Package index • IASDT.R

Package info

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

Data workflow - species distribution

Functions for preparing species observation data

GBIF

Process GBIF data

GBIF_Process(): GBIF Data Processing Function

GBIF_Download(): Download and Process GBIF Occurrence Data

GBIF_SpData(): Extract species data as sf and Raster and plot species distribution

GBIF_ReadChunk(): Read GBIF chunk data

GBIF_Check(): Check if GBIF login credentials exist

EASIN

Process EASIN data

EASIN_Process(): Extracts and processes EASIN data

EASIN_Taxonomy(): Extract EASIN Taxonomy Data

EASIN_Down(): Extract EASIN data using EASIN ID

EASIN_Plot(): Plotting cleaned EASIN data

eLTER

Process eLTER data

elTER_Process(): eLTER data processing function

Merging species observation data

IAS_Process(): Process IAS data

IAS_Distribution(): Prepare distribution maps and summary for Invasive Alien Species (IAS)

IAS_Plot(): Plot IAS distribution map

Others

GetAcceptedName(): Get accepted name of a taxon

GetSpeciesName(): Get Species Name or Information Based on IASDT Species ID

Data workflow - Predictors and other data

Functions for preparing predictors and other abiotic data

CLC

Process Corine Land Cover data to obtain % coverage of habitat types

CLC_Process(): Process Corine land cover (CLC) data

CHELSA

Process CHELSA data

CHELSA_Vars: Detailed information on CHELSA climate variables

CHELSA_Prepare(): Prepare and download CHELSA climate data

CHELSA_Process(): Process CHELSA climate data

CHELSA_Project(): Project CHELSA data to the study area

Sampling efforts

Request, prepare, and process sampling efforts data from GBIF

Efforts_Request(): Request and manage GBIF data for vascular plant orders

Efforts_Download(): Download and manage GBIF data for vascular plant orders

Efforts_Split(): Split Order data into smaller chunks

Efforts_Plot(): Plot the output of efforts maps

Efforts_Summarize(): Process and summarize GBIF data for vascular plants

Efforts_SummarizeMaps(): Summarize maps for efforts data

Efforts_Process(): Download and Process sampling efforts data

Railway, roads, and rivers

Processing railway and road intensity and the length of rivers per grid cell

Railway_Intensity(): Calculate railway intensity based on OpenStreetMap data

Road_Intensity(): Calculate road intensity

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

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

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

PrepKnots(): Prepare knot locations for Hmsc GPP models

Mod_PrepData(): Prepare habitat-specific data for Hmsc models

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

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

Mod_SLURM_Refit(): Prepare SLURM file for failed / Unfitted Models

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.

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

Merge_Chains(): Post-processing of model outputs

Mod_Summary(): Summary of Hmsc model parameters

RespCurv_PrepData(): Prepare and process response curve data for Hmsc models

RespCurv_PlotSpAll(): Plot all species response curves

RespCurv_PlotSp(): Plot species response curves

RespCurv_PlotSR(): Plot species richness response curves

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_Prep_TF(): Prepare batch scripts for latent factor prediction on GPU

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

Predict_Maps(): Predicts 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_Postprocess(): Model pipeline for Hmsc analysis

Mod_Postprocess_1_CPU(): Model pipeline for Hmsc analysis (using CPU)

Mod_Postprocess_2_CPU(): Model pipeline for Hmsc analysis (using CPU)

Mod_CV_Eval(): Evaluate cross-validated Hmsc Model

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

PlotBetaGG(): Heatmaps of parameter estimates or posterior support values of species' environmental responses (Beta parameters)

PlotOmegaGG(): Creates heatmaps of parameter estimates or posterior support values for species' residual association (Omega parameters).

PlotAlpha(): Plot convergence traceplots for the alpha parameter

PlotRho(): Plot convergence traceplots for the rho parameter

Convergence_Plot(): Plot model convergence of a selected model

Convergence_Plot_All(): Plot model convergence of multiple modelling alternatives

VarPar_Compute(): Computes variance partitioning of Hmsc models

VarPar_Plot(): Plot variance partitioning of Hmsc model

PlotGelman(): Plot Gelman-Rubin-Brooks

PlotGelman_Alpha(): Creates a Gelman-Rubin-Brooks plot for alpha parameters from an Hmsc object.

PlotGelman_Beta(): Gelman-Rubin-Brooks plot for beta parameters

PlotGelman_Omega(): Creates a Gelman-Rubin-Brooks plot for omega parameters.

PlotGelman_Rho(): Creates a Gelman-Rubin-Brooks plot for the rho parameter.

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 an 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

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

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

LoadMultiple(): Load multiple RData files together

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

CheckRData(): Check the Integrity of an RData File

CheckZip(): Check the Integrity of a ZIP File

CheckRDS(): Check the Integrity of an RDS File

CheckData(): Check the Integrity of RData / qs2 / rds / feather Files

CheckFeather(): Check the Integrity of an feather File

CheckQs(): Check the Integrity of an qs2 File

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

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 ≤ 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

SetChainName(): Set name of the chain to a vector of strings

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