Help for package geotopbricks

Maintainer:

Emanuele Cordano <emanuele.cordano@gmail.com>

License:

GPL (≥ 3)

Title:

An R Plug-in for the Distributed Hydrological Model GEOtop

Type:

Package

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 can be found in the provided documentation.

Version:

1.5.9.1

Date:

2025-04-18

Repository:

CRAN

Depends:

R (≥ 4.1.0),methods,raster,stringr,zoo,sf

Imports:

terra

Suggests:

soilwater

URL:

https://github.com/ecor/geotopbricks

RoxygenNote:

7.3.2

NeedsCompilation:

Packaged:

2025-04-18 17:34:58 UTC; ecor

Author:

Emanuele Cordano

[aut, cre, ctb]

Date/Publication:

2025-04-18 19:10:06 UTC

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")

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"),
  ...
)

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

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)

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.

Parser of an argument string

Description

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

Usage

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(",","="))

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)

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)

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

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
)

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)

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, ...)

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-classobject 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)

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,
  wpath = NULL,
  comment.lines = "default",
  header = "default",
  like.meteo.keywords = inherits(df, "sf"),
  coords_keywords = c("MeteoStationCoordinateX", "MeteoStationCoordinateY"),
  num_keyword = "NumberOfMeteoStations",
  ...
)

Arguments

df

data frame returend by declared.geotop.inpts.keywords

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.

like.meteo.keywords

logical. It is used in case df is a sf object (geospatial), it often used for meteorological stations

coords_keywords

keywords for station coordinates in case like.meteo.keywords==TRUE.

num_keyword

keyword for number of stations in case like.meteo.keywords==TRUE.

...

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)
#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)


df <- list(
## ! START METEO 

NumberOfMeteoStations=18,
MeteoStationCode = c("DWD_01735","DWD_01831",
"DWD_01832","DWD_01833","DWD_04354","DWD_04755",
"DWD_05306","DWD_05800","DWD_05802","DWD_06191",
"CHMI_C1BLAD01","CHMI_C1CHUR01","CHMI_C1HUSI01",
"CHMI_C1JELE01","CHMI_C1KHOR01","CHMI_C1STRZ01",
"CHMI_C1VOLR01","CHMI_L1HOJS01"),

MeteoStationElevation = c(628,1449,1436,1307,457,
847,940,615,615,684,893,1117.8,492,810,728,811,749,866),

MeteoStationLatitude = c(48.7894,49.1126,49.1129,
49.0851,48.7832,48.6819,48.9293,49.028,
49.0007,48.9023,48.9911111111111,49.0683333333333,49.0525,48.8030555555556,
49.1455555555556,48.9088888888889,48.9088888888889,49.2125),

MeteoStationLongitude = c(13.629,13.1353,13.1338,13.2801,13.3146,13.7351,
13.4641,13.2385,13.2137,13.1442,13.6683333333333,13.6152777777778,13.99,13.8897222222222,
13.55,13.7202777777778,13.8866666666667,13.1972222222222),
MeteoStationSource = c("DWD","DWD","DWD","DWD","DWD","DWD","DWD","DWD",
"DWD","DWD","CHMI","CHMI","CHMI","CHMI","CHMI","CHMI","CHMI","CHMI"),
MeteoStationWindVelocitySensorHeight = c(10,10,10,10,10,10,
10,10,10,10,10,10,10,10,10,10,10,10),
MeteoStationTemperatureSensorHeight = c(2,2,2,2,
2,2,2,2,2,2,2,2,2,2,2,2,2,2),
MeteoStationCoordinateX = c(399300.751483554,
363922.260272129,363813.623704389,374419.289552317,376193.768289692,
406895.244369364,387503.305318229,371234.500519548,
369350.262272179,364000.012870334,402582.414145364,
398857.930427203,426204.259500581,418472.448448941,
394254.345037428,406228.32523286,418420.252345735,368705.300573528),
MeteoStationCoordinateY = c(5404951.24399018,5441647.41925558,
5441683.4621225,5438340.55274848,5404725.536756,5392867.0291128,
5420733.31978365,5432063.12861282,5429070.90371837,
5418255.08734482,5427322.00086173,5435975.56352357,5433783.28344618,
5406157.18835262,5444648.8862922,5418116.78091222,5417924.86335169,
5452642.98443844)
###! END METEO
)


out1 <- create.geotop.inpts.keyword(df=df,comment.lines="")

###
library(terra)

meteo_sts <- terra::vect(system.file("ex_data/meteo_sts3.rds",package="geotopbricks")) |>
   st_as_sf()
   
   
out2 <- create.geotop.inpts.keyword(df=meteo_sts,comment.lines="")

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,
  ...
)

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

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("!>!", "!>>!"),
  ...
)

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,
  ...
)

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

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 = FALSE,
  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

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

## This step allows to put all keywords with their value in memory:
## it not mandataory but it can save running time in the session
inpts.frame <- declared.geotop.inpts.keywords(wpath=wpath) 

cond.time <- system.time({

prefix <- get.geotop.inpts.keyword.value("SoilLiqWaterPressTensorFile",wpath=wpath,
inpts.frame=inpts.frame)


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

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

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


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

})

cond2.time <- system.time({
if (cond.time[["elapsed"]]<0.01) {


##### spatial gridded covarege data (raster)
slope <- get.geotop.inpts.keyword.value("SlopeMapFile",raster=TRUE,wpath=wpath,
 inpts.frame=inpts.frame) 
bedrock_depth <- get.geotop.inpts.keyword.value("BedrockDepthMapFile",raster=TRUE,
wpath=wpath,
 inpts.frame=inpts.frame) 

}
})
cond3.time <- system.time({
if (cond2.time[["elapsed"]]<1) {


##### 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,inpts.frame=inpts.frame) 
end <- get.geotop.inpts.keyword.value("EndDateDDMMYYYYhhmm",
date=TRUE,wpath=wpath,tz=tz,inpts.frame=inpts.frame) 

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


##### 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 = ","
)

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)

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,
  ...
)

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)

It reads the CRS metadata utilized in a GEOtop Simulation

Description

It reads the CRS metadata utilized in a GEOtop Simulation

Usage

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)

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, ...)

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

max_value

Description

Gets the maximum (scalar) values of a GeotopRasterBrick object

Usage

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, ...)

Arguments

x

a GeotopRasterBrick object.

na.rm, ...

further arguments foe min.

Value

the minimum (scalar) values of a GeotopRasterBrick object

plot

Description

plot method for a GeotopRasterBrick object

Usage

## 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

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
)

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,
  ...
)

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

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, ...)

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 = "",
  ...
)

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

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,
  ...
)

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)

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, ...)

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

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,
  ...
)

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

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,
  ...
)

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

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",
  ...
)

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,
  ...
)

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

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,
  ...
)

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

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",
  ...
)

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)

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")

GeotopRasterBrick-class

Description

Details

Author(s)

See Also

Examples

KML

Description

Usage

Arguments

Note

Examples

Ops

Description

Usage

Arguments

Details

Note

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

Importing a GEOtop Keyword and its Value into R

Description

Usage

Arguments

Value

Note

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`