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funcoeslimpeza.R
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funcoeslimpeza.R
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library(taxize)
library(flora)
library(ggmap)
library(sp)
library(rgdal)
library(maptools)
library(dplyr) ## para manipular BD
library(rgbif)
##### functions cleaning data with geographic information
download.shp=function(all.records,level=2){
require(maps)
require(maptools)
require(raster)
require(rgdal)
require(rgeos)
require(spatialEco)
co=unique(all.records$country)
data(wrld_simpl)
codes=wrld_simpl@data[,1:5]
codes_use=as.character(codes$ISO3[which(codes$NAME %in% co)])
#cont.0=''#PHAM
if (length(codes_use)>0){
cont.0 <- getData("GADM", country = codes_use[1], level = level)
#url="http://biogeo.ucdavis.edu/data/gadm2.8/rds/"
for (i in 2:length(codes_use)){
cont=codes_use[i]
cont.1 <- getData("GADM", country = cont, level = level)
cont.0=rbind(cont.0,cont.1)} #join all the shps for contries in the dataset
}
return(cont.0)
}
# Criar variaveis sistema
info_geografica<-function(all.records){
init=download.shp(all.records, level=2)
HASC_0=HASC_1=HASC_2=rep(NA,nrow(init))
for (i in 1:nrow(init)){
print(i)
code=init$HASC_2[i]
HASC_S=unlist(strsplit(code,"[.]"))
HASC_0[i]=HASC_S[1]
HASC_1[i]=HASC_S[2]
HASC_2[i]=HASC_S[3]
}
init@data=cbind(init@data,HASC_0,HASC_1,HASC_2)
background.pol<<-download.shp(all.records, level=0)
paises<<-estado<<-mpios<<-init
#world cities
data(world.cities)
sedes<<-world.cities
#produce centroids
cents <- gCentroid(init,byid=T)
cents0<-as.data.frame(coordinates(cents))
cents1<<-SpatialPointsDataFrame(cents,data=cents0)
b=over(init, cents1)
centroid=init
centroid@data$Longmuncen<-b$x
centroid@data$Latmuncent<-b$y
}
###http://infocenter.ibi.com/wf8008/index.jsp?topic=%2Fpubdocs%2FRStat15%2Fsource%2Ftopic16.htm
### Revisar "overlay" de los registros con el "Shape" de departamento
corroboracion_pais=function(datos,mun){
CRS.new=CRS.new=background.pol@proj4string
#CRS.new=mun@proj4string
#CRS.new=CRS("+init=epsg:4326") # WGS 84
#projection(mun) <- projection("+proj=utm +zone=11 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0")
# proj4string(d) <- CRS("+init=epsg:4326") # WGS 84
# CRS.new <- CRS("+proj=somerc +lat_0=46.9524056 +lon_0=7.43958333 +ellps=bessel +x_0=2600000 +y_0=1200000 +towgs84=674.374,15.056,405.346 +units=m +k_0=1 +no_defs")
#CRS.new=CRS("+proj=longlat +datum=WGS84")
coordinates(datos)=~longitude+latitude
proj4string(datos) <- CRS.new
#proj4string(datos) <- CRS("+init=epsg:4326") # WGS 84
#ovm=overlay(datos,mun)
ovm=over(datos,mun)
#cntrm=as.character(mun@data$COUNTRY[ovm$PAIS]) #esta
cntrm=as.character(ovm$NAME_0)
if(length(which(!is.na(datos@data$state)))>0){
im=1:nrow(datos@data) # linea
tb=as.character(datos@data$country)# fala
CompareMun=cbind(im,cntrm,tb)
ma1=NULL
for ( i in 1:nrow(CompareMun)){
tmp<-agrep(CompareMun[i,2],CompareMun[i,3], max=4,value=F,ignore.case=T)
if (length(tmp)==0) tmp=0
ma<-c(CompareMun[i,1],tmp)
ma1=rbind(ma1,ma)
}
km=as.integer(ma1[which(is.na(ma1[,2])),1]) # pais diferente
lm=as.integer(ma1[which(ma1[,2]==1),1]) # pais igual
}else{
mm=rep(0,nrow(datos))
op=rep(NA,nrow(datos))
}
X=list()
X[[1]]=lm # pais correcto
X[[2]]=km #pais errado
X[[3]]=cntrm # sugerencia
return(X)
}
corroboracion_dep=function(datos,estado){
#CRS.new=estado@proj4string
#CRS.new=CRS("+proj=longlat +datum=WGS84")
#CRS.new=CRS("+init=epsg:4326") # WGS 84
CRS.new=CRS.new=background.pol@proj4string
coordinates(datos)=~longitude+latitude
proj4string(datos) <- CRS.new
ovm=over(datos,estado)
#cntrm=as.character(estado@data$HASC_1[ovm])
cntrm1=as.character(ovm$HASC_1)
cntrm2=as.character(ovm$NAME_1)
Encoding(cntrm2)="latin1"
if(length(which(!is.na(datos@data$stateprovince)))>0){
im=jm=NULL
for (j in 1:length(cntrm1)){
#print(j)
name.c=cntrm1[j]
name.c2=cntrm2[j]
name.dat=as.character(datos@data$stateprovince)[j]
Encoding(name.dat)="latin1"
if (!is.na(nchar(name.dat)==2)){ comp=name.dat==name.c} else{
comp=agrep(name.dat,name.c2,max.distance=3, ignore.case=T)
}
if (length(comp)==0){im=c(im,j) } else {## datos con diferente estado
jm=c(jm,j)}## datos con igual estado
}
diferente=as.data.frame(cbind(cntrm1,as.character(datos@data$stateprovince)))[im,]
#CompareDpto=cbind(im,diferente)
#MunCorrecto=cbind(cntrm,as.character(datos@data$state))[jm,]
} else{
im=rep(0,nrow(datos))
jm=rep(NA,nrow(datos))
}
X=list()
X[[1]]=jm # estado igual
X[[2]]=im# estado diferente
X[[3]]=cntrm1 #nombre estado correcto
return(X)
}
corroboracion=function(datos,mun){
#CRS.new=mun@proj4string
#CRS.new=CRS("+proj=longlat +datum=WGS84")
#CRS.new=CRS("+init=epsg:4326") # WGS 84
CRS.new=CRS.new=background.pol@proj4string
coordinates(datos)=~longitude+latitude
proj4string(datos) <- CRS.new
#ovm=overlay(datos,mun)
ovm=over(datos,mun)
#cntrm=as.character(mun@data$NAME_2[ovm])
cntrm=as.character(ovm$NAME_2)
Encoding(cntrm)="latin1"
if(length(which(!is.na(datos@data$county)))>0){
mm=op=NULL
for (j in 1:length(cntrm)){
#print(j)
name.c=cntrm[j]
name.dat=as.character(datos@data$county)[j]
Encoding(name.dat)="latin1"
# if(name.dat==""){name.dat=NA}else{name.dat=name.dat}
comp=''
if (!is.na(name.dat)& name.dat!=""){comp=agrep(name.dat,name.c,max.distance=4, ignore.case=T)}
if (length(comp)!=0){mm=c(mm,j) } else {##iqual municipality
op=c(op,j)} ## different municipality
}
}else{
mm=rep(0,nrow(datos))
op=rep(NA,nrow(datos))
}
X=list()
X[[1]]=mm
X[[2]]=op
X[[3]]=cntrm
return(X)
}