_richness_hotspots)))

srer = length( which(!is.na(na.omit(m$SR_ER_congruence_hotspots))) )
srbr = length( which(!is.na(na.omit(m$SR_BR_congruence_hotspots))) )
erbr = length( which(!is.na(na.omit(m$ER_BR_congruence_hotspots))) )

cum = length( which(!is.na(na.omit(m$cumul_congruence_hotspots))) )

## ------------------------------------------------------------------------
(srbr/(sr+br))*100

## ------------------------------------------------------------------------
(erbr/(er+br))*100

## ------------------------------------------------------------------------
(srer/(sr+er))*100

## ------------------------------------------------------------------------
(cum/(sr+er+br))*100