Package index • IASDT.R

Package info

IASDT.R IASDT.R-package: IASDT.R: Modelling the distribution of invasive alien plant species in Europe

Prepare species distribution data

GBIF_Process() GBIF_Check() GBIF_Download() GBIF_ReadChunk() GBIF_SpData(): Process GBIF occurrence data for the IAS-pDT

EASIN_Process() EASIN_Taxonomy() EASIN_Down() EASIN_Plot(): Process EASIN data for the IAS-pDT

eLTER_Process(): Process eLTER data for the IAS-pDT

IAS_Process() IAS_Distribution() IAS_Plot(): Process and map Invasive Alien Species (IAS) data for the IAS-pDT

GetSpeciesName(): Get species name or information of an IAS-pDT species ID

Prepare abiotic data

CLC_Process(): Process Corine Land Cover (CLC) data for the IAS-pDT

CHELSA_Vars: Detailed information on CHELSA climate variables

CHELSA_Process() CHELSA_Prepare() CHELSA_Project(): Process CHELSA Climate Data for the IAS-pDT

Efforts_Process() Efforts_Request() Efforts_Download() Efforts_Summarize() Efforts_Split() Efforts_Plot(): Process GBIF sampling effort data for the IAS-pDT

Railway_Intensity(): Calculate railway intensity based on OpenStreetMap data

Road_Intensity(): Calculate road intensity per grid cell

River_Length(): Calculate the length of rivers in each Strahler order per grid cell

BioReg_Process(): Process biogeographical regions dataset

Modelling functions

Functions for preparing data, running the models, and postprocessing of model outputs

Data preparation

Prepare input data and scripts for fitting Hmsc-HPC on GPU

Mod_GetCV(): Prepare spatial-block cross-validation folds for spatial analysis

Mod_PrepKnots(): Prepare knot locations for Hmsc GPP models

Mod_Prep4HPC() Mod_PrepData(): Prepare initial models for model fitting with Hmsc-HPC

Mod_SLURM() Mod_SLURM_Refit(): Prepare SLURM scripts for Hmsc-HPC model fitting

Mod_Fit_WS(): Fit Hmsc-HPC models on UFZ Windows Server

Mod_CV_Fit(): Prepare cross-validated Hmsc models for HPC fitting

Model postprocessing

Postprocessing model outputs, including checking for convergence, making spatial predictions, evaluation, and plotting.

Mod_GetPosts(): Combines posteriors exported by Hmsc-HPC into an Hmsc object

Mod_Merge_Chains(): Merge model chains

Mod_Summary(): Summary of Hmsc model parameters

RespCurv_PrepData() RespCurv_PlotSp() RespCurv_PlotSpAll() RespCurv_PlotSR(): Prepare and plot response curve data for Hmsc models

Mod_Predict_LF(): Draws samples from the conditional predictive distribution of latent factors

Mod_Plot_LF(): Plot spatial variation in site loadings of HMSC models

Mod_Postprocess_1_CPU() Mod_Prep_TF() Mod_Postprocess_2_CPU(): Model pipeline for post-processing fitted Hmsc models

Predict_Hmsc(): Calculates predicted values from a fitted Hmsc model

Predict_Maps(): Predict habitat suitability of Hmsc model across different climate options

Mod_Predict_Plot(): Plot species and level of invasion predictions as JPEG files using ggplot2

Mod_CV_Eval(): Evaluate cross-validated Hmsc Model

Mod_Eval_Plot(): Generate plots for the explanatory power of Hmsc models

Mod_Heatmap_Beta() Mod_Heatmap_Omega(): Heatmaps for the beta and omega parameters of the Hmsc model

Convergence_Plot() Convergence_Alpha() Convergence_Rho(): Plot model convergence of a selected model

Convergence_Plot_All(): Plot model convergence of multiple modelling alternatives

VarPar_Compute() VarPar_Plot(): Computes and visualize variance partitioning of Hmsc models

PlotGelman() PlotGelman_Alpha() PlotGelman_Beta() PlotGelman_Omega() PlotGelman_Rho(): Plot Gelman-Rubin-Brooks

Helper functions

Coda_to_tibble(): Convert a Coda object to a tibble with specified parameter transformations

exp_neg_div(): Exponential of Negative Division

fast_pnorm(): Fast Normal CDF

Solve1(): Invert a matrix

Solve2(): Solve a system of linear equations

Solve2vect(): Solve a system of linear equations for a vector

General functions

Data management / utility functions

Packages management

FunctionsInPackage(): List of functions in a package

LoadPackages(): Load or install multiple R packages

ReloadPackage(): Reload an R package

LoadedPackages(): List of loaded packages

Package_RemoteSha(): Get the remote SHA of R packages

AssignEnvVars(): Assign environment variables from a .env file

CheckCommands(): Check system commands availability

CheckArgs(): Check function arguments for specific types

CatFunArgs(): Print function Arguments

RecordArgs(): Capture and record evaluated function arguments

File operations

FileExt(): Get the file extension from a file path

FileSize(): File size in a human-readable format

FileType(): Determine the file type of a given file path

NormalizePath(): Normalize and quote file paths

Path(): Construct path to a file or directory

LoadAs(): Load objects from RData / qs2 / rds / feather file

LoadMultiple(): Load multiple .RData files together

CheckData() CheckRData() CheckQs() CheckRDS() CheckFeather(): Check the integrity of RData / qs2 / rds / feather files

CheckZip(): Check the Integrity of a ZIP File

SaveAs(): Save an object to a file with a new name

SaveMultiple(): Save multiple objects to their respective .RData files

List2RData(): Split list items into separate .RData files

Plotting

AddImg2Plot(): Add an image to an existing plot in R

AddLine(): Add a horizontal or vertical line to the current plot

integer_breaks(): Integer breaks for ggplot axis

Printing/logging functions

CatSep(): Print separator(s) to the console

CatTime(): Print text with time stamp

CatDiff(): Print time difference

Vector / data frame operations

AssignIfNotExist(): Assign a value to a variable if it does not already exist in the specified environment

cc(): Concatenate without quotes

ht(): Print head and tail of data frame

lapply_() sapply_(): Apply a function over a list or vector with optional silence

NDecimals(): Number of decimal places in a numeric value

ReplaceSpace(): Replace space with underscore in a string

ScrapLinks(): Extracts link texts and URLs from a web page

sort_(): Sort alphanumeric strings with enhanced options

SplitVector(): Split a vector into smaller chunks

SplitDF2Chunks(): Split a data.frame into smaller chunks

Range2NewVal(): Changes values within a specified range, or greater than or less than a specific value to a new value in a vector, data.frame, or raster

AllObjSizes(): Size of objects in memory

KeepOnly(): Keep only specified objects in the environment, removing all others.

SourceSilent(): Silently source R script with optional message and warning suppression

NUnique(): Number of unique values for all columns of a data frame

AddMissingCols(): Add missing columns to a data frame with specified fill values

Other functions

Set_parallel(): Set up or stop parallel processing plan

CurrOS(): Current operating system

System(): Run a system command in a cross-platform manner

CheckURL(): Check the validity of a URL

ScriptLocation(): Retrieve the location of the current R script.

ClearConsole(): Clear the console

CheckRStudioVersion(): Check if the installed RStudio version is up to date

CheckQuartoVersion(): Check if the installed Quarto version is up to date

InfoChunk(): Print Information chunk with time stamp

SaveSession(): Saves all non-function objects from the global environment to an RData file

SaveSessionInfo(): Save session information to a file

git_log(): Print or return a detailed git log of the git repository located in the specified directory.

GetBashVars(): Read command line arguments passed to an R script

Install_Hmsc(): Install Hmsc-HPC in a python virtual environment on Windows

DetectAlias(): Detect aliased variables in a linear model

GetMode(): Calculate the mode of a numeric vector

Spatial functions

CheckTiff(): Check if a tiff file corrupted

DownBoundary(): Determine the boundaries of the requested GBIF data

Polygon_Centroid(): Replace the geometry of a polygon with its centroid point

Rename_geometry(): Rename active geometry column of an sf object.

SplitRaster(): Split a raster object into a list of smaller rasters

setGeometry(): Set the geometry column of a simple feature (sf) data frame in the pipe pipeline.

Text2Coords(): Extract longitude and latitude from string

ClipRasterByPolygon(): Clip a raster layer by a spatial polygon

CheckStackInMemory(): Check if a raster stack reads from disk or memory

sf_add_coords(): Add longitude and latitude coordinates to an sf object

GridCross(): Create a multilinestring sf object representing cross in the middle of each grid cell

GridDiagOff(): Create a multilinestring sf object for the diagonal and off-diagonal lines for each grid cell

RastPA(): Convert raster map into binary (1/0)

NetCDFGlobalAttrs(): Get global attributes for NetCDF files

Scale_0_1(): Scale a SpatRaster object values to a range between 0 and 1

setRastCRS(): sets CRS for a SpatRaster

setRastVals(): Set values for SpatRaster Objects