R/meteodata.r
In alfcrisci/rAedesSim: Modeling Aedes Albopictus Mosquito populations by using
#' meteodata
#'
#' @description meteodata is the function to store raw weather information in a S3 object in order to performs the simulation.
#'
#' @param station_name character name of station or location
#' @param network character name or project or network which data corresponds.
#' @param data_type character weather data class: forecast,observation, sensor micrometeorological data, physical parameter simulation
#' @param standard character weather data standard class. Default is SYREP.
#' @param data_provider character institution -Private data manager.
#' @param data_maintaner character maintainer's name or contact or its contact .
#' @param data_licence character Licence of data.
#' @param lat numeric latitude coordinate.
#' @param lon numeric longitude coordinate.
#' @param elevation numeric Elevation corresponding to data collected. Default is 40.
#' @param timeformat numeric Time period of data aggregation. Default is "Daily".
#' @param sourcedata matrix or data.frame or ascii file of raw data. Frame must be daily with at least 6 fields. dates ( in YYYY-MM-DD format ),tmed,tmax,tmin,rhum prec.
#' @param field_delimiter chararter field delimiter of file. Default is comma ",".
#' @param date_format character Format of the dates in raw data. Default is YYYY-MM-DD.
#' @param timezone sring Timezone. Default is "Europe/Rome".
#' @param timeseries object xts R Timeseries of data
#' @param CRS character Projection of coordinates in proj4 format.
#' @return meteodata
#' @author Istituto di Biometeorologia Firenze Italy Alfonso crisci \email{a.crisci@@ibimet.cnr.it} ASL 2 LUCCA Marco Selmi \email{marco.selmi@@uslnordovest.toscana.it }
#' @keywords metorological data
#' @import sp
#' @import lubridate
#'
#' @export
meteodata<-function(station_name="Pisa San Giusto",
network="Aeronautica Militare",
data_type="Simulation",
standard="SYREP",
data_provider="IBIMET CNR",
data_maintainer="",
data_licence="",
date_format="YMD",
lat=43.0,
lon=11.0,
elevation=40,
timeformat="daily",
sourcedata=NULL,
field_delimiter=",",
timezone="Europe/Rome",
timeseries=NULL,
CRS="+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
)
{
#################################################################################################################
# location conversion
epgs4386="+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs";
splocation=data.frame(lon=lon,lat=lat)
coordinates(splocation) <- c('lon','lat')
proj4string(splocation) <- CRS
#################################################################################################################
newsp <-SpatialPointsDataFrame(splocation,data.frame(Elevation=elevation))
if (CRS != "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
{
newsp <- spTransform(splocation,CRS(epgs4386))
newsp <-SpatialPointsDataFrame(newsp,data.frame(Elevation=elevation))
}
lon_geo=as.numeric(coordinates(newsp))[1]
lat_geo=as.numeric(coordinates(newsp))[2]
if ( is.null(sourcedata)) {
stop( "To build meteodata valid object a data source is required in one of this two ways: \n
A) data.frame
B) csv ascii formatted file.\n
Format must be daily with fields :
[dates] Date of day better in YYYY-MM-DD format . \n
[tmed] Mean temperature. \n
[tmax] Maximum temperature.\n
[tmin] Minimum temperature.\n
[rhum] Mean relative humidity.\n
[prec] Cumulated rainfall.\n
Header name are indicated to avoid errors.
Mean temperature and minimum temperature fields are required."
)
}
#################################################################################################################
if (is.data.frame(sourcedata) || is.matrix(sourcedata))
{ filemeteo=as.data.frame(sourcedata)
}
else
{
filemeteo=read.table(sourcedata, header=TRUE, sep=field_delimiter,na.strings="NA", dec=".", strip.white=TRUE)
}
#################################################################################################################
if ( length(grep("tmed",names(filemeteo)))==0 || length( grep("dates",names(filemeteo)))== 0 || length( grep("rhum",names(filemeteo)))== 0)
{ stop( "Name field [dates] [tmed] [rhum] in datasource are requested. Please change the names of datafield including these ones.")
}
if ( length(grep("anno",names(filemeteo)))>0 && length(grep("mese",names(filemeteo)))>0 && length(grep("mese",names(filemeteo))>0 ))
{ names(filemeteo)<-gsub("anno","year",names(filemeteo))
names(filemeteo)<-gsub("mese","month",names(filemeteo))
names(filemeteo)<-gsub("giorno","day",names(filemeteo))
names(filemeteo)<-gsub("urel","rhum",names(filemeteo))
names(filemeteo)<-gsub("data","dates",names(filemeteo))
}
if ( !length(grep("year",names(filemeteo)))>0 && !length(grep("month",names(filemeteo)))>0 && length(grep("day",names(filemeteo))>0 ))
{ filemeteo$year<-year(filemeteo$dates)
filemeteo$month<-month(filemeteo$dates)
filemeteo$day<-day(filemeteo$dates)
}
#################################################################################################################
filemeteo$dates=as.Date(ymd(filemeteo$dates),tz=timezone)
if ( date_format == "DMY") {filemeteo$dates=dmy(filemeteo$dates)}
if ( date_format == "MDY") {filemeteo$dates=mdy(filemeteo$dates)}
filemeteo$dates=as.Date(filemeteo$dates,tz=timezone)
#################################################################################################################
rownames(filemeteo)<-1:nrow(filemeteo)
period=as.numeric(max(as.Date(filemeteo$dates,tz=timezone)))-as.numeric(min(as.Date(filemeteo$dates,tz=timezone)))
length_data_ini=nrow(filemeteo)
row_na=nrow(filemeteo[!complete.cases(filemeteo),])
perc_missing=(row_na/nrow(filemeteo))*100
if ( period > length_data_ini-1) {
fill_dates=data.frame(dates=seq(min(as.Date(filemeteo$dates,tz=timezone)),max(as.Date(filemeteo$dates,filemeteo$dates,tz=timezone)),1));
filemeteo=merge(fill_dates,filemeteo,by=c("dates"),all = T)
}
filemeteo$daylength = day_length(as.Date(filemeteo$dates,tz=timezone),lon_geo,lat_geo)$daylength;
#################################################################################################################
if (period < (length_data_ini-1)) {
stop( "Data source is not correcly time indexed! Suspect date duplicates.")
}
continuity=ifelse(period==length_data_ini-1,TRUE,FALSE)
#################################################################################################################
variables=names(filemeteo)[grep("tmed|tmax|tmin|rhum|prec",names(filemeteo))]
if ( is.null(timeseries) )
{
ts_zoo=try(as.xts(zoo(filemeteo[variables],as.Date(as.character(filemeteo$dates)))))
}
if ( !exists("ts_zoo"))
{
warning( "Timeseries creation invalid! Check data and dates in data sources")
}
#################################################################################################################
object <- list(station_name=station_name,
network=network,
data_type=data_type,
standard=standard,
data_provider=data_provider,
data_maintainer=data_maintainer,
data_licence=data_licence,
lat=lat_geo,
lon=lon_geo,
CRS=epgs4386,
elevation=elevation,
timeformat=timeformat,
tmed=filemeteo$tmed,
tmax=filemeteo$tmax,
tmin=filemeteo$tmin,
urel=filemeteo$rhum,
prec=filemeteo$prec,
dates=filemeteo$dates,
length_data_ini=length_data_ini,
ndays=length(filemeteo$dates),
daylenght=filemeteo$daylength,
continuity=continuity,
perc_missing_data=perc_missing,
timeseries=ts_zoo,
timezone=timezone,
sp_obj=newsp)
attr(object,"station_name") <- "Name of station"
attr(object,"network") <- "Network of station"
attr(object,"data_type")<-"Station Type"
attr(object,"standard")<-"Data class or relative reference standard"
attr(object,"data_provider")<-"Istitution or Private data manager"
attr(object,"data_maintainer")<-"Name or contact of data maintainer"
attr(object,"data_licence")<-"Licence of data"
attr(object,"lat")<-"Latitude in decimal degrees. Datum WGS 84"
attr(object,"lon")<-"Longitude in decimal degrees . Datum WGS 84"
attr(object,"CRS")<-"Projection used for the coordinate in proj4 string format"
attr(object,"elevation")<-"Elevation (m)"
attr(object,"timeformat")<-"Period of aggregation"
attr(object,"tmed")<-"Mean daily temperature"
attr(object,"tmax")<-"Maximum daily temperature"
attr(object,"tmin")<-"Minimum daily temperature"
attr(object,"urel")<-"Relative humidity daily average"
attr(object,"prec")<-"Rainfall cumulated in a day"
attr(object,"dates")<-"Dates of meteorological data matrix"
attr(object,"length_data_ini")<-"Initial data length of raw data"
attr(object,"ndays")<-"Number of days"
attr(object,"daylenght")<-"Day length for each date"
attr(object,"continuity")<-"If the temporal continuity of raw data is detected"
attr(object,"perc_missing_data")<-"Percentage of missing values"
attr(object,"timeseries")<-"Data timeseries as R xts object"
attr(object,"timezone")<-"Timezone"
attr(object,"sp_obj")<-"SpatialPointDataFrame"
class(object) <-"meteodata"
return(object)
}
alfcrisci/rAedesSim documentation built on May 10, 2019, 8:59 a.m.
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#' meteodata
#'
#' @description meteodata is the function to store raw weather information in a S3 object in order to performs the simulation.
#'
#' @param station_name character name of station or location
#' @param network character name or project or network which data corresponds.
#' @param data_type character weather data class: forecast,observation, sensor micrometeorological data, physical parameter simulation
#' @param standard character weather data standard class. Default is SYREP.
#' @param data_provider character institution -Private data manager.
#' @param data_maintaner character maintainer's name or contact or its contact .
#' @param data_licence character Licence of data.
#' @param lat numeric latitude coordinate.
#' @param lon numeric longitude coordinate.
#' @param elevation numeric Elevation corresponding to data collected. Default is 40.
#' @param timeformat numeric Time period of data aggregation. Default is "Daily".
#' @param sourcedata matrix or data.frame or ascii file of raw data. Frame must be daily with at least 6 fields. dates ( in YYYY-MM-DD format ),tmed,tmax,tmin,rhum prec.
#' @param field_delimiter chararter field delimiter of file. Default is comma ",".
#' @param date_format character Format of the dates in raw data. Default is YYYY-MM-DD.
#' @param timezone sring Timezone. Default is "Europe/Rome".
#' @param timeseries object xts R Timeseries of data
#' @param CRS character Projection of coordinates in proj4 format.
#' @return meteodata
#' @author Istituto di Biometeorologia Firenze Italy Alfonso crisci \email{a.crisci@@ibimet.cnr.it} ASL 2 LUCCA Marco Selmi \email{marco.selmi@@uslnordovest.toscana.it }
#' @keywords metorological data
#' @import sp
#' @import lubridate
#'
#' @export
meteodata<-function(station_name="Pisa San Giusto",
network="Aeronautica Militare",
data_type="Simulation",
standard="SYREP",
data_provider="IBIMET CNR",
data_maintainer="",
data_licence="",
date_format="YMD",
lat=43.0,
lon=11.0,
elevation=40,
timeformat="daily",
sourcedata=NULL,
field_delimiter=",",
timezone="Europe/Rome",
timeseries=NULL,
CRS="+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"
)
{
#################################################################################################################
# location conversion
epgs4386="+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs";
splocation=data.frame(lon=lon,lat=lat)
coordinates(splocation) <- c('lon','lat')
proj4string(splocation) <- CRS
#################################################################################################################
newsp <-SpatialPointsDataFrame(splocation,data.frame(Elevation=elevation))
if (CRS != "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
{
newsp <- spTransform(splocation,CRS(epgs4386))
newsp <-SpatialPointsDataFrame(newsp,data.frame(Elevation=elevation))
}
lon_geo=as.numeric(coordinates(newsp))[1]
lat_geo=as.numeric(coordinates(newsp))[2]
if ( is.null(sourcedata)) {
stop( "To build meteodata valid object a data source is required in one of this two ways: \n
A) data.frame
B) csv ascii formatted file.\n
Format must be daily with fields :
[dates] Date of day better in YYYY-MM-DD format . \n
[tmed] Mean temperature. \n
[tmax] Maximum temperature.\n
[tmin] Minimum temperature.\n
[rhum] Mean relative humidity.\n
[prec] Cumulated rainfall.\n
Header name are indicated to avoid errors.
Mean temperature and minimum temperature fields are required."
)
}
#################################################################################################################
if (is.data.frame(sourcedata) || is.matrix(sourcedata))
{ filemeteo=as.data.frame(sourcedata)
}
else
{
filemeteo=read.table(sourcedata, header=TRUE, sep=field_delimiter,na.strings="NA", dec=".", strip.white=TRUE)
}
#################################################################################################################
if ( length(grep("tmed",names(filemeteo)))==0 || length( grep("dates",names(filemeteo)))== 0 || length( grep("rhum",names(filemeteo)))== 0)
{ stop( "Name field [dates] [tmed] [rhum] in datasource are requested. Please change the names of datafield including these ones.")
}
if ( length(grep("anno",names(filemeteo)))>0 && length(grep("mese",names(filemeteo)))>0 && length(grep("mese",names(filemeteo))>0 ))
{ names(filemeteo)<-gsub("anno","year",names(filemeteo))
names(filemeteo)<-gsub("mese","month",names(filemeteo))
names(filemeteo)<-gsub("giorno","day",names(filemeteo))
names(filemeteo)<-gsub("urel","rhum",names(filemeteo))
names(filemeteo)<-gsub("data","dates",names(filemeteo))
}
if ( !length(grep("year",names(filemeteo)))>0 && !length(grep("month",names(filemeteo)))>0 && length(grep("day",names(filemeteo))>0 ))
{ filemeteo$year<-year(filemeteo$dates)
filemeteo$month<-month(filemeteo$dates)
filemeteo$day<-day(filemeteo$dates)
}
#################################################################################################################
filemeteo$dates=as.Date(ymd(filemeteo$dates),tz=timezone)
if ( date_format == "DMY") {filemeteo$dates=dmy(filemeteo$dates)}
if ( date_format == "MDY") {filemeteo$dates=mdy(filemeteo$dates)}
filemeteo$dates=as.Date(filemeteo$dates,tz=timezone)
#################################################################################################################
rownames(filemeteo)<-1:nrow(filemeteo)
period=as.numeric(max(as.Date(filemeteo$dates,tz=timezone)))-as.numeric(min(as.Date(filemeteo$dates,tz=timezone)))
length_data_ini=nrow(filemeteo)
row_na=nrow(filemeteo[!complete.cases(filemeteo),])
perc_missing=(row_na/nrow(filemeteo))*100
if ( period > length_data_ini-1) {
fill_dates=data.frame(dates=seq(min(as.Date(filemeteo$dates,tz=timezone)),max(as.Date(filemeteo$dates,filemeteo$dates,tz=timezone)),1));
filemeteo=merge(fill_dates,filemeteo,by=c("dates"),all = T)
}
filemeteo$daylength = day_length(as.Date(filemeteo$dates,tz=timezone),lon_geo,lat_geo)$daylength;
#################################################################################################################
if (period < (length_data_ini-1)) {
stop( "Data source is not correcly time indexed! Suspect date duplicates.")
}
continuity=ifelse(period==length_data_ini-1,TRUE,FALSE)
#################################################################################################################
variables=names(filemeteo)[grep("tmed|tmax|tmin|rhum|prec",names(filemeteo))]
if ( is.null(timeseries) )
{
ts_zoo=try(as.xts(zoo(filemeteo[variables],as.Date(as.character(filemeteo$dates)))))
}
if ( !exists("ts_zoo"))
{
warning( "Timeseries creation invalid! Check data and dates in data sources")
}
#################################################################################################################
object <- list(station_name=station_name,
network=network,
data_type=data_type,
standard=standard,
data_provider=data_provider,
data_maintainer=data_maintainer,
data_licence=data_licence,
lat=lat_geo,
lon=lon_geo,
CRS=epgs4386,
elevation=elevation,
timeformat=timeformat,
tmed=filemeteo$tmed,
tmax=filemeteo$tmax,
tmin=filemeteo$tmin,
urel=filemeteo$rhum,
prec=filemeteo$prec,
dates=filemeteo$dates,
length_data_ini=length_data_ini,
ndays=length(filemeteo$dates),
daylenght=filemeteo$daylength,
continuity=continuity,
perc_missing_data=perc_missing,
timeseries=ts_zoo,
timezone=timezone,
sp_obj=newsp)
attr(object,"station_name") <- "Name of station"
attr(object,"network") <- "Network of station"
attr(object,"data_type")<-"Station Type"
attr(object,"standard")<-"Data class or relative reference standard"
attr(object,"data_provider")<-"Istitution or Private data manager"
attr(object,"data_maintainer")<-"Name or contact of data maintainer"
attr(object,"data_licence")<-"Licence of data"
attr(object,"lat")<-"Latitude in decimal degrees. Datum WGS 84"
attr(object,"lon")<-"Longitude in decimal degrees . Datum WGS 84"
attr(object,"CRS")<-"Projection used for the coordinate in proj4 string format"
attr(object,"elevation")<-"Elevation (m)"
attr(object,"timeformat")<-"Period of aggregation"
attr(object,"tmed")<-"Mean daily temperature"
attr(object,"tmax")<-"Maximum daily temperature"
attr(object,"tmin")<-"Minimum daily temperature"
attr(object,"urel")<-"Relative humidity daily average"
attr(object,"prec")<-"Rainfall cumulated in a day"
attr(object,"dates")<-"Dates of meteorological data matrix"
attr(object,"length_data_ini")<-"Initial data length of raw data"
attr(object,"ndays")<-"Number of days"
attr(object,"daylenght")<-"Day length for each date"
attr(object,"continuity")<-"If the temporal continuity of raw data is detected"
attr(object,"perc_missing_data")<-"Percentage of missing values"
attr(object,"timeseries")<-"Data timeseries as R xts object"
attr(object,"timezone")<-"Timezone"
attr(object,"sp_obj")<-"SpatialPointDataFrame"
class(object) <-"meteodata"
return(object)
}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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