Package 'BioSIM'

Title: 'BioSIM' Client for 'BioSIM' Web API
Description: Provide a client that retrieves the climate variables from the original 'BioSIM' application hosted on a server. The 'BioSIM' application is being developed and maintained by the Canadian Forest Service.
Authors: Mathieu Fortin [aut, cre] (ORCID: <https://orcid.org/0000-0002-6436-2727>), Remi Saint-Amant [ctb], His Majesty the King in right of Canada [cph]
Maintainer: Mathieu Fortin <[email protected]>
License: LGPL-3
Version: 1.1.0
Built: 2026-05-14 09:25:24 UTC
Source: https://github.com/RNCan/BioSimClient_R

Help Index

The list of all months

Description

The list of all months

Usage

allMonths

Format

An object of class character of length 12.

Configure the client

Description

The forceClimateGenerationEnabled argument forces BioSIM to generate climate for past dates instead of using the observations from the climate stations. By default this option is set to false. The nbNearestNeighbours argument sets the number of stations for the imputation of climate variables.

Usage

biosimclient.config(
  forceClimateGenerationEnabled = NULL,
  nbNearestNeighbours = NULL,
  isLocalConnectionEnabled = NULL,
  isTestModeEnabled = NULL
)

Arguments

forceClimateGenerationEnabled

a logical
nbNearestNeighbours

an integer
isLocalConnectionEnabled

a logical (only for test purposes)
isTestModeEnabled

a logical (only for test purpose)

Details

If an argument is set to null, there is no effect at all. If all the arguments are set to null, then the configuration is reset to its default value: the climate variables of past dates relies on observations and the number of climate stations is set to 4.

Examples

## Not run: 
### enables the climate generation for past dates and uses 20 climate stations
biosimclient.config(T, 20)

### reset the configuration
biosimclient.config() 
## End(Not run)

Report of the climate generation settings

Description

The isForceClimateGenerationEnabled setting forces BioSIM to generate climate for past dates instead of using the observations from the climate stations. By default this option is set to false. The nbNearestNeighbours setting is the number of stations used to impute climate variables to a particular location.

Usage

biosimclient.getConfiguration()

Details

All the settings can be changed through the biosimclient.config function.

Value

a data.frame object

Generate a meteorological time series and apply one or many models.

Description

This function generated a meteorological time series for some locations and applies one or many models on this series. Default RCP and Climate model are RCP45 and RCM4. The CONSTANT_CLIMATE rcp option actually reproduces the climate observed between 1991 and 2020.

Usage

generateWeather(
  modelNames,
  fromYr,
  toYr,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  rep = 1,
  repModel = 1,
  rcp = "RCP45",
  climModel = "RCM4",
  additionalParms = NULL
)

Arguments

modelNames

a character or a vector of character. Should be one or some models listed in the available models (see the getModelList() method)
fromYr

the starting date (yr) of the period (inclusive)
toYr

the ending date (yr) of the period (inclusive)
id

a vector with the ids of the plots
latDeg

the latitudes of the plots
longDeg

the longitudes of the plots
elevM

the elevations of the plots (can contain some NA or can be NULL, in which cases BioSim relies on a digital elevation model)
rep

number of replicates of generated climate (is set to 1 by default)
repModel

number of replicates on the model end (is set to 1 by default)
rcp

an representative concentration pathway (either "CONSTANT_CLIMATE", "RCP45" or "RCP85")
climModel

a climatic model (either "RCM4", "GCM4" or "Hadley")
additionalParms

a list of named vectors with the additional parameters if needed

Value

a list of data.frame objects

Examples

locations <- BioSIM::twoLocationsInSouthernQuebec
addParms <- c("LowerThreshold"=5)
## Not run: 
degreeDays <- generateWeather("DegreeDay_Annual", 2017, 2021, locations$Name, locations$Latitude,
                   locations$Longitude, locations$Elevation,
                   rcp = "RCP85", climModel = "GCM4",
                   additionalParms = list(addParms))
## End(Not run)

Return the annual normals for a period

Description

Return the annual normals for a period

Usage

getAnnualNormals(
  period,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  rcp = "RCP45",
  climModel = "RCM4"
)

Arguments

period

a string representing the period (either "1951_1980", "1961_1990", "1971_2000", "1981_2010" up to "2071_2100")
id

a vector with the ids of the plots
latDeg

the latitudes of the plots
longDeg

the longitudes of the plots
elevM

the elevations of the plots (can contain some NA, in which case BioSim relies on a digital elevation model)
rcp

an representative concentration pathway (either "RCP45" or "RCP85")
climModel

a climatic model (either "RCM4", "GCM4" or "Hadley")

Value

a data.frame object

Examples

locations <- BioSIM::twoLocationsInSouthernQuebec
## Not run: 
annualNormals <- getAnnualNormals("1981_2010", locations$Name, locations$Latitude,
                                     locations$Longitude, locations$Elevation)
## End(Not run)

Provide help for a particular model

Description

Provide help for a particular model

Usage

getModelDefaultParameters(modelName)

Arguments

modelName

should be one of the character string returned by the getModelList function

Examples

## Not run: 
getModelHelp("Spruce_Budworm_Biology")
## End(Not run)

Provide help for a particular model

Description

Provide help for a particular model

Usage

getModelHelp(modelName)

Arguments

modelName

should be one of the character string returned by the getModelList function

Examples

## Not run: 
getModelHelp("Spruce_Budworm_Biology")
## End(Not run)

Return the list of models available in BioSim

Description

Provide the list of model that can be used in BioSIM after generating the climate for some locations.

Usage

getModelList()

Examples

## Not run: 
getModelList()
## End(Not run)

Return the monthly normals for a period

Description

Return the monthly normals for a period

Usage

getMonthlyNormals(
  period,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  rcp = "RCP45",
  climModel = "RCM4"
)

Arguments

period

a string representing the period (either "1951_1980", "1961_1990", "1971_2000", "1981_2010" up to "2071_2100")
id

a vector with the ids of the plots
latDeg

the latitudes of the plots
longDeg

the longitudes of the plots
elevM

the elevations of the plots (can contain some NA, in which case BioSim relies on a digital elevation model)
rcp

an representative concentration pathway (either "RCP45" or "RCP85")
climModel

a climatic model (either "RCM4", "GCM4" or "Hadley")

Value

a data.frame object

Examples

locations <- BioSIM::twoLocationsInSouthernQuebec
## Not run: 
monthlyMeans <- getMonthlyNormals("1981_2010", locations$Name, locations$Latitude,
                                   locations$Longitude, locations$Elevation)
## End(Not run)

Return the normals for a period

Description

If the argument averageOverTheseMonths is left NULL or empty, the monthly normals are provided. If this argument is filled with some months, then the normal are aggregated over these months.

Usage

getNormals(
  period,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  averageOverTheseMonths,
  rcp = "RCP45",
  climModel = "RCM4"
)

Arguments

period

a string representing the period (either "1951_1980", "1961_1990", "1971_2000", "1981_2010" up to "2071_2100")
id

a vector with the ids of the plots
latDeg

the latitudes of the plots
longDeg

the longitudes of the plots
elevM

the elevations of the plots (can contain some NA, in which case BioSim relies on a digital elevation model)
averageOverTheseMonths

a vector with some months if there is a need for aggregating the climate varibles
rcp

an representative concentration pathway (either "RCP45" or "RCP85")
climModel

a climatic model (either "RCM4", "GCM4" or "Hadley")

Value

a data.frame object

Examples

locations <- BioSIM::twoLocationsInSouthernQuebec
## Not run: 
summerMean <- getNormals("1981_2010", locations$Name, locations$Latitude,
                          locations$Longitude, locations$Elevation,
                          c("June", "July", "August"))
## End(Not run)

The settings environment for this package

Description

This environment contains the general settings of the package.

Usage

settingEnv

Format

An object of class environment of length 0.

Shut down the Java server

Description

This method overrides the original function of the J4R package. It only adds a call to the clearCache function before calling the original function of the J4R package.

Usage

shutdownClient()

Examples

## Not run: 
shutdownClient()
## End(Not run)

Shut down the Java server

Description

This method overrides the original function of the J4R package. It only adds a call to the clearCache function before calling the original function of the J4R package.

Usage

shutdownJava()

Examples

## Not run: 
shutdownJava()
## End(Not run)

A list of two plots located in southern Quebec

Description

A list of two plots located in southern Quebec

Usage

data(twoLocationsInSouthernQuebec)

Format

An object of class data.frame with 2 rows and 5 columns.

Examples

data(twoLocationsInSouthernQuebec)