Coding style | checklist default | Rules for coding style | Static code analysis checks | Using a different coding style | References

Rules for folder names | Rules for file names | Rules for graphical file names

Available checks | Extensive report on checks | Errors, warnings and notes | Changes | Session info | Making code findable and citable | Integration with Zenodo and ORCID | Bundling your code in a package | Benefits of using a package for your analysis

Coding style | pkgdown style | License files

Starting an R package from scratch | Prepare online setup | Local setup | Finalise online setup in GitHub | Get it working with an existing package or update the checklist | Prerequisites | Online setup on GitHub | Troubleshooting | Failing check package on GitHub Actions

Starting a new project from scratch | Add or update checklist tools in an existing project | To do once after activating version control | Failing checks in the GitHub Action

Configuration | Basic usage | Custom dictionary | Rd files | Quarto projects

General implementation | Read | Manipulate | Write | Schema properties implementation | fields | missingValues | primaryKey | foreignKeys | Field properties implementation | name | type and format | title | description | example | constraints | rdfType | Field types implementation | string | number | integer | boolean | object | array | datetime | date | time | year | yearmonth | duration | geopoint | geojson | any

Introduction | Interactive Input Functions | Yes/No Questions | ORCID Identifiers | ROR Identifiers | Email Addresses | URLs | Language Codes | Licenses | Menu Selection | Validation Functions | ORCID Validation | ROR Validation | Email Validation | URL Validation | Language Code Validation | Integration with Interactive Functions | Non-Interactive Behaviour | Error Handling | Best Practices | Common Patterns | Validating User Input | Cleaning Existing Data | Optional Fields | Batch Processing | Related Functions

Why bother setting up an org_list? | The org_item class | Roles: rightsholder, funder, and publisher | The org_list class | Creating an org_list programmatically | Creating an org_list interactively | Getting the default org_list for a project | Adding an org_item to an existing org_list | The built-in INBO organisation list | FAQ

Introduction | Why Use Individual Helper Functions? | Storing Individual Information | Selecting and Reusing Individuals | Converting Individual Information | To Person Objects | To Badge Format | To Data Frames | Adding Individuals to Files | Role Mapping for Different File Types | Helper Functions for Roles | Checking Person Roles | Selecting Roles Interactively | Typical Workflow | Working with Multiple Languages | Best Practices | Related Functions

zen4R - R Interface to Zenodo REST API | 1. Overview and vision | 2. Development status | 3. Credits | 4. User guide | 4.1 How to install zen4R in R | 4.2 Connect to Zenodo REST API | 4.3 Query Zenodo deposited records | 4.3.1 Get Depositions | 4.3.2 Get Deposition By Concept DOI | 4.3.3 Get Deposition By DOI | 4.3.4 Get Deposition By Zenodo ID | 4.3.4 Get versions of a Zenodo record | 4.4 Manage Zenodo record depositions | 4.4.1 Create an empty record | 4.4.2 Fill a record | 4.4.3 Deposit/update a record | 4.4.4 Delete a record | 4.4.5 Publish a record | 4.4.6 Edit/Update a published record | 4.4.7 Discard changes of a draft record | 4.4.8 Create a new version record | 4.5 Manage Zenodo record deposition files | 4.5.1 Upload file | 4.5.2 Get files | 4.5.3 Delete file | 4.6 Manage Zenodo record deposition files | 4.6.1 Submit a published record to communities | 4.6.2 Submit a draft record to a community | 4.7 Export Zenodo record metadata | 4.7.1 Export Zenodo record metadata by format | 4.7.2 Export Zenodo record metadata - all formats | 4.8 Browse Zenodo controlled vocabularies | 4.8.1 Communities | 4.8.2 Licenses | 4.8.3 Funders | 4.8.4 Grants / Awards | 4.9 Query Zenodo published records | 4.9.1 Get Records | 4.9.2 Get Record By Concept DOI | 4.9.3 Get Record By DOI | 4.9.4 Get Record By Zenodo ID | 4.10 Download files from Zenodo records | 4.11 Manage requests | 5. Issue reporting | 6. User support

Make a Movebank dataset "frictionless" | Transform a Movebank dataset to Darwin Core | Transform a Movebank dataset to Ecological Metadata Language (EML) | Example dataset

Leeswijzer | Doelstellingen en inhoud package | Inhoud package | Doelstellingen | Installatie van het package | Gebruik basisfuncties | Wegwijs in R | R, RStudio, scripts en projecten | Packages en documentatie | Wat met gegenereerde gegevens in tabelvorm? | Hoe eigen gegevens inlezen in R? | Wat met een list van tabellen? | Basis van LSVI-package | Connecteren met de databank | Gebruik van de functies zelf

Inleiding | Beschikbare gegevens en informatie | Algemene workflow | Berekening van voorwaarden | Rekenregels | AnalyseVariabele | aantal | bedekking | bedekkingExcl <!-- spell-check: ignore --> | bedekkingLaag | bedekkingLaagExcl | bedekkingLaagPlus | bedekkingSom <!-- spell-check: ignore --> | maxBedekking | maxBedekking2s <!-- spell-check: ignore --> | maxBedekkingExcl <!-- spell-check: ignore --> | aandeel | aandeelKruidlaag | aandeelLaagExcl | aantalGroepen | scoresom <!-- spell-check: ignore --> | meting | Afhandeling taxonlijsten | Bedekking en schalen | Status | Distance-to-target

Introduction | Aim | Packages and connection | Functionality | Survey information | Header information | Recording information | Classification information | Qualifiers information | Layer information | Layer qualifiers | Parent-child relationships between recordings | Processing the retrieved data | More complex queries | Closing the connection

Introduction | Aim | Data issues or missing taxonlist | Packages and connection | Functionality | Taxonlists overview | Taxonlist features | Taxonlist items | More complex queries | Closing the connection | Database philosophy | Taxonlijst | TaxonlijstVersie | Taxonlijstitem | TaxonlijstitemInterpretatie | Taxon | Kenmerk (= feature) | Kenmerkwaarde | TaxonlijstItemAttribuut | Full data model

Where do you find your credentials? | Store your credentials | Forgot your credentials? | Don't have an account to ETN?

Introduction | Basic usage | Package contents | Schema information | Important notes | CSV format required | Metadata integration | Recursive search | Use cases | Data sharing | Data validation | Data catalogs | See also

Introduction | Basic usage | Example: case conversion | Multiple columns | Use cases | Unsupported data type | Storage optimization | Data standardization | Important notes | Limitations

DHMV Data | Situation/Motivation | Limits of ows4R Package | The Lead: QGIS | The Solution: Query Building | Using Version 2.0.1 | The "inbospatial" Way | Post Mortem | Table of Contents

Introduction | Overview of Spatial Web Services | Vector data examples | Simple use case without filter | Apply a CQL-Filter to filter on a field | Request a subset of fields | Meteorological data example | Spatial filtering using a bounding box | Spatial filters using spatial binary predicates | Intersects a point | Raster data examples

Retrieve chemical data from Watina | Plot the ionic ratio against the electrical conductivity (Van Wirdum)

Connecting | Selecting locations | Disconnecting

Overview | The basics: obtaining hydrochemical data | Processing hydrochemical data and selecting locations

Overview | The basics: obtaining XG3 values | Processing XG3 values and selecting locations

General implementation | Read | Manipulate | Write | Properties implementation | resources | profile | name | id | licenses | title | description | homepage | image | version | created | keywords | contributors | sources

General implementation | Read | Manipulate | Write | Properties implementation | name | path | data | profile | schema | dialect | title | description | format | mediatype | encoding | bytes | hash | sources | licenses | compression

What is a Data Package? | Read a Data Package | Create and edit a Data Package | Write a Data Package

General implementation | Read | Manipulate | Write | Properties implementation | delimiter | lineTerminator | quoteChar | doubleQuote | escapeChar | nullSequence | skipInitialSpace | header | commentChar | caseSensitiveHeader | csvddfVersion

Introduction | User credentials | Select project(s) of interest | Animals | Detections | Stations | Acoustic tags | Acoustic network projects | Acoustic deployments | Data visualization

Setting options | Available options

Goal | Benefits of writing with bookdown | Available templates in INBOmd | Installation | Using INBOmd | Recommended way to start a new report | Legacy way to start a new document from RStudio templates | Rendering a document | Examples of INBOmd

What is Zenodo? | What is ORCID? | Why integrate Zenodo and ORCID with GitHub? | Setup ORCID | Once | Setup Zenodo | Once per repository | What happens next? | Managing Zenodo metadata via DESCRIPTION | Contributor roles | Funding information

Load data | Time of introduction | Number of introductions per year | Cumulative number of alien species | Native range | Pathways of introduction | Pathway data | Visualize pathways at level 1 | Visualize pathways over time at level 1 | Visualize pathways at level 2 | Visualize pathways over time at level 2 | Pathway count table | Additional resources

Introduction | Decision rules approach | Example data | Apply decision rules | Understanding the results | GAM approach | Apply GAM | Understanding GAM results | Correcting for research effort | Choosing between approaches | Additional resources

Introduction | Reading metadata | Updating the optional metadata

Introduction | Data Storage | On a File System | In Git Repositories | Timings | Writing Data | Reading Data

Introduction | Setup | Structuring Git2rdata Objects Within a Project | Storing Dataframes ad Hoc into a Git Repository | First Commit | Second Commit | Third Commit | Scripted Workflow for Storing Dataframes | R Package Workflow for Storing Dataframes | Analysis Workflow with Reproducible Data | Long running analysis

Introduction | Palettes | inbo_palette() | vlaanderen_palette() | traffic_palette() | Flanders colours | Simulate effect of colour blindness on the perception of palettes | Named INBO colours | Named Flanders colours

Inleiding | Situering | Doelstellingen | Definities | Praktische werkwijze | Vuistregels voor de metingen | Aantal op te meten bomen | Vuistregels voor selectie van de bomen | Proefvlak | Clusteren van boomsoorten en/of domeinen | Berekenen van curves | Initiatie | Fit | Validatie | Stap 1: afwijkende metingen | Stap 2: afwijkende curves | outputIVANHO | resultaat | uitbreiding naar hogere omtrekklassen | Standaardstramien voor berekeningen | Bruikbaar interval | Omtrekklassen | Scope voor omtrekklassen | Bruikbaar interval: Q5k en Q95k | Functie initiatie() | Keuze van modellen | Algemeen | Basismodel | Afgeleid model | Lokaal model | Kwaliteitsbeoordeling | RMSE | Afwijkende metingen | Afwijkende curvevorm | Berekening resultaat | output voor implementatie in IVANHO | modelparameters per domein

Introduction | Aim | Packages and connection | Functionality | Information on monitoring schemes | Locations and sublocation of monitoring schemes | Visits | Observations | Closing the connection | Data policy

The multimput package | Very short intro to multiple imputation | Short intro to multiple imputation | The dataset | Create the imputation model | Apply the imputation model | Aggregate the imputed dataset | Model the aggregated imputed dataset | Simple example | Return only the parameters associated with fYear | Predict a smoother for predefined values | Compare the results using different imputation models | Modelling aggregated data with glm.nb | Modelling aggregated data with inla | References

Minimal setup for using read_soilmap() | Install and load n2khab | Create (or locate) the n2khab_data directory with 2 subdirectories | Download the soilmap_simple data source in the correct place | Explore the soilmap_simple data source! | Access more information: the soilmap data source | Download the soilmap data source in the correct place | Explore the soilmap data source

Introduction | Installation | Recommended use of the package | Load data from Fieldmap database | Calculations (aggregations) | Umbrella functions | Subfunctions | Additional functions | Save and retrieve data | Update forresdat | References

Introduction | Maintaining Variable Classes | Efficiency Relative to Storage and Time | Optimizing File Storage | Optimized for Version Control | Basic Usage | Storing Optimized | Storing Verbose | Efficiency Relative to File Storage | Reading Data | Missing Values

Introduction | Setup | Assumptions | Sorting Observations | Sorting Variables | Handling Factors Optimized | Relabelling a Factor

Description of the problem | Some background on SQL Server and odbc data types | Consulting data types

Overview | Descriptions

Concept | Workflow | Import the relevant data | Generate the analysis objects | Fit the models | Extract the results | Traceable and auditable | Portable | Efficient | Metadata | Definition of the model | Scheme, species and location | Time-stamp | Used packages | Linked analyses | Available models | n2k_import() | n2k_inla() | n2k_inla_comparison() | n2k_composite() | n2k_hurdle_imputed() | n2k_aggregate() | n2k_modelimputed() | Manifest | Docker

Overview | More on list contents and package functionality | Multilanguage support | Get the reference lists in R

Introduction | Distribution of the data sources used by n2khab functions | More about Zenodo | Local data storage | Getting started for your (collaborative) workflow

Intro | Data sources | Using the read_...() functions | Returning raw data sources | Returning processed data sources | read_habitatmap_stdized() | read_habitatmap_terr() | read_watersurfaces_hab() | Matching interpreted data sources with a data frame column of types | References

Intro | Data sources | Get the data in R | read_GRTSmh() | read_GRTSmh_diffres() | read_GRTSmh_base4frac() | References

Setup | Station names | Session and camera IDs

Setup | Species record table | Temporal independence | Exclude some species | Station names | Remove duplicates | Use filter predicates | Other arguments needed?

A Simple, Stable and Transparent Classification of Effects | A Detailed Classification | Classification Using effectclass | Suggestion for Displaying Effects in a Tabular Format

stat_fan() | stat_effect() and scale_effect() | format_ci() and classification() | References

Setup | Get taxonomic information | Create maps | Basic usage | Number of species | Number of observations | Number of individuals | RAI | RAI (individuals) | Effort | Clustering and hovering | Visualize deployments without detected animals | Use a color palette | Use a specific icon and color for zero values | Modify circle size | Use absolute scale | Use filter predicates

Setup | One argument - one value predicates | pred(), pred_not() | pred_gt(), pred_gte(), pred_lt(), pred_lte() | One argument - no value predicates | One argument - multiple value predicates | multiple predicates: pred_and() and pred_or() | How to use filter predicates | One predicate | Multiple predicates

Do not use absolute file paths | Easiest solution: use relative paths within the project | Alternative solution: use relative paths between projects | Fallback solution: ask the user to specify the path

Introduction | Important | Using the default theme from INBOtheme | Using a non-default theme from INBOtheme | Prepare the code and data | Default: theme_inbo() | theme_inbo() with default background | theme_inbo() with transparent background | theme_vlaanderen2015() | theme_vlaanderen2015() with default background | theme_vlaanderen2015() with transparent background | theme_elsevier()

Introduction | Default: theme_inbo() | theme_vlaanderen2015() | theme_elsevier()

Introduction | KNMI data | MOW-HIC data | KMI data | Google maps kml files | Closure

Introduction | Aim | Functionality | Dependencies | Guess CRS function

Introduction | Aim | Functionality

For a simple R project | A more complex project | A project with several reports with different data and media

Generate data | Overdispersion | Fitting the models | Distribution checks | Dispersion checks | Zero inflation | Underdispersion

1-D Random walks | Simulating random walks | Inspecting simulated random walks | Summarising and subsetting | Transformations | Centring

Simulating random intercepts | Inspecting simulated random intercepts | Link functions | Centring and quantiles | Priors for fixed effects

Overview | Installation | Getting Started | LaTeX packages used in this package | Plain LaTeX | LaTeX table with booktabs | Table Styles | LaTeX options | Striped | Hold position | Scale down | Repeat header in longtable | Full width? | Position | Font Size | Column / Row Specification | Column spec | Insert Images into Columns | Row spec | Header Rows | Cell/Text Specification | Conditional logic | Visualize data with Viridis Color | Text Specification | Grouped Columns / Rows | Add header rows to group columns | Group rows via labeling | Row indentation | Group rows via multi-row cell | Table Footnote | LaTeX Only Features | Linebreak processor | Table on a Landscape Page | Decimal Alignment | Use LaTeX table in HTML or Word | From other packages | tables | xtable

Overview | Installation | Getting Started | Basic HTML table | Bootstrap theme | Alternative themes | Table Styles | Bootstrap table classes | Full width? | Position | Font size | Fixed Table Header Row | Column / Row Specification | Column spec | Insert Images into Columns | Row spec | Header Rows | Cell/Text Specification | Conditional logic | Visualize data with Viridis Color | Text Specification | Tooltip | Popover Message | Links | Integration with formattable | Grouped Columns / Rows | Add header rows to group columns | Group rows via labeling | Row indentation | Group rows via multi-row cell | Table Footnote | HTML Only Features | Scroll box | Save HTML table directly | Use it with sparkline | From other packages | tables | xtable

Introduction | When to Split the Dataframe

Short introduction to Generalized Random Tessellation Stratified sampling (GRTS) | Quadrant recursive map | Reverse hierarchical ordering | Randomisation | Selection of the sample | Benefits of the normal hierarchical order | Benefits of the revese hierarchical order | Main functionality of grtsdb | Nested samples | Repeated samples | n-dimensional GRTS

Introduction | Download with known ts identifier | Search identifier based on variable name | Search identifier based on station name | Check the URL used to request the data

codemetar: generate codemeta metadata for R packages | Why create a codemeta.json for your package? | Installation and usage requirements | Create a codemeta.json in one function call | Keep codemeta.json up-to-date | A brief intro to common terms we'll use: | How to improve your package's codemeta.json? | Going further

Introduction | Which combinations? | How to define the from/to dates | How to define the period | Examples

Introduction | Download all stations for a given variable | Download set of variables from a station

Text wrapping | Insert linebreak in table | Linebreak in other kableExtra functions

Unrecommended Features | add_footnote | Notation systems | Alphabet | Number | Symbol | In-table markers