Package 'BioSIM' reference manual

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] , Remi Saint-Amant [ctb], His Majesty the King in right of Canada [cph]
Maintainer:	Mathieu Fortin <[email protected]>
License:	LGPL-3
Version:	1.0.5
Built:	2024-11-10 03:13:56 UTC
Source:	https://github.com/RNCan/BioSimClient_R

The list of all months

Description

The list of all months

Usage

allMonths
allMonths

Format

An object of class character of length 12.

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
)
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)

## 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()
biosimclient.getConfiguration()

Details

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

Value

a data.frame object

Clear the cache of the client (DEPRECATED).

Description

When using the weather generator, some objects are stored in memory on the server and a reference is stored in the client, so that subsequent calls on models for the same location and time interval does not have to generate the climate over and over again. After a while it may happen that a large number of objects are kept in memory. This method clears this cache on both the server and the client ends.

Usage

clearCache()
clearCache()

Examples


## Not run: 
clearCache()
## End(Not run)

## Not run: 
clearCache()
## End(Not run)

Generate climate and apply a model (DEPRECATED).

Description

This function generated the basic climate variables for some locations and applies a particular model on this generated climate.

Usage

generateModelOutput(
  modelName,
  fromYr,
  toYr,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  isEphemeral = T,
  rep = 1,
  repModel = 1,
  rcp = "RCP45",
  climModel = "RCM4",
  additionalParms = NULL
)
generateModelOutput(
  modelName,
  fromYr,
  toYr,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  isEphemeral = T,
  rep = 1,
  repModel = 1,
  rcp = "RCP45",
  climModel = "RCM4",
  additionalParms = NULL
)

Arguments

`modelName`	a character. Should be one of the 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)
`isEphemeral`	a logical. If set to true, the generated climate is not stored on the server, which implies a greater computational burden and inconsistencies if different models are applied on the same locations. By default, it is set to true.
`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 "RCP45" or "RCP85")
`climModel`	a climatic model (either "RCM4", "GCM4" or "Hadley")
`additionalParms`	a named vector with the additional parameters if needed

Value

a data.frame object

Examples


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

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

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.

Usage

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

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"
)
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)

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)
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)

## 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)
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)

## 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()
getModelList()

Examples


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

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

Generate climate and apply a model (DEPRECATED).

Description

This function generated the basic climate variables for some locations and applies a particular model on this generated climate.

Usage

getModelOutput(
  fromYr,
  toYr,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  modelName,
  isEphemeral = T,
  rep = 1,
  repModel = 1,
  rcp = "RCP45",
  climModel = "RCM4",
  additionalParms = NULL
)
getModelOutput(
  fromYr,
  toYr,
  id,
  latDeg,
  longDeg,
  elevM = rep(NA, length(longDeg)),
  modelName,
  isEphemeral = T,
  rep = 1,
  repModel = 1,
  rcp = "RCP45",
  climModel = "RCM4",
  additionalParms = NULL
)

Arguments

`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, in which case BioSim relies on a digital elevation model)
`modelName`	a character. Should be one of the models listed in the available models (see the getModelList() method)
`isEphemeral`	a logical. If set to true, the generated climate is not stored on the server, which implies a greater computational burden and inconsistencies if different models are applied on the same locations. By default, it is set to true.
`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 "RCP45" or "RCP85")
`climModel`	a climatic model (either "RCM4", "GCM4" or "Hadley")
`additionalParms`	a named vector with the additional parameters if needed

Value

a data.frame object

Examples


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

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

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"
)
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)

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
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()
shutdownClient()

Examples

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

## 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()
shutdownJava()

Examples

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

## 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)
data(twoLocationsInSouthernQuebec)

Format

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

Examples

data(twoLocationsInSouthernQuebec)
data(twoLocationsInSouthernQuebec)

Package 'BioSIM'

Help Index

The list of all months

Description

Usage

Format

Configure the client

Description

Usage

Arguments

Details

Examples

Report of the climate generation settings

Description

Usage

Details

Value

Clear the cache of the client (DEPRECATED).

Description

Usage

Examples

Generate climate and apply a model (DEPRECATED).

Description

Usage

Arguments

Value

Examples

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

Description

Usage

Arguments

Value

Examples

Return the annual normals for a period

Description

Usage

Arguments

Value

Examples

Provide help for a particular model

Description

Usage

Arguments

Examples

Provide help for a particular model

Description

Usage

Arguments

Examples

Return the list of models available in BioSim

Description

Usage

Examples

Generate climate and apply a model (DEPRECATED).

Description

Usage

Arguments

Value

Examples

Return the monthly normals for a period

Description

Usage

Arguments

Value

Examples

Return the normals for a period

Description

Usage

Arguments

Value

Examples

The settings environment for this package

Description

Usage

Format

Shut down the Java server

Description

Usage

Examples

Shut down the Java server