Package 'geotopbricks' reference manual

Title:	An R Plug-in for the Distributed Hydrological Model GEOtop
Description:	It analyzes raster maps and other information as input/output files from the Hydrological Distributed Model GEOtop. It contains functions and methods to import maps and other keywords from geotop.inpts file. Some examples with simulation cases of GEOtop 2.x/3.x are presented in the package. Any information about the GEOtop Distributed Hydrological Model source code is available on www.geotop.org. Technical details about the model are available in Endrizzi et al (2014) <https://gmd.copernicus.org/articles/7/2831/2014/gmd-7-2831-2014.html>.
Authors:	Emanuele Cordano
Maintainer:	Emanuele Cordano <[email protected]>
License:	GPL (>= 3)
Version:	1.5.8.2
Built:	2024-11-11 04:45:02 UTC
Source:	https://github.com/ecor/geotopbricks

Parser of an argument string

Description

This command parses ...DESCRITION TO DO !!!

Usage

argsParser(option, args, sep = " ", novalue_response = NULL)
argsParser(option, args, sep = " ", novalue_response = NULL)

Arguments

`option`	character strings containg options (or flag) whose values
`args`	String containing all the arguments of an R script
`sep`	separator character. Default is `" "`. If it is of length 2, the first is seperator among different options, the second is betwwen option name and its value.
`novalue_response`	value used in case the option is missing. Default is `NULL`.

Examples


args <- "--value  6  --fruit apple"

option <- "--fruit"

value <- argsParser(option=option,args=args)

option2 <- "--jobs"

value2 <- argsParser(option=option2,args=args)
value22 <- argsParser(option=option2,args=args,novalue_response="./")
 args_b <- "value=6 , fruit=apple"
option3 <- "value"
value <- argsParser(option=option3,args=args_b,sep=c(",","="))

args <- "--value  6  --fruit apple"

option <- "--fruit"

value <- argsParser(option=option,args=args)

option2 <- "--jobs"

value2 <- argsParser(option=option2,args=args)
value22 <- argsParser(option=option2,args=args,novalue_response="./")
 args_b <- "value=6 , fruit=apple"
option3 <- "value"
value <- argsParser(option=option3,args=args_b,sep=c(",","="))

Bondone Dataset

Description

It contains hourly meteorological data observed at MeteoTrentino T0327 station located at Monte Bondone-Viotte (Trentino, Easter Alps, Italy) from August 2004 to December 2012.\

The zoo object 'meteo' contains:

Iprec: Hourly Precipitation Depth expressed in millimeters

AirT: Air Temperature expressed in Celsius Degree

RH: Relative Humidity in PerCent

WinDir: Wind Direction expressed in Degrees North Clockwise

WinSp: Wind Direction expressed in meters per second

Swglob: Short-Wave Radiation expressed in Watts per square meters

The corresponding time axis vector for each observation can be printed by typing index(meteo).

Usage

data(bondone)
data(bondone)

Format

Data frame , 'zoo' object

Details

This data set stores all meteorological information useful for a GEOtop simulation. The user can easily use the package with his/her own data after replacing the values of such variables.

Source

Original data are provided by Provincia Autonoma di Trento (https://www.meteotrentino.it/)).

This dataset is intended for research purposes only, being distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

brick

Description

Added implemetation for 'brick' S4 method

@title brick

Usage

## S4 method for signature 'zoo'
brick(
  x,
  layer = 1,
  timerange = NULL,
  time = NULL,
  rows = 1:nrow(x),
  crs = NULL,
  use.read.raster.from.url = TRUE
)

## S4 method for signature 'GeotopRasterBrick'
brick(x)
## S4 method for signature 'zoo'
brick(
  x,
  layer = 1,
  timerange = NULL,
  time = NULL,
  rows = 1:nrow(x),
  crs = NULL,
  use.read.raster.from.url = TRUE
)

## S4 method for signature 'GeotopRasterBrick'
brick(x)

Arguments

`x`	a 'zoo' object returned by function `pointer.to.maps.xyz.time` or `pointer.to.maps.xy.time` or a `GeotopRasterBrick-class` object
`layer`	layer at which raster maps are imported. If is `NULL`, maps ara no-zlayer distributed and `zoo` must be returend by `pointer.to.maps.xy.time`
`timerange`	two-elememts vector containing the time range at which geotop maps are imported
`time`	vector of time instants at which geotop maps are imported
`rows`	rows of `zoo` correspondig to the geotop maps that are imported. By default all rows of `zoo` are considered. It is calculated by `time` or `timerange` if they are not set as `NULL`.
`crs`	coordinate system see `RasterBrick-class`
`use.read.raster.from.url`	logical value. Default is `TRUE`. If `TRUE` the RasterLayer are read with `read.raster.from.url`, istead of `raster` (otherwise). It is recomended in case the files whose paths are contained in `x` are remote and are 'http' addresses. In this cases the stand-alone method `raster(x)` does not always work and `use.read.raster.from.url` is necessary.

Value

a RasterBrick-class containing the geopop maps indicated by x, which is already in a GeotopRasterBrick-class object or a 'zoo' object returned by function pointer.to.maps.xyz.time or pointer.to.maps.xy.time.

Examples

# TON TOSS 
# See the examples in the functions listed in the 'SeeAlso' section
# TON TOSS 
# See the examples in the functions listed in the 'SeeAlso' section

Imports a brick of raster ascii maps into a 'brick' object

Description

Imports a brick of raster ascii maps into a 'brick' object

Usage

brick.decimal.formatter(
  file = NULL,
  file_prefix,
  formatter = "%04d",
  file_extension = ".asc",
  nlayers = 10,
  use.read.raster.from.url = FALSE,
  crs = NULL,
  start.from.zero = FALSE
)
brick.decimal.formatter(
  file = NULL,
  file_prefix,
  formatter = "%04d",
  file_extension = ".asc",
  nlayers = 10,
  use.read.raster.from.url = FALSE,
  crs = NULL,
  start.from.zero = FALSE
)

Arguments

`file`	fileneme of the 'brick' files containing the decimal formatter. It is `NULL` by default, otherwise it replaces `file_suffix`, `formatter` and `file_extension`.
`file_prefix`	character string suffix name of the 'brick' files.
`formatter`	string value. Default is `"%04d"` .
`file_extension`	strinf value. Default is `".asc"`
`nlayers`	number of layers
`use.read.raster.from.url`	logical value. Default is `FALSE`. (this is recommended in this function). If `TRUE` the RasterLayer are read with `read.raster.from.url`, istead of `raster` (otherwise). It is recomended in case the files whose paths are contained in `x` are remote and are 'http' addresses. In this cases the stand-alone method `raster(x)` does not always work and `use.read.raster.from.url` is necessary.
`crs`	coordinate system see `RasterBrick-class`,`brick`, Default is `NULL`.
`start.from.zero`	logical value. Default is `FALSE`. If `TRUE` the formatter starts from `0000`, otherwise it starts from `0001`.

Value

the output is returned as a RasterBrick-class object

Examples

library(geotopbricks)
library(raster)
file <- system.file("example_files/examples/snowthickness",package="geotopbricks")
file <- paste(file,"SnowThickness0000L%04d.asc",sep="/")
# nlayers=15
nlayers <- 6 ## Only 6 layers are read to minimize the elapsed time of the example!!
b <- brick.decimal.formatter(file=file,nlayers=nlayers)
nlayers(b)
names(b)
library(geotopbricks)
library(raster)
file <- system.file("example_files/examples/snowthickness",package="geotopbricks")
file <- paste(file,"SnowThickness0000L%04d.asc",sep="/")
# nlayers=15
nlayers <- 6 ## Only 6 layers are read to minimize the elapsed time of the example!!
b <- brick.decimal.formatter(file=file,nlayers=nlayers)
nlayers(b)
names(b)

brickFromOutputSoil3DTensor

Description

Extracts a brick or a raster layer from a output 3D Tensor or 2D map respectively

Usage

brickFromOutputSoil3DTensor(
  x,
  when,
  layers = "SoilLayerThicknesses",
  one.layer = FALSE,
  suffix = "L%04dN%04d.asc",
  time_formatter = "N%04d",
  suffix_one.layer = "N%04d.asc",
  wpath = NULL,
  tz = "A",
  start_date_key = "InitDateDDMMYYYYhhmm",
  end_date_key = "EndDateDDMMYYYYhhmm",
  timestep = "OutputSoilMaps",
  use.read.raster.from.url = FALSE,
  crs = NULL,
  projfile = "geotop.proj",
  start.from.zero = FALSE,
  secondary.suffix = NULL,
  only.map.filename = FALSE,
  add_suffix_dir = NULL,
  ...
)

rasterFromOutput2DMap(x, when, ...)
brickFromOutputSoil3DTensor(
  x,
  when,
  layers = "SoilLayerThicknesses",
  one.layer = FALSE,
  suffix = "L%04dN%04d.asc",
  time_formatter = "N%04d",
  suffix_one.layer = "N%04d.asc",
  wpath = NULL,
  tz = "A",
  start_date_key = "InitDateDDMMYYYYhhmm",
  end_date_key = "EndDateDDMMYYYYhhmm",
  timestep = "OutputSoilMaps",
  use.read.raster.from.url = FALSE,
  crs = NULL,
  projfile = "geotop.proj",
  start.from.zero = FALSE,
  secondary.suffix = NULL,
  only.map.filename = FALSE,
  add_suffix_dir = NULL,
  ...
)

rasterFromOutput2DMap(x, when, ...)

Arguments

`x`	string. GEOtop keyword reletated to the 3D or 2D variable to be imported in R.
`when`	`POSIXct-class` for date and time on which the variable `x` is requested.
`layers`	number of soil layer or geotop keyword for soil layer (e.g. `SoilLayerThicknesses` or `SoilFile`). Default is `SoilLayerThicknesses`.
`one.layer`	logical value. If `TRUE` a `RasterLayer-class` object is imported, otherwise a `RasterBrick-class`object is returened. Default for `brickFromOutputSoil3DTensor` is `FALSE`
`suffix`	charachter string containing the decimal formatter used by GEOtop in the output file names. Default is `"L%04dN%04.asc"`. A simple user is recommended not to modify the value of this argument and use the default value.
`time_formatter`, `suffix_one.layer`	charachter string (`suffix_one.layer` is used for 2Dxy map) containing the decimal formatter used by GEOtop in the output file names to indicate time instant. Default is `"N%04.asc"`. A simple user is recommended not to modify the value of this argument and use the default value.
`wpath`, `tz`, `use.read.raster.from.url`	see `get.geotop.inpts.keyword.value`
`start_date_key`, `end_date_key`	initial and final detes and times of the GEOtop simulation or alternatively the respective keywords of `*.inpts` file (Default)
`timestep`	time step expressed in seconds every which the raster file has been created. It can be a string corresponding to the geotop keyword in the inpts file. Default value is `"OutputSoilMaps"`.
`crs`, `start.from.zero`	see `brick.decimal.formatter`. If `crs` is not `NULL` (Default) , `projfile` is ignored.
`projfile`	name of the `.proj` file containing CRS information. See `get.geotop.inpts.keyword.value`. Default is `"geotop.proj"`. If is `NULL` or `NA` or this file does not exist, it is not searched and read.. In case `use.read.raster.from.url` is `TRUE` and no `NULL` or `NA` values are assinged, the `.proj` file is searched.
`secondary.suffix`	String secondary suffix which can be added at the end of the Map file name (optional). Default is `NULL` and no secondary suffix is added.
`only.map.filename`	logical value. If it is `TRUE`, only map file names are returned and maps are not imported. Default is `FALSE`.
`add_suffix_dir`, `...`	additional arguments for `get.geotop.inpts.keyword.value` or `brickFromOutputSoil3DTensor`

Details

These functions brickFromOutputSoil3DTensor and rasterFromOutput2DMap return 3D or 2D Raster-class objects respectively. rasterFromOutput2DMap is a wrapper function of brickFromOutputSoil3DTensor with the option one.layer==TRUE. The functionswork with the following output keywords:

"SoilTempTensorFile",

"SoilAveragedTempTensorFile",

"SoilLiqContentTensorFile",

"SoilAveragedLiqContentTensorFile",

"SoilIceContentTensorFile",

"SoilAveragedIceContentTensorFile",

"SoilLiqWaterPressTensorFile",

"SoilTotWaterPressTensorFile" for brickFromOutputSoil3DTensor;

"FirstSoilLayerTempMapFile",

"FirstSoilLayerAveragedTempMapFile",

"FirstSoilLayerLiqContentMapFile",

"FirstSoilLayerIceContentMapFile",

"LandSurfaceWaterDepthMapFile",

"ChannelSurfaceWaterDepthMapFile",

"NetRadiationMapFile",

"InLongwaveRadiationMapFile",

"NetLongwaveRadiationMapFile",

"NetShortwaveRadiationMapFile",

"InShortwaveRadiationMapFile",

"DirectInShortwaveRadiationMapFile",

"ShadowFractionTimeMapFile",

"SurfaceHeatFluxMapFile",

"SurfaceSensibleHeatFluxMapFile",

"SurfaceLatentHeatFluxMapFile",

"SurfaceTempMapFile",

"PrecipitationMapFile",

"CanopyInterceptedWaterMapFile",

"SnowDepthMapFile",

"GlacierDepthMapFile",

"SnowMeltedMapFile",

"SnowSublMapFile",

"GlacierMeltedMapFile",

"GlacierSublimatedMapFile",

"AirTempMapFile",

"WindSpeedMapFile",

"WindDirMapFile",

"RelHumMapFiladd_suffix_dir=NULLe",

"SWEMapFile",

"GlacierWaterEqMapFile"

"SnowDurationMapFile",

"ThawedSoilDepthMapFile",

"ThawedSoilDepthFromAboveMapFile",

"WaterTableDepthMapFile",

"WaterTableDepthFromAboveMapFile",

"NetPrecipitationMapFile",

"EvapotranspirationFromSoilMapFile" for rasterFromOutput2DMap.

Author(s)

Emanuele Cordano

Examples


library(geotopbricks)
## Not run: 
# The data containing in the link are only for educational use
wpath <- 'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/idroclim_test1'
## URL path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/idroclim_test1
x <- "SoilLiqContentTensorFile"
tz <-  "Etc/GMT-1"
when <- as.POSIXct("2002-03-22",tz=tz)

# Not Run because it elapses too long time!!! 
# Please Uncomment the following lines to run by yourself!!!
 b <- brickFromOutputSoil3DTensor(x,when=when,wpath=wpath,tz=tz,use.read.raster.from.url=TRUE)

# a 2D map: 
x_e <- "SnowDepthMapFile"
# Not Run: uncomment the following line

m <- rasterFromOutput2DMap(x_e,when=when,wpath=wpath,timestep="OutputSnowMaps",
                            tz=tz,use.read.raster.from.url=TRUE)
## NOTE: set use.read.raster.from.url=FALSE (default) 
# if the "wpath" directorty is in the local file system.
# Not Run: uncomment the following line
plot(m)

## End(Not run)
library(geotopbricks)
## Not run: 
# The data containing in the link are only for educational use
wpath <- 'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/idroclim_test1'
## URL path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/idroclim_test1
x <- "SoilLiqContentTensorFile"
tz <-  "Etc/GMT-1"
when <- as.POSIXct("2002-03-22",tz=tz)

# Not Run because it elapses too long time!!! 
# Please Uncomment the following lines to run by yourself!!!
 b <- brickFromOutputSoil3DTensor(x,when=when,wpath=wpath,tz=tz,use.read.raster.from.url=TRUE)

# a 2D map: 
x_e <- "SnowDepthMapFile"
# Not Run: uncomment the following line

m <- rasterFromOutput2DMap(x_e,when=when,wpath=wpath,timestep="OutputSnowMaps",
                            tz=tz,use.read.raster.from.url=TRUE)
## NOTE: set use.read.raster.from.url=FALSE (default) 
# if the "wpath" directorty is in the local file system.
# Not Run: uncomment the following line
plot(m)

## End(Not run)

Creates an 'geotop.inpts' files the keyword and their values of a date.frame like the one returned by `declared.geotop.inpts.keywords`

Description

Creates an 'geotop.inpts' files the keyword and their values of a date.frame like the one returned by declared.geotop.inpts.keywords

Usage

create.geotop.inpts.keyword(
  df,
  file = "geotop.inpts.copy",
  wpath = NULL,
  comment.lines = "default",
  header = "default",
  ...
)
create.geotop.inpts.keyword(
  df,
  file = "geotop.inpts.copy",
  wpath = NULL,
  comment.lines = "default",
  header = "default",
  ...
)

Arguments

`df`	data frame returend by `declared.geotop.inpts.keywords`
`file`	connetion or file name where to write 'df'
`wpath`	complere path to `file` (optional). Default is `NULL`.
`comment.lines`	string or vector of strings to add as comments for each keyword. If it is `NULL` the comment lines are omitted.
`header`	string or vector of strings to add as a header. If it is `NULL` the header is omitted.
`...`	further arguments for `writeLines`

Details

In case comment.lines and header are set equal to "default", they are suitably modified within the function code. See the example output.

Examples


library(geotopbricks)
## Not run: 
#Simulation working path
wpath <- 
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/panola13_run2xC_test3'
## URL path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/panola13_run2xC_test3
df <- declared.geotop.inpts.keywords(wpath=wpath)
create.geotop.inpts.keyword(df=df)

## End(Not run)


library(geotopbricks)
## Not run: 
#Simulation working path
wpath <- 
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/panola13_run2xC_test3'
## URL path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/panola13_run2xC_test3
df <- declared.geotop.inpts.keywords(wpath=wpath)
create.geotop.inpts.keyword(df=df)

## End(Not run)

Creates geotop meteo files from (a list of) 'zoo' objects

Description

Creates geotop meteo files from (a list of) 'zoo' objects

Usage

create.geotop.meteo.files(
  x,
  format = "%d/%m/%Y %H:%M",
  file_prefix = "meteo",
  file_extension = ".txt",
  formatter = "%04d",
  na = "-9999",
  col.names = TRUE,
  row.names = FALSE,
  date_field = "Date",
  sep = ",",
  level = NULL,
  quote = FALSE,
  ...
)
create.geotop.meteo.files(
  x,
  format = "%d/%m/%Y %H:%M",
  file_prefix = "meteo",
  file_extension = ".txt",
  formatter = "%04d",
  na = "-9999",
  col.names = TRUE,
  row.names = FALSE,
  date_field = "Date",
  sep = ",",
  level = NULL,
  quote = FALSE,
  ...
)

Arguments

`x`	'zoo' object or a list of 'zoo' object representing the meteorological station
`format`	string format representing the date, see `as.POSIXlt`. Default is `"%d/%m/%Y %H:%M"` (which is the same format used in `geotop.inpts` keyword `InitDateDDMMYYYYhhmm`)
`file_prefix`	string containing file prefix (full path). It correspos to the value of in `geotop.inpts` keyword `MeteoFile`)
`file_extension`	string containing the extensions of final files. Default is `c(".txt")`
`formatter`	string value. It is the decimal formatter contained in the file name and used in case the tabular data are referred at several points. Default is `"%04d"` . See `sprintf` .
`na`	NA value indicator. Default is `"-9999"`. See `write.table`.
`col.names`	logical parameter. Default is `TRUE`. See `write.table`.
`row.names`	logical parameter. Default is `FALSE`. See `write.table`.
`date_field`	string value. Default is "Date", otherwise defined by the value of `HeaderDateDDMMYYYYhhmmMeteo` geotop keyword.
`sep`	string value. Default is `","`. See `write.table`.
`level`	integer argument. See `get.geotop.inpts.keyword.value` for major details. Default is `NULL` and is ignored.
`quote`	logical parameter. Default is `TRUE`. See `write.table`.
`...`	further arguments for `write.table`

Examples


library(geotopbricks)
data(bondone) ## It contains a "meteo" zoo object.


set.seed(12)

file_prefix <- paste(tempdir(),"meteo",sep="/") 
level=2
out <- create.geotop.meteo.files(x=meteo,file_prefix=file_prefix,level=level) 
## It exports the "meteo" zoo object into a ASCII file for GEOtop
head(readLines(out))
out




library(geotopbricks)
data(bondone) ## It contains a "meteo" zoo object.


set.seed(12)

file_prefix <- paste(tempdir(),"meteo",sep="/") 
level=2
out <- create.geotop.meteo.files(x=meteo,file_prefix=file_prefix,level=level) 
## It exports the "meteo" zoo object into a ASCII file for GEOtop
head(readLines(out))
out

Collects all keywords contained in the 'getop.inpts' configuration files and their values in a data frame object.

Description

Collects all keywords contained in the 'getop.inpts' configuration files and their values in a data frame object.

Usage

declared.geotop.inpts.keywords(
  wpath,
  inpts.file = "geotop.inpts",
  comment = "!",
  exceptions = "Date",
  warn = FALSE,
  no.comment = c("!>!", "!>>!"),
  ...
)
declared.geotop.inpts.keywords(
  wpath,
  inpts.file = "geotop.inpts",
  comment = "!",
  exceptions = "Date",
  warn = FALSE,
  no.comment = c("!>!", "!>>!"),
  ...
)

Arguments

`wpath`	working directory containing GEOtop files
`inpts.file`	name of the GEOtop configuration file. Default is `"geotop.inpts"`
`comment`	comment indicator charcater. Default is `"!"`
`exceptions`	string vector. If keywords contain an element of this vector, the blank spaces in Value `" "` will not be removed.
`warn`	logical argument of `readLines`. Default is `FALSE`.
`no.comment`	string indicatos read as comment ones by GEOtop but they do not indicate comments by "geotopbricks" package.
`...`	further arguments of `readLines`

Value

a data frame with two columns: Keyword and Value

geotopbrick

Description

geotopbrick method bla bla bla

Usage

geotopbrick(x = NULL, ...)

## Default S3 method:
geotopbrick(x, ...)

## S3 method for class 'zoo'
geotopbrick(x, layer = NULL, time = NULL, crs = NULL, timerange = NULL, ...)

## S3 method for class 'RasterLayer'
geotopbrick(x, layer = NULL, time = NULL, ascpath = zoo(NULL), ...)

## S3 method for class 'RasterBrick'
geotopbrick(x, layer = NULL, time = NULL, ascpath = zoo(NULL), ...)

## S3 method for class 'GeotopRasterBrick'
geotopbrick(
  x,
  layer = NULL,
  time = NULL,
  crs = NULL,
  timerange = NULL,
  ascpath = NULL,
  ...
)
geotopbrick(x = NULL, ...)

## Default S3 method:
geotopbrick(x, ...)

## S3 method for class 'zoo'
geotopbrick(x, layer = NULL, time = NULL, crs = NULL, timerange = NULL, ...)

## S3 method for class 'RasterLayer'
geotopbrick(x, layer = NULL, time = NULL, ascpath = zoo(NULL), ...)

## S3 method for class 'RasterBrick'
geotopbrick(x, layer = NULL, time = NULL, ascpath = zoo(NULL), ...)

## S3 method for class 'GeotopRasterBrick'
geotopbrick(
  x,
  layer = NULL,
  time = NULL,
  crs = NULL,
  timerange = NULL,
  ascpath = NULL,
  ...
)

Arguments

`x`	a 'zoo' object returned by function `pointer.to.maps.xyz.time` or `pointer.to.maps.xy.time` or a `GeotopRasterBrick-class` object
`...`	further arguments.
`layer`	layer at which raster maps are imported. If is `NULL`, maps ara no-zlayer distributed and `zoo` must be returend by `pointer.to.maps.xy.time`
`time`	vector of time instants at which geotop maps are imported
`crs`	coordinate system see `RasterBrick-class`
`timerange`	two-elememts vector containing the time range at which geotop maps are imported
`ascpath`	`NULL` object or a `"zoo"` S3 object containing the names of ascii maps provided by GEOtop

Value

a GeotopRasterBrick-class

GeotopRasterBrick-class

Description

A GeotopRasterBrick: an object to manage raster maps provied by GEOtop!!

Details

ascpath:: A "zoo" S3 object containing the names of ascii maps provided by GEOtop
index:: A "POSIXt" S3 object containing time or dates on which raster layers of brick are referred
layer:: character. Name of the vertical layer at which raster map are referred
brick:: A "RasterBrick-class" S4 object containing the Raster-Layer maps imported from GEOtop output files

#' @note A GeotopRasterBrick object can be created by new("GeotopRasterBrick", ...)

Author(s)

Emanuele Cordano

Examples

showClass("GeotopRasterBrick")


 
showClass("GeotopRasterBrick")

Importing a GEOtop Keyword and its Value into R

Description

It returns the values of a keyword of "geotop.inpts" file or data frame with the suitable format.

Usage

get.geotop.inpts.keyword.value(
  keyword,
  inpts.frame = NULL,
  vector_sep = NULL,
  col_sep = ",",
  numeric = FALSE,
  format = "%d/%m/%Y %H:%M",
  date = FALSE,
  tz = "Etc/GMT-1",
  raster = FALSE,
  file_extension = ".asc",
  add_wpath = FALSE,
  wpath = NULL,
  use.read.raster.from.url = TRUE,
  data.frame = FALSE,
  formatter = "%04d",
  level = 1,
  date_field = "Date",
  isNA = -9999,
  matlab.syntax = TRUE,
  projfile = "geotop.proj",
  start_date = NULL,
  end_date = NULL,
  ContinuousRecovery = 0,
  ContinuousRecoveryFormatter = "_crec%04d",
  zlayer.formatter = NULL,
  z_unit = c("centimeters", "millimeters"),
  geotop_z_unit = "millimeters",
  add_suffix_dir = NULL,
  MAXNROW = 4,
  header.only = FALSE,
  ...
)
get.geotop.inpts.keyword.value(
  keyword,
  inpts.frame = NULL,
  vector_sep = NULL,
  col_sep = ",",
  numeric = FALSE,
  format = "%d/%m/%Y %H:%M",
  date = FALSE,
  tz = "Etc/GMT-1",
  raster = FALSE,
  file_extension = ".asc",
  add_wpath = FALSE,
  wpath = NULL,
  use.read.raster.from.url = TRUE,
  data.frame = FALSE,
  formatter = "%04d",
  level = 1,
  date_field = "Date",
  isNA = -9999,
  matlab.syntax = TRUE,
  projfile = "geotop.proj",
  start_date = NULL,
  end_date = NULL,
  ContinuousRecovery = 0,
  ContinuousRecoveryFormatter = "_crec%04d",
  zlayer.formatter = NULL,
  z_unit = c("centimeters", "millimeters"),
  geotop_z_unit = "millimeters",
  add_suffix_dir = NULL,
  MAXNROW = 4,
  header.only = FALSE,
  ...
)

Arguments

`keyword`	keyword name
`inpts.frame`	data frame returned by `declared.geotop.inpts.keywords` or `NULL`. Default is `NULL`.
`vector_sep`	character value for the separator character if Keyword Value must be returned as a vector, otherwise it is `NULL`. Default is `NULL`, but if `numeric` or `date` are `FALSE`, `vector_sep` is set `","` by default.
`col_sep`	character value for the separator character of columuns. It is used if Keyword Value is returned as a data frema or zoo object or list of these objects. Default is `NULL`, but is set `","`.
`numeric`	logical value. If `TRUE` the Value has numeric type, otherwise it is a string or string vector. Default is `FALSE`.
`format`	string format representing the date, see `as.POSIXlt`, used if `date` is `TRUE`. Default is `"%d/%m/%Y %H:%M"` (which is the format used in `geotop.inpts` keyword `InitDateDDMMYYYYhhmm`)
`date`	logical value. If `TRUE` the Value is retured as `POSIXlt` date, otherwise it is a string or string vector. Default is `FALSE`.
`tz`	format string representing the time zone, see `as.POSIXlt`, used if `date` is `TRUE`. Default is `"Etc/GMT-1"` (until the previous version it was `"A"`) which meens UTC +1.
`raster`	logical value. Default is `FALSE`. If `TRUE` function returns direclty the raster map as `Raster-class` object built with `raster` method.
`file_extension`	Extension to be added to the keyword if keyword is a file name. Default is `".asc"`
`add_wpath`	logical value. Default is `FALSE`. If `TRUE`, the `wpath` string is attached to the keyword string value. It is automatically set `TRUE` if `raster` is `TRUE`.
`wpath`	working directory containing GEOtop files (included the inpts file). It is mandatory if `raster` is `TRUE`. See `declared.geotop.inpts.keywords`.
`use.read.raster.from.url`	logical value. Default is `TRUE`. If `TRUE` the RasterLayer are read with `read.raster.from.url`, istead of `raster` (otherwise). It is recomended in case the files whose paths are contained in `x` are remote and are 'http' addresses. In this cases the stand-alone method `raster(x)` does not always work and `use.read.raster.from.url` is necessary.
`data.frame`	logical value. It is an option for tabular data. If `TRUE` function returns direclty a data frame or a list of data frames as `data.frame` or `zoo` objects imported from the keyword-related files using `read.table` function. In this case the argument `wpath` (see `declared.geotop.inpts.keywords`) is mandatory. Default is `FALSE`.
`formatter`	string value. It is the decimal formatter contained in the file name and used in case the tabular data are referred at several points. Default is `"%04d"` . It is used in case `data.frame` is `TRUE`.
`level`	integer values. Numbers incating all the identandification numbers of the files containing the requested data frames. Default is 1, correspondig to the decimal formatter `"0001"`. See examples.
`date_field`	string value. Default is "Date", otherwise defined by the value of `HeaderDateDDMMYYYYhhmmMeteo` geotop keyword. It is used only if the argument `data.frame` is `TRUE`. If it is `NULL` or `NA` the function return a list of generic `data.frame` object(s), otherwise `link{zoo}` object(s). See the arguments `tz` and `format` for Date formatting.
`isNA`	numeric value indicating NA in geotop ascii files. Default is -9999.00
`matlab.syntax`	logical value. Default is `FALSE`. If `TRUE` a vector is written in a string according to *.m file syntax. Warning: this synstax is not read by GEOtop.
`projfile`	fileneme of the GEOtop projection file. Default is `geotop.proj`.
`start_date`, `end_date`	null objects or dates in `POSIXlt` format between which the variables are returned. It is enabled in case that `date_field` is not `NULL` or `NA` and `data.frame` is `TRUE`. Default is `NULL`.
`ContinuousRecovery`	integer value. Default is 0. It is used for tabular output data and is the number of times GEOtop simulation broke during its running and was re-launched with 'Contiuous Recovery' option.
`ContinuousRecoveryFormatter`	character string. Default is `'_crec%04d'`. It is used only for tabular output data and if `ContinuousRecovery` is equal or greater than 1.
`zlayer.formatter`	decimal formatter. It is used if `data.frame==TRUE` and the columns refers to different soil depths. Default is `NULL`.
`z_unit`	z coordinate measurement unit. GEOtop values expressed in millimeters which are converted to centimeters by default. Default is `c("centimeters","millimeters")`. Otherwise can be the ratio between the unit and one meter. It is used if `zlayer.formatter=="z%04d"` or similar.
`geotop_z_unit`	z coordinate measurement unit used by GEOtop. Default is `millimeters`. It is used if `zlayer.formatter=="z%04d"` or similar.
`add_suffix_dir`	character string. Add a suffix at the directory reported in the keyword value
`MAXNROW`	maximum number accepted for `data.frema` output. Default is 4. It is used in case of `data.frame==TRUE`. In case the number of records in the function output is less than `MAXNROW` , function returns neither `data.frame` nor `zoo` objects but only the keyword value.
`header.only`	logical value. Default is `FALSE`. If it is `TRUE` and `data.frame==TRUE`, only file hedaer with variable names is returned by the function.
`...`	further arguments of `declared.geotop.inpts.keywords`

Value

the keyword value

Note

If inpts.frame is NULL, inpts.frame will be obtained by calling the function declared.geotop.inpts.keywords with ... arguments.

Examples


library(geotopbricks)

#Simulation working path
 


wpath <- 
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/panola13_run2xC_test3'
## URL path (RAW VERSION) of
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/panola13_run2xC_test3
prefix <- get.geotop.inpts.keyword.value("SoilLiqWaterPressTensorFile",wpath=wpath)

slope <- get.geotop.inpts.keyword.value("SlopeMapFile",raster=TRUE,wpath=wpath) 
bedrock_depth <- get.geotop.inpts.keyword.value("BedrockDepthMapFile",raster=TRUE,wpath=wpath) 

layers <- get.geotop.inpts.keyword.value("SoilLayerThicknesses",numeric=TRUE,wpath=wpath)
names(layers) <- paste("L",1:length(layers),sep="")

##### set van genuchten parameters to estimate water volume 
theta_sat <- get.geotop.inpts.keyword.value("ThetaSat",numeric=TRUE,wpath=wpath)
theta_res <- get.geotop.inpts.keyword.value("ThetaRes",numeric=TRUE,wpath=wpath)
alphaVG <-  get.geotop.inpts.keyword.value("AlphaVanGenuchten",
numeric=TRUE,wpath=wpath) # expressed in mm^-1

nVG <-  get.geotop.inpts.keyword.value("NVanGenuchten",numeric=TRUE,wpath=wpath) 


##### end set van genuchten parameters to estimate water volume


##### set meteo data


tz <- "Etc/GMT-1"  ## See help(timezones) In particular:
## Most platforms support time zones of the form Etc/GMT+n 
## and Etc/GMT-n (possibly also without prefix Etc/), 
## which assume a fixed offset from UTC (hence no DST). 
## Contrary to some expectations 
## (but consistent with names such as PST8PDT), negative offsets are times ahead of (east of) UTC, 
## positive offsets are times behind (west of) UTC.
start <-  get.geotop.inpts.keyword.value("InitDateDDMMYYYYhhmm",
date=TRUE,wpath=wpath,tz=tz) 
end <- get.geotop.inpts.keyword.value("EndDateDDMMYYYYhhmm",
date=TRUE,wpath=wpath,tz=tz) 

nmeteo <- get.geotop.inpts.keyword.value("NumberOfMeteoStations",
numeric=TRUE,wpath=wpath)
level <- 1:nmeteo

## set meteo data

 meteo <- get.geotop.inpts.keyword.value("MeteoFile",wpath=wpath,data.frame=TRUE,
       level=level,start_date=start,end_date=end,tz=tz)


##### end set meteo data

## IMPORTING AN OUTPUT SOIL MOISTURE PROFILE: 


wpath <-  paste0(
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/',
'master/simulations/Muntatschini_pnt_1_225_B2_004')
## URL Path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/Muntatschini_pnt_1_225_B2_004

	SMC  <- get.geotop.inpts.keyword.value("SoilLiqContentProfileFile",
          wpath=wpath,data.frame=TRUE,date_field="Date12.DDMMYYYYhhmm.",
          formatter="%04d")

    SMCz  <- get.geotop.inpts.keyword.value("SoilLiqContentProfileFile",
         wpath=wpath,data.frame=TRUE,date_field="Date12.DDMMYYYYhhmm.",
          formatter="%04d",zlayer.formatter="z%04d")



		




library(geotopbricks)

#Simulation working path
 


wpath <- 
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/panola13_run2xC_test3'
## URL path (RAW VERSION) of
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/panola13_run2xC_test3
prefix <- get.geotop.inpts.keyword.value("SoilLiqWaterPressTensorFile",wpath=wpath)

slope <- get.geotop.inpts.keyword.value("SlopeMapFile",raster=TRUE,wpath=wpath) 
bedrock_depth <- get.geotop.inpts.keyword.value("BedrockDepthMapFile",raster=TRUE,wpath=wpath) 

layers <- get.geotop.inpts.keyword.value("SoilLayerThicknesses",numeric=TRUE,wpath=wpath)
names(layers) <- paste("L",1:length(layers),sep="")

##### set van genuchten parameters to estimate water volume 
theta_sat <- get.geotop.inpts.keyword.value("ThetaSat",numeric=TRUE,wpath=wpath)
theta_res <- get.geotop.inpts.keyword.value("ThetaRes",numeric=TRUE,wpath=wpath)
alphaVG <-  get.geotop.inpts.keyword.value("AlphaVanGenuchten",
numeric=TRUE,wpath=wpath) # expressed in mm^-1

nVG <-  get.geotop.inpts.keyword.value("NVanGenuchten",numeric=TRUE,wpath=wpath) 


##### end set van genuchten parameters to estimate water volume


##### set meteo data


tz <- "Etc/GMT-1"  ## See help(timezones) In particular:
## Most platforms support time zones of the form Etc/GMT+n 
## and Etc/GMT-n (possibly also without prefix Etc/), 
## which assume a fixed offset from UTC (hence no DST). 
## Contrary to some expectations 
## (but consistent with names such as PST8PDT), negative offsets are times ahead of (east of) UTC, 
## positive offsets are times behind (west of) UTC.
start <-  get.geotop.inpts.keyword.value("InitDateDDMMYYYYhhmm",
date=TRUE,wpath=wpath,tz=tz) 
end <- get.geotop.inpts.keyword.value("EndDateDDMMYYYYhhmm",
date=TRUE,wpath=wpath,tz=tz) 

nmeteo <- get.geotop.inpts.keyword.value("NumberOfMeteoStations",
numeric=TRUE,wpath=wpath)
level <- 1:nmeteo

## set meteo data

 meteo <- get.geotop.inpts.keyword.value("MeteoFile",wpath=wpath,data.frame=TRUE,
       level=level,start_date=start,end_date=end,tz=tz)


##### end set meteo data

## IMPORTING AN OUTPUT SOIL MOISTURE PROFILE: 


wpath <-  paste0(
'https://raw.githubusercontent.com/ecor/geotopbricks_doc/',
'master/simulations/Muntatschini_pnt_1_225_B2_004')
## URL Path (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/Muntatschini_pnt_1_225_B2_004

	SMC  <- get.geotop.inpts.keyword.value("SoilLiqContentProfileFile",
          wpath=wpath,data.frame=TRUE,date_field="Date12.DDMMYYYYhhmm.",
          formatter="%04d")

    SMCz  <- get.geotop.inpts.keyword.value("SoilLiqContentProfileFile",
         wpath=wpath,data.frame=TRUE,date_field="Date12.DDMMYYYYhhmm.",
          formatter="%04d",zlayer.formatter="z%04d")

Get a `sf` object for Meteorological Stations or Control Points in a GEOtop simulation

Description

Get a sf object for Meteorological Stations or Control Points in a GEOtop simulation

Usage

get.geotop.points(
  prefix = c("MeteoStation", "CoordinatePoint"),
  suffixes = c("Code", "Elevation", "Source"),
  coord_suffixes = list(MeteoStation = c("CoordinateX", "CoordinateY"), CoordinatePoint =
    c("X", "Y")),
  wpath,
  ...,
  vector_sep = ","
)
get.geotop.points(
  prefix = c("MeteoStation", "CoordinatePoint"),
  suffixes = c("Code", "Elevation", "Source"),
  coord_suffixes = list(MeteoStation = c("CoordinateX", "CoordinateY"), CoordinatePoint =
    c("X", "Y")),
  wpath,
  ...,
  vector_sep = ","
)

Arguments

`prefix`	keyword prefix
`suffixes`	keyword suffixes
`coord_suffixes`	coordinate keyword suffixes. Default is `c("PointX","PointY")`
`wpath`	GEOtop simulation path
`vector_sep`, `...`	further arguments for `get.geotop.inpts.keyword.value`

Examples



###See simulation template: "https://github.com/ecor/geotopbricks_doc/tree/master/template/sumava"
wpath <- "https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/template/sumava/"
## system.file("template/sumava",package="geotopbricks") 
out <- get.geotop.points(wpath=wpath)
out <- get.geotop.points(prefix="CoordinatePoint",suffix=c("Code","Source"),wpath=wpath)
out <- get.geotop.points(prefix="MeteoStation",suffix=c("Code","Source"),wpath=wpath)


###See simulation template: "https://github.com/ecor/geotopbricks_doc/tree/master/template/sumava"
wpath <- "https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/template/sumava/"
## system.file("template/sumava",package="geotopbricks") 
out <- get.geotop.points(wpath=wpath)
out <- get.geotop.points(prefix="CoordinatePoint",suffix=c("Code","Source"),wpath=wpath)
out <- get.geotop.points(prefix="MeteoStation",suffix=c("Code","Source"),wpath=wpath)

This function saves all spatially distrubuted information contained in the recovery folder into a comprehensive `list` object.

Description

This function saves all spatially distrubuted information contained in the recovery folder into a comprehensive list object.

Usage

get.geotop.recovery.state(
  recFolder,
  xx = "0000",
  formatter = "L%04d",
  extension = ".asc",
  nsoillayers = 10,
  layersFromDir = FALSE,
  ...
)
get.geotop.recovery.state(
  recFolder,
  xx = "0000",
  formatter = "L%04d",
  extension = ".asc",
  nsoillayers = 10,
  layersFromDir = FALSE,
  ...
)

Arguments

`recFolder`	directory when recvery maps are set. In GEOtop it is ...
`xx`	charcter String. Default is `"0000"`
`formatter`	string character for the the decimal formatter to be used. Default is `"L%04d"`.
`extension`	file estension used for asccii recovery map files. It must contains `'.'` as the first character. Defaut is `".asc"` .
`nsoillayers`	number of soil layers used in the GEOtop simulation.
`layersFromDir`	logical value. If is `TRUE` the number of soil/snow (vertical) layers used in the GEOtop simulation is automatically calculated and cannot be assigned through `nsoillayers`.
`...`	further arguments

Value

a list object containining all recovery raster maps.

Note

This function has been used with the built 1.225-9 of GEOtop .

Author(s)

Emanuele Cordano

Examples

library(geotopbricks)
example_Rscript <- system.file('template/example.geotop.recovery.state.R',package="geotopbricks")
example_Rscript

# Not Run because it elapses too long time!!! 
# Please Uncomment the following line to run by yourself!!!
# source(example_Rscript)

library(geotopbricks)
example_Rscript <- system.file('template/example.geotop.recovery.state.R',package="geotopbricks")
example_Rscript

# Not Run because it elapses too long time!!! 
# Please Uncomment the following line to run by yourself!!!
# source(example_Rscript)

It reads the CRS metadata utilzed in a GEOtop Simulation

Description

It reads the CRS metadata utilzed in a GEOtop Simulation

Usage

getProjection(x, cond = TRUE, ...)
getProjection(x, cond = TRUE, ...)

Arguments

`x`	name and full path of the file containimg CRS information
`cond`	logical value. If `FALSE` the function returns `NA`. Default is `TRUE`.
`...`	futher arguments

Value

A string corresponding the projection and CRS if the argument cond is TRUE.

Examples

library(geotopbricks)

wpath <- 'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/idroclim_test1'
## URL path  (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/idroclim_test1
## Not run: 

x <- paste(wpath,"geotop.proj",sep="/")


crs <- getProjection(x)

## End(Not run)
library(geotopbricks)

wpath <- 'https://raw.githubusercontent.com/ecor/geotopbricks_doc/master/simulations/idroclim_test1'
## URL path  (RAW VERSION) of 
## https://github.com/ecor/geotopbricks_doc/tree/master/simulations/idroclim_test1
## Not run: 

x <- paste(wpath,"geotop.proj",sep="/")


crs <- getProjection(x)

## End(Not run)

Interpolates the values of a 'brick' at a certain depth and returns the map of brick values at the "depth" level

Description

Interpolates the values of a 'brick' at a certain depth and returns the map of brick values at the "depth" level

Usage

getvalues.brick.at.depth(x, depth, layers, i0 = NULL, verify = FALSE, ...)
getvalues.brick.at.depth(x, depth, layers, i0 = NULL, verify = FALSE, ...)

Arguments

`x`	a 'RasterBrick' or a three-dimensional array
`depth`	depth map, generally a 'RasterLayer' object
`layers`	vector of layer thickness
`i0`	a 'Raster' containing the number of soil laver just over the bedrock. Default is `NULL` and is then calculated.
`verify`	logical. Default is `FALSE`. If it is `TRUE`, it verifies that function is working correctly.
`...`	further argument

Value

a list of 'Raster' maps:

i0 a 'Raster' containing the number of soil laver just over the bedrock

val_z0 a 'Raster' containing the values of x at the i0-th layer

val_z1 a 'Raster' containing the values of x at the (i0+1)-th layer

z0 a 'Raster' containing the depth of the center of the i0-th layer

z1 a 'Raster' containing the depth of the center of the (i0+1)-th layer

Note

x and depth or i0 must cover the same spatial region.

Examples


library(geotopbricks)
# The examples is the following R script conteined in a 'inst' directory of the package source
f <- system.file("doc/examples/example.getvalues.brick.at.depth.R",package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation
library(geotopbricks)
# The examples is the following R script conteined in a 'inst' directory of the package source
f <- system.file("doc/examples/example.getvalues.brick.at.depth.R",package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation

KML

Description

KML method for a GeotopRasterBrick object

Usage

## S4 method for signature 'GeotopRasterBrick'
KML(
  x,
  filename,
  crs = as.character("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"),
  ...
)
## S4 method for signature 'GeotopRasterBrick'
KML(
  x,
  filename,
  crs = as.character("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"),
  ...
)

Arguments

`x`	the `GeotopRasterBrick` object
`filename`	mane of the KML file to produce
`crs`	character string containing the LatLon reference system. Default is `"+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"` (see https://spatialreference.org/ref/epsg/4326/).
`...`	further argument for S4 method `KLM` for Raster object.

Note

A coordinate transformation is made with projectRaster.

Examples



library(geotopbricks)
# The examples is the following R script contained in a 'inst' directory of the package source
f <- system.file("doc/examples/example.KML.GeotopRasterBrick.R",package="geotopbricks")
## Not run: 
  source(f) # Uncomment this line to run the example. 

## End(Not run) 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation
library(geotopbricks)
# The examples is the following R script contained in a 'inst' directory of the package source
f <- system.file("doc/examples/example.KML.GeotopRasterBrick.R",package="geotopbricks")
## Not run: 
  source(f) # Uncomment this line to run the example. 

## End(Not run) 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation

max_value

Description

Gets the maximum (scalar) values of a GeotopRasterBrick object

Usage

max_value(x, na.rm = TRUE, ...)
max_value(x, na.rm = TRUE, ...)

Arguments

`x`	a `GeotopRasterBrick` object.
`na.rm`, `...`	further arguments for `max`.

Value

the maximum (scalar) values of a GeotopRasterBrick object

min_value

Description

Gets the minimum (scalar) values of a GeotopRasterBrick object

Usage

min_value(x, na.rm = TRUE, ...)
min_value(x, na.rm = TRUE, ...)

Arguments

`x`	a `GeotopRasterBrick` object.
`na.rm`, `...`	further arguments foe `min`.

Value

the minimum (scalar) values of a GeotopRasterBrick object

Ops

Description

Ops

Usage

## S4 method for signature 'GeotopRasterBrick,GeotopRasterBrick'
Ops(e1, e2)

## S4 method for signature 'GeotopRasterBrick,numeric'
Ops(e1, e2)

## S4 method for signature 'numeric,GeotopRasterBrick'
Ops(e1, e2)
## S4 method for signature 'GeotopRasterBrick,GeotopRasterBrick'
Ops(e1, e2)

## S4 method for signature 'GeotopRasterBrick,numeric'
Ops(e1, e2)

## S4 method for signature 'numeric,GeotopRasterBrick'
Ops(e1, e2)

Arguments

e1, e2

the GeotopRasterBrick or numeric objects

Details

Ops method for a GeotopRasterBrick object

Note

If e1 or e2 time index is not taken into account.

plot

Description

plot method for a GeotopRasterBrick object

Usage

## S4 method for signature 'GeotopRasterBrick,ANY'
plot(x, y = NULL, ...)
## S4 method for signature 'GeotopRasterBrick,ANY'
plot(x, y = NULL, ...)

Arguments

`x`	the `GeotopRasterBrick` object
`y`	further argument
`...`	further argument for S4 method `plot` for Raster object.

Examples



library(geotopbricks)
# The examples is the following R script conteined in a 'inst' directory of the package source
f <- system.file("doc/examples/example.plot.GeotopRasterBrick.R",package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation







library(geotopbricks)
# The examples is the following R script conteined in a 'inst' directory of the package source
f <- system.file("doc/examples/example.plot.GeotopRasterBrick.R",package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation

pointer.to.maps.xyz.time

Description

'pointer.to.maps.xyz.time' function (obsolete)

Usage

pointer.to.maps.xyz.time(
  wpath,
  map.prefix = "thetaliq",
  suffix = "L%04dN%04d.asc",
  zoo.index = NULL,
  ntime,
  nlayers
)
pointer.to.maps.xyz.time(
  wpath,
  map.prefix = "thetaliq",
  suffix = "L%04dN%04d.asc",
  zoo.index = NULL,
  ntime,
  nlayers
)

Arguments

`wpath`	complete working path to *.asc maps are saved
`map.prefix`	string prefix name map before
`suffix`	z-time or time suffix plus file extention character string. Default for GEOtop application is `"L%04dN%04d.asc"` for xy+z+time maps or `"N%04d.asc"` for xy+time maps.
`zoo.index`	time or date index. Default is `NULL` , otherwise function returns a zoo object with `zoo.index` as index.
`ntime`	number of time instant. If `zoo.index` is not `NULL`, it is calculated from `zoo.index` length.
`nlayers`	number of vertical layers.

Value

A data.frame or zoo object containig the paths to maps fpr each time and z layer.

Author(s)

Emanuele Cordano

Read a text file containing values and matedata of a z-layer brick referred to a time instant (e.g. date). The file is formatted like an ascii format like `'geotop.inpts'` file.

Description

Read a text file containing values and matedata of a z-layer brick referred to a time instant (e.g. date). The file is formatted like an ascii format like 'geotop.inpts' file.

Usage

read.ascii.vectorized.brick(
  file = NULL,
  comment = "!",
  crs = "",
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)
read.ascii.vectorized.brick(
  file = NULL,
  comment = "!",
  crs = "",
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)

Arguments

`file`	file name to write
`comment`	character. Comment indicator. Default is `"!"`.
`crs`	Character or object of class CRS. PROJ4 type description of a Coordinate Reference System (map projection) (optional). See `brick` or `raster`.
`NAflag`	numeric. Dafauli is -9999, see `writeRasterxGEOtop`.
`matlab.syntax`	logical value. Default is `FALSE`. If `TRUE` the file syntax is like the one of a *.m Matlab script file.
`...`	further aguments inserted as attribute

Value

the RasterBrick-class object

Examples

# see the examples of read.ascii.vectorized.brick
# see the examples of read.ascii.vectorized.brick

It imports a 'RasterLayer' object in Escri-Asci format from a URL 'http(s)://....<FILENAME>.asc

Description

It imports a 'RasterLayer' object in Escri-Asci format from a URL 'http(s)://....<FILENAME>.asc

Usage

read.raster.from.url(x, header_nrow = 6, ...)
read.raster.from.url(x, header_nrow = 6, ...)

Arguments

`x`	the charcater string containing the URL address
`header_nrow`	Number of header in the ASCII grid format. Deafault is 6. See https://en.wikipedia.org/wiki/Esri_grid
`...`	additional arguments

Value

a 'RasterLayer' object

Note

This function reads a local or remote text files formatted as https://en.wikipedia.org/wiki/Esri_grid and creates a 'RasterLayer' object.

Reads a text file like the one generated by `write.vectorized.geotop.recovery`

Description

#. containing values and matedata of a z-layer brick referred to a time instant (e.g. date). The file is formatted like an ascii format like 'geotop.inpts' file.

Usage

read.vectorized.geotop.recovery(
  file = file,
  comment = "!",
  matlab.syntax = TRUE,
  xx = "0000",
  formatter = "L%04d",
  extension = ".asc",
  NAflag = -9999,
  crs = "",
  ...
)
read.vectorized.geotop.recovery(
  file = file,
  comment = "!",
  matlab.syntax = TRUE,
  xx = "0000",
  formatter = "L%04d",
  extension = ".asc",
  NAflag = -9999,
  crs = "",
  ...
)

Arguments

`file`	file name to write
`comment`	character. Comment indicator. Default is `"!"`.
`matlab.syntax`	logical value. Default is `TRUE`. If `TRUE` the file syntax is like the one of a *.m Matlab script file.
`formatter`, `extension`, `xx`	see `get.geotop.recovery.state`.
`NAflag`	numeric. Default is -9999, see `writeRasterxGEOtop`.
`crs`	Character or object of class CRS. PROJ4 type description of a Coordinate Reference System (map projection) (optional). See `brick` or `raster`.
`...`	further aguments inserted as attribute

Value

a list object like get.geotop.recovery.state

Examples

# see the examples of read.ascii.vectorized.brick
# see the examples of read.ascii.vectorized.brick

It replaces some keyword values of `geotop.inpts` file with the ones of anoter `*.inpts` value

Description

It replaces some keyword values of geotop.inpts file with the ones of anoter *.inpts value

Usage

replace.keyword(
  x,
  y = "geotop.inpts",
  file.output = NULL,
  write.file.output = TRUE,
  wpath = NULL,
  ...
)
replace.keyword(
  x,
  y = "geotop.inpts",
  file.output = NULL,
  write.file.output = TRUE,
  wpath = NULL,
  ...
)

Arguments

`x`	filename of the `*.inpts` with the "new" keyword value
`y`	filename of the `*.inpts` with the "old" keyword value. Default is `"geotop.inpts"`.
`file.output`	filename where to write the comprehensive new `geotop.inpts` file. If it is `NULL` (default), the fileneme is assigned by `y`.
`write.file.output`	logical value. If it is `TRUE`, the output of the function is written in he file `file.output`.
`wpath`	working path to the GEOtop simulation folder containing the `x` and `y` files.
`...`	further arguments

Details

This function repleces some keword values of y with the ones indicated in y. It is useful to replace the meteo station metedata, for instance, when the meteorological station of a study cases are modified. The function returns the new geotop.inpts file as a vector of character strings. If write.file.output==TRUE, the output is written in an extarnal file, e.g. "geotop.inpts" newly (this option is suggested).

Author(s)

Emanuele Cordano

Examples


library(geotopbricks)
wpath <- system.file('template/meteo_ex',package="geotopbricks")
x <- "meteo.inpts"
zl <- replace.keyword(x,wpath=wpath,write.file.output=FALSE)



library(geotopbricks)
wpath <- system.file('template/meteo_ex',package="geotopbricks")
x <- "meteo.inpts"
zl <- replace.keyword(x,wpath=wpath,write.file.output=FALSE)

This function re-writes the recovery ascii raster maps in a given folder

Description

This function re-writes the recovery ascii raster maps in a given folder

Usage

set.geotop.recovery.state(rec, newRecFolder, ...)
set.geotop.recovery.state(rec, newRecFolder, ...)

Arguments

`rec`	a `list` object returened by `get.geotop.recovery.state`
`newRecFolder`	directory where to write all recovery raster asccii maps
`...`	further arguments

Author(s)

Emanuele Cordano

Examples

# See the examples of the 'get.geotop.recovery.state' function
# See the examples of the 'get.geotop.recovery.state' function

Aggregates with a mean or an addition on the vertical profile the values of a 'brick' within a certain depth and returns the vertical aggregated map

Description

Aggregates with a mean or an addition on the vertical profile the values of a 'brick' within a certain depth and returns the vertical aggregated map

Usage

vertical.aggregate.brick.within.depth(
  x,
  depth = NULL,
  layers = NULL,
  i0 = NULL,
  verify = FALSE,
  FUN = identity,
  divide.by.depth = FALSE,
  ...
)
vertical.aggregate.brick.within.depth(
  x,
  depth = NULL,
  layers = NULL,
  i0 = NULL,
  verify = FALSE,
  FUN = identity,
  divide.by.depth = FALSE,
  ...
)

Arguments

`x`	a 'RasterBrick' or a three-dimensional array
`depth`	depth map, generally a 'RasterLayer' object
`layers`	vector of layer thickness
`i0`	a 'Raster' containing the number of soil laver just over the bedrock. Default is `NULL` and is then calculated.
`verify`	logical. Default is `FALSE`. If it is `TRUE`, it verifies that function is working correctly.
`FUN`	function used for aggregation. If missing, `identity` is the default value.
`divide.by.depth`	logical. If `TRUE` the function returns the 'mean' value, otherwise a a cumulate value. Default is `FALSE`.
`...`	further argument for `FUN`

Value

a list of 'Raster' maps:

i0 a 'Raster' containing the number of soil laver just over the bedrock

z0 a 'Raster' containing the depth of the center of the i0-th layer

result a 'Raster' containing the aggregated map

Note

x and depth or i0 must cover the same spatial region.

Examples


library(geotopbricks)
# The examples is the following R script conteined 
# in a 'inst' directory of the package source
f <- system.file("doc/examples/example.vertical.aggregate.brick.within.depth.R",
package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation







library(geotopbricks)
# The examples is the following R script conteined 
# in a 'inst' directory of the package source
f <- system.file("doc/examples/example.vertical.aggregate.brick.within.depth.R",
package="geotopbricks")
#  source(f) # Uncomment this line to run the example. 
# You can copy the example file using file.copy(from=f,to=....,...) See file.copy documentation

Writes a z-layer brick referred to a time instant (e.g. date) in an ascii format like `'geotop.inpts'` file.

Description

Writes a z-layer brick referred to a time instant (e.g. date) in an ascii format like 'geotop.inpts' file.

Usage

write.ascii.vectorized.brick(
  b,
  file = NULL,
  header = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)
write.ascii.vectorized.brick(
  b,
  file = NULL,
  header = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)

Arguments

`b`	a `RasterBrick-class` or `GeotopRasterBrick-class` object
`file`	file name to write
`header`	character string vector for header text lines. If missing, a default header is written. #Default is `c("! header")`.
`overwrite`	logical. Default is `TRUE`, see `writeRaster`.
`NAflag`	numeric. Default is -9999, see `writeRasterxGEOtop`.
`matlab.syntax`	logical value. Default is `FALSE`. If `TRUE` the file syntax is like the one of a *.m Matlab script file.
`...`	further aguments inserted as attribute

Value

the string vector possibly written in file.

Note

Add Quote if necessary. This function is NOT maintained and will be DEPRECATED.

Examples

## Not Run
## library(geotopbricks)
## library(raster)
## file <- system.file("doc/examples/snowthickness",package="geotopbricks")
## file <- paste(file,"SnowThickness0000L%04d.asc",sep="/")
## b <- brick.decimal.formatter(file=file,nlayers=15)
## nlayers(b)
## names(b)
## file <- "snow.txt"
## btext <- write.ascii.vectorized.brick(b,Date="1/1/2009",file="snow.txt")
## The printed object
## str(btext)
## bb <- read.ascii.vectorized.brick(file = file) 
## bf <- abs(as.matrix(bb[[1]]-b[[1]]))<.Machine$double.eps^0.5
## Not Run
## library(geotopbricks)
## library(raster)
## file <- system.file("doc/examples/snowthickness",package="geotopbricks")
## file <- paste(file,"SnowThickness0000L%04d.asc",sep="/")
## b <- brick.decimal.formatter(file=file,nlayers=15)
## nlayers(b)
## names(b)
## file <- "snow.txt"
## btext <- write.ascii.vectorized.brick(b,Date="1/1/2009",file="snow.txt")
## The printed object
## str(btext)
## bb <- read.ascii.vectorized.brick(file = file) 
## bf <- abs(as.matrix(bb[[1]]-b[[1]]))<.Machine$double.eps^0.5

Writes an R object (`data.frame` or `zoo`) into a CSV file readible by GEOtop.

Description

Writes an R object (data.frame or zoo) into a CSV file readible by GEOtop.

Usage

write.geotop.table(
  x,
  file,
  wpath = NULL,
  tz = "Etc/GMT-1",
  date_field = "Date12.DDMMYYYYhhmm.",
  file_end = "",
  sep = ",",
  format = "%d/%m/%Y %H:%M",
  na = "-9999",
  ...
)
write.geotop.table(
  x,
  file,
  wpath = NULL,
  tz = "Etc/GMT-1",
  date_field = "Date12.DDMMYYYYhhmm.",
  file_end = "",
  sep = ",",
  format = "%d/%m/%Y %H:%M",
  na = "-9999",
  ...
)

Arguments

`x`	R object (`data.frame` or `zoo`) to be exported and written.
`file`	filename
`wpath`	working path to the GEOtop simlation. If `wpath` is not `NULL` , `filename` will be put in `wpath`.
`tz`	time zone. Default is `"Etc/GMT-1"`. See `get.geotop.inpts.keyword.value` fur further details.
`date_field`	string used for date-time field. Deafult is `"Date12.DDMMYYYYhhmm."`. See `get.geotop.inpts.keyword.value` fur further details.
`file_end`	suffix of the file name (`file`) (optional). Default is `""`.
`sep`	separator character. Default is `","`. See `write.table` fur further details.
`format`	date time format. Default is `"%d/%m/%Y %H:%M"`. See `get.geotop.inpts.keyword.value` fur further details.
`na`	string for unassigned values. Defaults is `"-9999"`. See `write.table` fur further details.
`...`	further arguments for `write.table`.

It writes a `list` object returened by `get.geotop.recovery.state` as a string vector or in a text file, following `*.inpts` or Matlab-like syntax.

Description

It writes a list object returened by get.geotop.recovery.state as a string vector or in a text file, following *.inpts or Matlab-like syntax.

Usage

write.vectorized.geotop.recovery(
  rec,
  file = NULL,
  header = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  matlab.syntax = TRUE,
  ...
)
write.vectorized.geotop.recovery(
  rec,
  file = NULL,
  header = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  matlab.syntax = TRUE,
  ...
)

Arguments

`rec`	a `list` object returened by `get.geotop.recovery.state`
`file`	ascii text file name whrere to write the string vector
`header`	character string vector for header text lines. If missing, a default header is written. Default is `c("! header")` or he one assigned by `matlab.syntax`.
`overwrite`	logical. Default is `TRUE`, see `writeRaster`.
`NAflag`	numeric. Default is -9999, see `writeRasterxGEOtop`.
`matlab.syntax`	logical value. Default is `TRUE`. If `TRUE` the file syntax is like the one of a *.m Matlab script file.
`...`	further aguments inserted as attribute

Value

a string vector containg the rec variables.

Note

Add Quote if necessary

Examples

# See the examples of the 'get.geotop.recovery.state' function



# See the examples of the 'get.geotop.recovery.state' function

Writes one or more variables (scalars, vectors or Rasters) in a string each, following `*.inpts` or Matlab-like syntax.

Description

Writes one or more variables (scalars, vectors or Rasters) in a string each, following *.inpts or Matlab-like syntax.

Usage

write.vectorized.variable.in.string(
  l,
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)
write.vectorized.variable.in.string(
  l,
  NAflag = -9999,
  matlab.syntax = FALSE,
  ...
)

Arguments

`l`	a `list` object contained the variables (scalars, vectors or Rasters) which will be written in a string each.
`NAflag`	numeric. Default is -9999, see `writeRasterxGEOtop`.
`matlab.syntax`	logical value. Default is `FALSE`. If `TRUE` the file syntax is like the one of a *.m Matlab script file.
`...`	further aguments

Value

the string vector <NAME_VARIABLE>==<VALUES_VARIABLE>.

Note

Add Quote if necessary

Examples

a <- 1:5
l <- list(v=a,a=a)
out <- write.vectorized.variable.in.string(l,matlab.syntax=TRUE)
out 


a <- 1:5
l <- list(v=a,a=a)
out <- write.vectorized.variable.in.string(l,matlab.syntax=TRUE)
out

This function uses `writeRaster` to create .asc maps which can be read by GEOtop

Description

This function uses writeRaster to create .asc maps which can be read by GEOtop

Usage

writeRasterxGEOtop(
  x,
  filename = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  use.decimal.formatter = FALSE,
  start.from.zero = FALSE,
  keyword,
  wpath,
  suffix.ext = ".asc",
  ...
)
writeRasterxGEOtop(
  x,
  filename = NULL,
  overwrite = TRUE,
  NAflag = -9999,
  use.decimal.formatter = FALSE,
  start.from.zero = FALSE,
  keyword,
  wpath,
  suffix.ext = ".asc",
  ...
)

Arguments

`x`	a Raster object, see `writeRaster`. It can be also a `RasterBrick-class` object.
`filename`	see `writeRaster`. It is a vector of string or one string containing a decimal formatter (see `brick.decimal.formatter`) in case `x` is a `RasterBrick-class` object.
`overwrite`	logical. Default is `TRUE`, see `writeRaster`.
`NAflag`	numeric. Dafauli is -9999, see `writeRaster`.
`use.decimal.formatter`	logical value. Default is `FALSE`. If it is `TRUE` or `x` is a `RasterBrick-class` object with `nlayers(x)!=length(filename)` , `filename` is considered as one string containing a decimal formatter (e.g. `"%04d"`, see `brick.decimal.formatter`). Otherwise, if `filename` is considered as a vector string.
`start.from.zero`	logical value. Default is `FALSE`. If `TRUE` the formatter starts from `0000`, otherwise it starts from `0001`.
`keyword`	geotop keyword to be used to extract the raster file name from `geotop.inpts` file. This is enabled if `filename` is equal to `NULL`.
`wpath`	simulation folder containing `geotop.inpts` file.
`suffix.ext`	charachter string to be added to the `keyword` value,e.g. possible suffix and extension of the raster file name. Default is `".asc"`.
`...`	further arguments of `get.geotop.inpts.keyword.value` or `writeRaster`

Note

It makes use of system functons. It uses *.asc format for raster files. In case the file name filename is missing and then NULL, it must be imported by the simulation geotop.inpts file.

Examples



file <- system.file("ex/elev.tif", package="terra")
elev <- raster(file)


elevfile <- rasterTmpFile()
extension(elevfile) <- ".asc"

writeRasterxGEOtop(x=elev,file=elevfile)



file <- system.file("ex/elev.tif", package="terra")
elev <- raster(file)


elevfile <- rasterTmpFile()
extension(elevfile) <- ".asc"

writeRasterxGEOtop(x=elev,file=elevfile)

A GeotopRasterBrick: an object to manage raster maps provied by GEOtop!!

Description

A GeotopRasterBrick: an object to manage raster maps provied by GEOtop!!

Examples

showClass("zoo")
showClass("zoo")

Package 'geotopbricks'

Help Index

Parser of an argument string

Description

Usage

Arguments

Examples

Bondone Dataset

Description

Usage

Format

Details

Source

brick

Description

Usage

Arguments

Value

See Also

Examples

Imports a brick of raster ascii maps into a 'brick' object

Description

Usage

Arguments

Value

Examples

brickFromOutputSoil3DTensor

Description

Usage

Arguments

Details

Author(s)

See Also

Examples

Creates an 'geotop.inpts' files the keyword and their values of a date.frame like the one returned by declared.geotop.inpts.keywords

Description

Usage

Arguments

Details

See Also

Examples

Creates geotop meteo files from (a list of) 'zoo' objects

Description

Usage

Arguments

See Also

Examples

Collects all keywords contained in the 'getop.inpts' configuration files and their values in a data frame object.

Description

Usage

Arguments

Value

See Also

geotopbrick

Description

Usage

Arguments

Value

GeotopRasterBrick-class

Description

Details

Author(s)

See Also

Examples

Importing a GEOtop Keyword and its Value into R

Description

Usage

Arguments

Value

Note

Examples

Get a sf object for Meteorological Stations or Control Points in a GEOtop simulation

Description

Usage

Arguments

Examples

This function saves all spatially distrubuted information contained in the recovery folder into a comprehensive list object.

Description

Usage

Arguments

Creates an 'geotop.inpts' files the keyword and their values of a date.frame like the one returned by `declared.geotop.inpts.keywords`

Get a `sf` object for Meteorological Stations or Control Points in a GEOtop simulation

This function saves all spatially distrubuted information contained in the recovery folder into a comprehensive `list` object.

Read a text file containing values and matedata of a z-layer brick referred to a time instant (e.g. date). The file is formatted like an ascii format like `'geotop.inpts'` file.

Reads a text file like the one generated by `write.vectorized.geotop.recovery`