In this tutorial we describe how to use ModestR to model species distribution in different climatic change scenarios. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension.
24. Creating virtual species with ModestR (Version ModestR 6.4 or higher)modestrsoftware
This tutorial describes how to easily create virtual species and importing them directly in ModestR. Virtual species are a procedure increasingly used in ecology to improve species distribution models. This feature uses the R virtualspecies package from Leroy et al (https://cran.r-project.org/web/packages/virtualspecies/index.html)
15. Locating species occupied river basins with ModestR (Version ModestR 5.3...modestrsoftware
In this tutorial we'll explain how to automatically find the river basins that are occupied by a species, using the species known occurences. River basins are very interesting because they can be considered a natural geographical extent for a species.
18. Estimating species composition in one or more regions with KnowBr and Mo...modestrsoftware
In this tutorial we describe how to use ModestR with KnowBR results to estimate species composition by region. Using SDM results for several species and the expected richness estimated by KnowBR, ModestR can determine the most suitable composition of species of a region.
20. Calculating most probable distribution of a species with Niche of Occurr...modestrsoftware
In this tutorial we describe how to perform species distribution modelling (SDM) with Niche Of Occurrence (NOO) in ModestR. NOO is a new proposed SDM that offers a very good performance and it's easier to perform and understand than other existing SDM's
4.- How to use data cleaning, EOO estimation and environmental of occurrence ...modestrsoftware
How to use data cleaning, EOO estimation and environmental occurrence features in ModestR.
Describes data cleaning; EOO methods supported in ModestR (convex hull, alpha shape, kernel density); environmental occurrence in ModestR.
7.- ModestR tools for taxonomy (Version ModestR v5.3 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
24. Creating virtual species with ModestR (Version ModestR 6.4 or higher)modestrsoftware
This tutorial describes how to easily create virtual species and importing them directly in ModestR. Virtual species are a procedure increasingly used in ecology to improve species distribution models. This feature uses the R virtualspecies package from Leroy et al (https://cran.r-project.org/web/packages/virtualspecies/index.html)
15. Locating species occupied river basins with ModestR (Version ModestR 5.3...modestrsoftware
In this tutorial we'll explain how to automatically find the river basins that are occupied by a species, using the species known occurences. River basins are very interesting because they can be considered a natural geographical extent for a species.
18. Estimating species composition in one or more regions with KnowBr and Mo...modestrsoftware
In this tutorial we describe how to use ModestR with KnowBR results to estimate species composition by region. Using SDM results for several species and the expected richness estimated by KnowBR, ModestR can determine the most suitable composition of species of a region.
20. Calculating most probable distribution of a species with Niche of Occurr...modestrsoftware
In this tutorial we describe how to perform species distribution modelling (SDM) with Niche Of Occurrence (NOO) in ModestR. NOO is a new proposed SDM that offers a very good performance and it's easier to perform and understand than other existing SDM's
4.- How to use data cleaning, EOO estimation and environmental of occurrence ...modestrsoftware
How to use data cleaning, EOO estimation and environmental occurrence features in ModestR.
Describes data cleaning; EOO methods supported in ModestR (convex hull, alpha shape, kernel density); environmental occurrence in ModestR.
7.- ModestR tools for taxonomy (Version ModestR v5.3 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
11.- Calculating species distribution for different periods with ModestR (Ve...modestrsoftware
In this tutorial we’ll describe how to calculate species distribution for different periods. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension
19. Calculating 3D species distribution in marine habitats with ModestR (Ver...modestrsoftware
In this tutorial we describe how to calculate species distribution along depth (3D) in marine habitats with ModestR. In this way, if you have occurrences with depth information from a species, and environmental/climatic data for different depths (such as those from NOAA or Copernicus), with ModestR you can calculate species distribution in 3D, for each depth where the species is present
21.- Creating virtual species and calculating simple ensemble models with R ...modestrsoftware
In this tutorial we describe two simple scripts in R to generate random virtual species, and to calculate species distribution models (SDM's) using ensemble models.
Those scripts may be useful to test hypotesis, or to work with ModestR or other tools
25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)modestrsoftware
This tutorial describes how to donwload DNA barcoding data from BOLD to ModestR for any species, and how to use those data to calculate phylogenetic distances and build phylogenetic trees
1. How to create a database (Version ModestR v6.5 or higher)modestrsoftware
In this tutorial we’ll describe how to create a new ModestR database, how to populate it using taxonomic data stored in a CSV file.
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
12.- Recommendations for marine environments and Economic Exclusive Zones (Ve...modestrsoftware
In this tutorial we’ll give you some tips to work with ModestR in marine environments, different sources of information and how to use the marine Economic Exclusive Zones.
16. Importing different climatic change scenarios from WorldClim to ModestR ...modestrsoftware
In this tutorial we describe how to import different climatic change scenarios from WorldClim to ModestR. This is necessary for example to use the 3D Niche capability of ModestR to model species distribution along those scenarios.
Quantitative Analysis of 3D Refractive Index MapsMathieuFRECHIN
Nanolive’s 3D Cell Explorer allows for the creation of high-content 3D images of living cells with very
high spatio-temporal resolution (x, y:180nm; z:400nm; t:1.7sec). Being able to extract quantitative
data describing the objects (population of cells, cells, organelles) contained in such images is at
the core of leading-edge cell biology research. This application note will start where application
note 2 (AppNote2017-2) stopped by looking at how meaningful numbers can be extracted from
segmented objects using FIJI. We will then bring some cellular features in perspective to help you to
start elegant quantitative studies with the 3D Cell Explorer.
7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)modestrsoftware
This tutorial describes some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS taxonomic database to explore and export taxonomic data.
It can also use GBIF to check and complete taxonomic data from a list of species.
11.- Calculating species distribution for different periods with ModestR (Ve...modestrsoftware
In this tutorial we’ll describe how to calculate species distribution for different periods. To do that, we’ll use the 3D Niche capability of ModestR, taking time as 3th dimension
19. Calculating 3D species distribution in marine habitats with ModestR (Ver...modestrsoftware
In this tutorial we describe how to calculate species distribution along depth (3D) in marine habitats with ModestR. In this way, if you have occurrences with depth information from a species, and environmental/climatic data for different depths (such as those from NOAA or Copernicus), with ModestR you can calculate species distribution in 3D, for each depth where the species is present
21.- Creating virtual species and calculating simple ensemble models with R ...modestrsoftware
In this tutorial we describe two simple scripts in R to generate random virtual species, and to calculate species distribution models (SDM's) using ensemble models.
Those scripts may be useful to test hypotesis, or to work with ModestR or other tools
25. Phylogenetics trees with ModestRr and bold (Version ModestR 6.5 or higher)modestrsoftware
This tutorial describes how to donwload DNA barcoding data from BOLD to ModestR for any species, and how to use those data to calculate phylogenetic distances and build phylogenetic trees
1. How to create a database (Version ModestR v6.5 or higher)modestrsoftware
In this tutorial we’ll describe how to create a new ModestR database, how to populate it using taxonomic data stored in a CSV file.
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
12.- Recommendations for marine environments and Economic Exclusive Zones (Ve...modestrsoftware
In this tutorial we’ll give you some tips to work with ModestR in marine environments, different sources of information and how to use the marine Economic Exclusive Zones.
16. Importing different climatic change scenarios from WorldClim to ModestR ...modestrsoftware
In this tutorial we describe how to import different climatic change scenarios from WorldClim to ModestR. This is necessary for example to use the 3D Niche capability of ModestR to model species distribution along those scenarios.
Quantitative Analysis of 3D Refractive Index MapsMathieuFRECHIN
Nanolive’s 3D Cell Explorer allows for the creation of high-content 3D images of living cells with very
high spatio-temporal resolution (x, y:180nm; z:400nm; t:1.7sec). Being able to extract quantitative
data describing the objects (population of cells, cells, organelles) contained in such images is at
the core of leading-edge cell biology research. This application note will start where application
note 2 (AppNote2017-2) stopped by looking at how meaningful numbers can be extracted from
segmented objects using FIJI. We will then bring some cellular features in perspective to help you to
start elegant quantitative studies with the 3D Cell Explorer.
COMPUTATIONAL ENGINEERING OF FINITE ELEMENT MODELLING FOR AUTOMOTIVE APPLICAT...IAEME Publication
Modals with complicated geometry, complex loads and boundary condition are difficult to analyse and evaluate in the terms of strain, stress, displacement and reaction forces by using theoretical methods. A given modal can be analysed by using Finite Element Method easily with the help of computer software ABAQUS CAE and can get approximate solutions. This report is about modelling two dimensional and three dimensional analyses with the ABAQUS CAE for plane stress, plane strain, shell, and beam and 3d solid modal elements.
NetSim MANETs component can be interfaced with
Component 6 (IOT) module to run 802.15.4 in MAC/PHY
Component 9 (VANETs) module to run IEEE 1609 WAVE in MAC/PHY
Military Radio Add on to run TDMA/DTDMA in MAC/PHY
Modeling of the age old problem of bipedal locomotion using a hybrid automaton and integrating it with the BIP (Behavior,Interaction,Priority) framework
AlarmClock/AlarmClock/AlarmClock.Designer.vb
<Global.Microsoft.VisualBasic.CompilerServices.DesignerGenerated()> _
Partial Class AlarmClockForm
Inherits System.Windows.Forms.Form
'Form overrides dispose to clean up the component list.
<System.Diagnostics.DebuggerNonUserCode()> _
Protected Overrides Sub Dispose(ByVal disposing As Boolean)
Try
If disposing AndAlso components IsNot Nothing Then
components.Dispose()
End If
Finally
MyBase.Dispose(disposing)
End Try
End Sub
'Required by the Windows Form Designer
Private components As System.ComponentModel.IContainer
'NOTE: The following procedure is required by the Windows Form Designer
'It can be modified using the Windows Form Designer.
'Do not modify it using the code editor.
<System.Diagnostics.DebuggerStepThrough()> _
Private Sub InitializeComponent()
Me.components = New System.ComponentModel.Container
Me.timeLabel = New System.Windows.Forms.Label
Me.setButton = New System.Windows.Forms.Button
Me.resetButton = New System.Windows.Forms.Button
Me.alarmTimer = New System.Windows.Forms.Timer(Me.components)
Me.alarmLabel = New System.Windows.Forms.Label
Me.currentTimeLabel = New System.Windows.Forms.Label
Me.SuspendLayout()
'
'timeLabel
'
Me.timeLabel.AutoSize = True
Me.timeLabel.Location = New System.Drawing.Point(11, 15)
Me.timeLabel.Name = "timeLabel"
Me.timeLabel.Size = New System.Drawing.Size(37, 15)
Me.timeLabel.TabIndex = 0
Me.timeLabel.Text = "Time:"
'
'setButton
'
Me.setButton.Location = New System.Drawing.Point(173, 11)
Me.setButton.Name = "setButton"
Me.setButton.Size = New System.Drawing.Size(55, 23)
Me.setButton.TabIndex = 2
Me.setButton.Text = "Set"
Me.setButton.UseVisualStyleBackColor = True
'
'resetButton
'
Me.resetButton.Enabled = False
Me.resetButton.Location = New System.Drawing.Point(173, 47)
Me.resetButton.Name = "resetButton"
Me.resetButton.Size = New System.Drawing.Size(55, 23)
Me.resetButton.TabIndex = 3
Me.resetButton.Text = "Reset"
Me.resetButton.UseVisualStyleBackColor = True
'
'alarmTimer
'
Me.alarmTimer.Enabled = True
Me.alarmTimer.Interval = 1000
'
'alarmLabel
'
Me.alarmLabel.AutoSize = True
Me.alarmLabel.Location = New System.Drawing.Point(12, 50)
Me.alarmLabel.Name = "alarmLabel"
Me.alarmLabel.Size = New System.Drawing.Size(42, 15)
Me.alarmLabel.TabIndex = 4
Me.alarmLabel.Text = "Alarm:"
'
'currentTimeLabel
'
Me.currentTimeLabel.BorderStyle = System.Windows.Forms.BorderStyle.Fixed3D
Me.currentTimeLabel.Location = New System.Drawing.Point(59, 11)
Me.currentTimeLabe.
Willie Nelson Net Worth: A Journey Through Music, Movies, and Business Venturesgreendigital
Willie Nelson is a name that resonates within the world of music and entertainment. Known for his unique voice, and masterful guitar skills. and an extraordinary career spanning several decades. Nelson has become a legend in the country music scene. But, his influence extends far beyond the realm of music. with ventures in acting, writing, activism, and business. This comprehensive article delves into Willie Nelson net worth. exploring the various facets of his career that have contributed to his large fortune.
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Introduction
Willie Nelson net worth is a testament to his enduring influence and success in many fields. Born on April 29, 1933, in Abbott, Texas. Nelson's journey from a humble beginning to becoming one of the most iconic figures in American music is nothing short of inspirational. His net worth, which estimated to be around $25 million as of 2024. reflects a career that is as diverse as it is prolific.
Early Life and Musical Beginnings
Humble Origins
Willie Hugh Nelson was born during the Great Depression. a time of significant economic hardship in the United States. Raised by his grandparents. Nelson found solace and inspiration in music from an early age. His grandmother taught him to play the guitar. setting the stage for what would become an illustrious career.
First Steps in Music
Nelson's initial foray into the music industry was fraught with challenges. He moved to Nashville, Tennessee, to pursue his dreams, but success did not come . Working as a songwriter, Nelson penned hits for other artists. which helped him gain a foothold in the competitive music scene. His songwriting skills contributed to his early earnings. laying the foundation for his net worth.
Rise to Stardom
Breakthrough Albums
The 1970s marked a turning point in Willie Nelson's career. His albums "Shotgun Willie" (1973), "Red Headed Stranger" (1975). and "Stardust" (1978) received critical acclaim and commercial success. These albums not only solidified his position in the country music genre. but also introduced his music to a broader audience. The success of these albums played a crucial role in boosting Willie Nelson net worth.
Iconic Songs
Willie Nelson net worth is also attributed to his extensive catalog of hit songs. Tracks like "Blue Eyes Crying in the Rain," "On the Road Again," and "Always on My Mind" have become timeless classics. These songs have not only earned Nelson large royalties but have also ensured his continued relevance in the music industry.
Acting and Film Career
Hollywood Ventures
In addition to his music career, Willie Nelson has also made a mark in Hollywood. His distinctive personality and on-screen presence have landed him roles in several films and television shows. Notable appearances include roles in "The Electric Horseman" (1979), "Honeysuckle Rose" (1980), and "Barbarosa" (1982). These acting gigs have added a significant amount to Willie Nelson net worth.
Television Appearances
Nelson's char
Micro RNA genes and their likely influence in rice (Oryza sativa L.) dynamic ...Open Access Research Paper
Micro RNAs (miRNAs) are small non-coding RNAs molecules having approximately 18-25 nucleotides, they are present in both plants and animals genomes. MiRNAs have diverse spatial expression patterns and regulate various developmental metabolisms, stress responses and other physiological processes. The dynamic gene expression playing major roles in phenotypic differences in organisms are believed to be controlled by miRNAs. Mutations in regions of regulatory factors, such as miRNA genes or transcription factors (TF) necessitated by dynamic environmental factors or pathogen infections, have tremendous effects on structure and expression of genes. The resultant novel gene products presents potential explanations for constant evolving desirable traits that have long been bred using conventional means, biotechnology or genetic engineering. Rice grain quality, yield, disease tolerance, climate-resilience and palatability properties are not exceptional to miRN Asmutations effects. There are new insights courtesy of high-throughput sequencing and improved proteomic techniques that organisms’ complexity and adaptations are highly contributed by miRNAs containing regulatory networks. This article aims to expound on how rice miRNAs could be driving evolution of traits and highlight the latest miRNA research progress. Moreover, the review accentuates miRNAs grey areas to be addressed and gives recommendations for further studies.
"Understanding the Carbon Cycle: Processes, Human Impacts, and Strategies for...MMariSelvam4
The carbon cycle is a critical component of Earth's environmental system, governing the movement and transformation of carbon through various reservoirs, including the atmosphere, oceans, soil, and living organisms. This complex cycle involves several key processes such as photosynthesis, respiration, decomposition, and carbon sequestration, each contributing to the regulation of carbon levels on the planet.
Human activities, particularly fossil fuel combustion and deforestation, have significantly altered the natural carbon cycle, leading to increased atmospheric carbon dioxide concentrations and driving climate change. Understanding the intricacies of the carbon cycle is essential for assessing the impacts of these changes and developing effective mitigation strategies.
By studying the carbon cycle, scientists can identify carbon sources and sinks, measure carbon fluxes, and predict future trends. This knowledge is crucial for crafting policies aimed at reducing carbon emissions, enhancing carbon storage, and promoting sustainable practices. The carbon cycle's interplay with climate systems, ecosystems, and human activities underscores its importance in maintaining a stable and healthy planet.
In-depth exploration of the carbon cycle reveals the delicate balance required to sustain life and the urgent need to address anthropogenic influences. Through research, education, and policy, we can work towards restoring equilibrium in the carbon cycle and ensuring a sustainable future for generations to come.
UNDERSTANDING WHAT GREEN WASHING IS!.pdfJulietMogola
Many companies today use green washing to lure the public into thinking they are conserving the environment but in real sense they are doing more harm. There have been such several cases from very big companies here in Kenya and also globally. This ranges from various sectors from manufacturing and goes to consumer products. Educating people on greenwashing will enable people to make better choices based on their analysis and not on what they see on marketing sites.
Characterization and the Kinetics of drying at the drying oven and with micro...Open Access Research Paper
The objective of this work is to contribute to valorization de Nephelium lappaceum by the characterization of kinetics of drying of seeds of Nephelium lappaceum. The seeds were dehydrated until a constant mass respectively in a drying oven and a microwawe oven. The temperatures and the powers of drying are respectively: 50, 60 and 70°C and 140, 280 and 420 W. The results show that the curves of drying of seeds of Nephelium lappaceum do not present a phase of constant kinetics. The coefficients of diffusion vary between 2.09.10-8 to 2.98. 10-8m-2/s in the interval of 50°C at 70°C and between 4.83×10-07 at 9.04×10-07 m-8/s for the powers going of 140 W with 420 W the relation between Arrhenius and a value of energy of activation of 16.49 kJ. mol-1 expressed the effect of the temperature on effective diffusivity.
Diabetes is a rapidly and serious health problem in Pakistan. This chronic condition is associated with serious long-term complications, including higher risk of heart disease and stroke. Aggressive treatment of hypertension and hyperlipideamia can result in a substantial reduction in cardiovascular events in patients with diabetes 1. Consequently pharmacist-led diabetes cardiovascular risk (DCVR) clinics have been established in both primary and secondary care sites in NHS Lothian during the past five years. An audit of the pharmaceutical care delivery at the clinics was conducted in order to evaluate practice and to standardize the pharmacists’ documentation of outcomes. Pharmaceutical care issues (PCI) and patient details were collected both prospectively and retrospectively from three DCVR clinics. The PCI`s were categorized according to a triangularised system consisting of multiple categories. These were ‘checks’, ‘changes’ (‘change in drug therapy process’ and ‘change in drug therapy’), ‘drug therapy problems’ and ‘quality assurance descriptors’ (‘timer perspective’ and ‘degree of change’). A verified medication assessment tool (MAT) for patients with chronic cardiovascular disease was applied to the patients from one of the clinics. The tool was used to quantify PCI`s and pharmacist actions that were centered on implementing or enforcing clinical guideline standards. A database was developed to be used as an assessment tool and to standardize the documentation of achievement of outcomes. Feedback on the audit of the pharmaceutical care delivery and the database was received from the DCVR clinic pharmacist at a focus group meeting.
WRI’s brand new “Food Service Playbook for Promoting Sustainable Food Choices” gives food service operators the very latest strategies for creating dining environments that empower consumers to choose sustainable, plant-rich dishes. This research builds off our first guide for food service, now with industry experience and insights from nearly 350 academic trials.
Artificial Reefs by Kuddle Life Foundation - May 2024punit537210
Situated in Pondicherry, India, Kuddle Life Foundation is a charitable, non-profit and non-governmental organization (NGO) dedicated to improving the living standards of coastal communities and simultaneously placing a strong emphasis on the protection of marine ecosystems.
One of the key areas we work in is Artificial Reefs. This presentation captures our journey so far and our learnings. We hope you get as excited about marine conservation and artificial reefs as we are.
Please visit our website: https://kuddlelife.org
Our Instagram channel:
@kuddlelifefoundation
Our Linkedin Page:
https://www.linkedin.com/company/kuddlelifefoundation/
and write to us if you have any questions:
info@kuddlelife.org
17. An example using ModestR to assess species distribution in different climatic change scenarios (Version ModestR 5.6 or higher)
1. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Step by step tutorial:
An example using ModestR to
model species distribution in
different climatic change
scenarios
2. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
What do you need for this tutorial:
1. ModestR v.5.6 or higher installed
2. Internet connection
3. About 40 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR
3. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
We’ll describe how to use ModestR to
assess species distribution in different
climatic change scenarios. To do that, we’ll
use the 3D Niche capability of ModestR,
taking time as 3th dimension. Follow the
next steps!
4. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
For this tutorial we’ll use a climate change scenario from
WorldClim. In order to follow the tutorial, you already have
this climate change scenario integrated in ModestR.
If you still haven’t done this, please see Tutorial 16 in the
ModestR Tutorials page
5. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
First step of NOO3D is loading occurrences from a species. With ModestR you can
download data from GBIF or import them from a CSV file. For this example we’ll use a
sample file with occurrences from a virtual species generated using the “virtualspecies”
package from R, using the variables BIO2, BIO8 and BIO15 of WorldClim
Here is the suitability map of this
species. As you can see, it has been
limited to a rectangular area in France
6. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1) Select menu “Options / Preferences”
2) To use Spanish format (default):
Decimal separator “ , “
Field separator “ ; “
To use English format :
Decimal separator “ . “
Field separator “ , “
For this tutorial you’ll find a sample file “VirtualSpecies_Original_for_Tutorial_17”.
You can choose it between two CSV options: Format Spanish / Format English
You may select the format depending on the configuration in the "Options / Preferences" menu of the "CSV Exportation
Options" section of any of the ModestR applications.
For example in ModestR DataBase Manager you can find it:
7. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
2) Go to menu “File/Import/Occurrence
data from CSV file” then select the
downloaded CSV file
Download the file “VirtualSpecies_Original_for_Tutorial_17” from next link:
CSV in Spanish Format / CSV in English Format
Then import it from MapMaker
1) Run ModestR MapMaker
8. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
When importing occurrences to ModestR, you have to select the valid habitats for the species
1) In the dialog box just
check the “Land” habitat
2)Then click on “Accept”
3) Once the import
completed, click on
“Accept”
9. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Once occurrences imported, you can zoom on the area. ModestR checks the habitats and indicates when
occurrences are in an invalid habitat for the species using another color. Those occurrences are shown but are
not used in any analysis or calculation
Invalid occurrences (here in black) are
occurrences located in habitats not valid for the
species. As we indicated that only land was valid
for this species, invalid occurrences are those
located in marine or freshwater habitats.
10. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
NOO3D can be used to calculate a density map that shows species suitability , of to calculate a distribution.
We’ll first start with the density map
1) Go to menu Mapping/Niche of occurrence/Density Map
11. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Next step is creating or selecting an existing 2D or 3D CEL (Compounded Environmental Layer).
A CEL will bind together several enviromental variables in a single multidimensional variable. In this case we’ll
create a new 3D CEL using the WorldClim data we have imported previously
1) Select “Create a new 3D CEL”
More details about what are compounded
environmental layers can be found in ModestR
User’s Manual on ModestR website.
A tutorial about compounded environmental layers
creation can also be found at
http://www.ipez.es/ModestR/Manual_Tutorial.html
2) Click “Accept”
If other previously created and stored
CEL’s exist, they will be show here
12. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
When creating a 3D CEL, only 3D datasets will be displayed among the candidate variables.
You have to select the whished variables you want to work with.
1) For this example, in the dialog box
that will be shown, select all the
variables from a WorldClim climate
change scenario (i.e. those for RCP26,
or RCP45…)
By default, NOO3D modelling will be done
for the whole range covered by the
selected variables, which in this case are
the years from 2000 to 2070.
13. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
You also have to select the geographical extent you want to work with
2) Select “Extent of Occurrence”
as geographical extent .
By default, alpha
shape is used.
3) Click on “Preview” to see the Extent of
Occurrence to be used in the World map.
4) Click on “Continue”
14. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
1) Click on “Calculate VIF “
In the next step you can calculate VIF (Variance Inflation Factor)
of the variables to detect collinearity and, optionally, delete
some variables that may be redundant
15. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
You can select a variable an delete it from the list.
VIF will be recalculated with the remaining variables. You can
continue deleting other variables, until VIF is considered acceptable
(tipically when VIF<30)
For this example we’ll keep only BIO2, BIO4, BIO8, BIO9, BIO15,
BIO18 and BIO19. Delete all other variables
VIF of each variable is shown
VIF >30 is shown in red.
3) Click on “Continue”
2) Select a variable and click on “Delete selected“
(keep only BIO2, BIO4, BIO8, BIO9, BIO15, BIO18 and BIO19)
Note.- to select several variables keep Ctrl key pressed while
selecting.
16. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
In the next step you can calculate the relative relevance of each variable regarding the species distribution using a
Instability Index (see https://doi.org/10.1016/j.ecoinf.2016.11.004 for more information). This can help you selecting the
most relevant variables for the species
1) Select “Use all occurrences” and uncheck the
option “Use occurrences Z value if exists”
2) Select “Use custom Z value” then select 2000 as value. This means
that all current occurrences are manually assigned to year 2000.
In other context, for example when modelling species in a depth
range, we’ll most likely use the depth value of each occurrence.
3) Select “EOO” to use only the values of
the variables within the EOO
4) Click on “Analyse”
Z meaning is set by default to “Year”
because this is the Z meaning we
previously assigned to the variables
we imported.
17. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Contribution of each variable will appear
5) Click on “Continue”
Most relevant variables
will be automatically
selected.
18. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
In the next step variables are optimally ordered in the polar space using they correlation matrix.
You can eventually reorder variables, but the most of the time you’ll just continue
Click on “Continue”
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In the next step, the 3DCEL is generated and shown in the polar coordinates system
Here the current environmental data are projected on polar coordinates system.
The result is a tridimensional representation of the different environmental
conditions that occur in the world for each year..
2) Click on “3D View” to
open a 3D viewer and
show the 3DCEL in a 3D
view.
1) Click on those cursor
buttons to see the
different layers of the
3DCEL. There is one layer
for each year of the used
variables
3) Click on “Continue”
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In the last step, you can optionally save this 3D CEL to be used later. Or you can just load it for the current worksession.
For this example we’ll save it to use it later
1) Enter a name
2) Click on “Save layer”
4) Click on “Continue”
3) When save completed,
click on “Continue”
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3) Click on “Continue”
This Z value indicates here which year (thus, which
environmental data) corresponds to the current species
occurrences. For example, if we assign them 2000, that
means that the occurrences should be considered as
corresponding to the environmental data assigned to Z
(Year)=2000 in the 3D CEL we are using.
This indicates that NOO3D will generate a model for the whole
range of years included in the 3DCEL (2000,2050, 2070).
In other contexts, for example when modelling species in a depth
range, we’ll most likely use the depth range where the species is
present, but not the whole depth range available.
1) Select “Use all occurrences”
and uncheck the option “Use
occurrences Z value if exists”
Z meaning is set to Year because this is the Z meaning
we previously assigned to the variables we imported.
2) Select “Use custom Z value”
to the current occurrences
Once a 3DCEL selected or built, we can perform the NOO3D for the species.
We’ll have to set that the Z axis is Year and assign a Z value to the current occurrences, as in
this context they don’t have a value. In other contexts, for example when modelling species in
a depth range, we’ll most likely use the depth value of each occurrence
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2) Click “Run” to calculate density
1) Set “Smoothing” to 3
NOO3D uses a kernel density function to calculate the suitability of the species.
Therefore a smoothing parameter can be adjusted to take into account the
environmental tolerance of the species. The more a species is tolerant, the
higher we may adjust smoothing. Typical values range between 1 and 3
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Results will be displayed both in the world map, showing geographic density, and in the dialog box, showing polar density map
You can see the density for each Z (year)
value of the 3D CEL using the button bar
You can also open the 3D view using the
3D View button
Probability and density rasters can
be saved to files using this button
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If you click the 3D View button you’ll see a 3D viewer with the niche density data of the species
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Going back to MapMaker, you can move the dialog box to be able to show the world map, and see the species
suitability for different years
1) Drag the dialog box to a side
to be able to see the world map
2) Click on those cursor buttons to
see the different layers of the
3DCEL. There is one layer for each
year of the used variables
You can see in the world map the
density for each Z (year) value of
the 3D CEL using the button bar to
change year
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Close the dialog box and go back to main MapMaker window. We’ll now calculate Distribution map
1) Go to menu
“Mapping/Niche of occurrence/ Distribution map”
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Thanks to having saved previously the 3DCEL we built, we’ll now just have to select it to calculate NOO3D distribution
2) Select the previously saved CEL
3) Click on “Accept”
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The parameters to set are the same than for the density map
This indicates that NOO3D will generate a model for the whole
range of years included in the 3DCEL (2000,2050, 2070).
In other contexts, for example when modelling species in a depth
range, we’ll most likely use the depth range where the species is
present, but not the whole depth range available.
1) Select “Use all occurrences” and
uncheck the option “Use occurrences
Z value if exists”
Z meaning is set to Year because this is the Z meaning
we previously assigned to the variables we imported.
2) Select “Use custom Z value” to
the current occurrences
3) Click on “Continue”
29. MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
5) Click on “Run”. You’ll be asked to enter a file
name to save results. Then calculation will start
4) Set “Smoothing” to 3
Kernel density hull options
“Add area” option (by default) indicates that the
estimated area will be added to the distribution map. The
other option, “Hull simulation”, adds just a shape only
for visualization purposes, not as part of the species
distribution.
Range can be “Full layer” or “EOO”.
In this case, as the CEL we are using
is already limited to the EOO, we
can leave the defaults
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Once ended, results will include a file that can be opened with MRMapping
MRMapping is another application of ModestR that
can show several distribution maps at the same time,
while MapMaker is intended to work with a single
distribution map
Click to “Open MRMapping”
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The file generated for MRMapping contains a distribution map for each Z value (year) of the 3D CEL used to calculate
niche. In this case, this means a distribution map for each year for which we added environmental data to the 3D CEL
Zoom to France
Uncheck valid occurrences to
only see the range distribution
The distribution of the species
for each year is displayed with a
different color
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Go to menu “Edit / Distribution list editor”
Double click on land colors to modify
them
Use those checkboxes to show / hide
individual distribution maps
Select a distribution and use those
buttons to change their display order
You can modify the distribution colors and order to explore the species distribution by year
The list of distributions is shown here
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You can also use slideshow feature to see how species niches will change in time
Go to “View / Slideshow”
A floating toolbar will be displayed, to easily move around the distribution maps
for each Z value (year), much like moving from a slide to another in a slideshow
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The procedure previously described is useful when working with one or few species, and when we want to see the results
of each step, test several parameters, etc.
But when working with many species, it may be more useful to use DataManager application from ModestR, that
allows working with databases of hundreds or thousands of species. In DataManager you can perform NOO3D in batch
mode and obtain for example the distribution of many species for different years
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It was the Step by step tutorial:
An example using ModestR to model species distribution in
different climatic change scenarios
Thank you for your interest.
You can find this one and other tutorials in http://www.ipez.es/ModestR
By the ModestR team