sylvainschmitt / phd

Personnal repository for my PhD code and documentation.

👋 Hi there!

I'm Sylvain, an ecologist at CIRAD (https://www.cirad.fr), a French research center working with developing countries on environmental and development issues. I am currently conducting research into modeling the joint effect of climate change and anthropogenic disturbance on the dynamics of Amazonian tropical forests.

More info at https://sylvainschmitt.netlify.app/.

phd's Issues

Topography genomics

Topography genomics

• Firs draft
• Supplementary materials
• Cover letter
• Reviews
• Submission
• Review
• Co-authors approval
• Resubmission
• Data archiving
• Response to reviews

Anne internship

• Sampling
  • Field preparation
  • Collection management (silicagel, dry leaves, flower, wood samples)
• Measures
  • Dry weights
  • LA with scans
  • Data Cleaning
• Analysis (linked to functional ecology modelling)
  • Formation
    • Bayes & Stan
    • R, Rmarkdown, R projects, and R packages (tydiverse)
    • Git, GitHub
  • Model(s) building
    • Ontogeny
    • Abiotic
    • Biotic interactions
    • Ecological levels
    • Full
  • Bayesian inference
    • Sub-models
    • Full model
    • Random effects variance
  • Writing
    • Introduction
    • Mat & Met
    • Results (figure production)
    • Discussion

environment.Rmd

J'ai essayé de faire tourner ton script , et je suis bloquée pour ici pour avec les données gapcar créer le fichier gap.Rdata il faut dcm.

Si non pour le reste ca c'est bien passer il va juste pas oublié de charger le package rgeos

Concept document

Low priority or abandoned

• Integrate Myriam last review
• Integrate ideas from GTÖ poster
• Integrate Bruno's meeting idea
• Integrate CST bibliography

Symcapture

Symcapture

• Design probes
• Extract DNA
• Prepare libraries
• Capture
• Sequencing
• Raw data analysis
• Populations structure
• Populations history
• Annotation
• Populations genomics
• Environmental genomics
• Growth genomics
• Functional genomics
• Introgression
• analyses scenario speciation @x. Vekemans

Sampling

Ecuador

• Check needed material
• Command material

Eschweilera

• Dates: September-October
• Anne internship
• FTH project
• Saint-Omer availabilities
• Check needed material
• Define sampling
• Sampling

Symphonia

• Sampling

Other

• APA form

Parvicapture

Parvicapture

• Sampling
• Select target sequence to be captured
• Design probes (target sequences to be sent to the company)
• Extract DNA
• Prepare libraries
• Sequencing
• Raw data analysis
• Populations structure
• Populations history
• Populations genomics
• Environmental genomics
• Growth genomics

Eschweilera functional

Anne internship

• Sampling
  • Field preparation
  • Collection management (silicagel, dry leaves, flower, wood samples)
• Measures
  • Dry weights
  • LA with scans
  • Data Cleaning
• Introduction
  • Bibliography
  • Theory
  • Question / Hypothesis
• Analysis
• Discussion

Growth genomics

Growth genomics

• Outlines
• Christophe review
• Choose journal
• Expand discussion
• First draft
• Supplementary materials
• Reviews
• Reinforce
• Code to GitHub
• Data to Zenodo
• Sequences to SRA
• Co-authors approval
• Direct submission to PNAS
• Submission inquiry to Current Biology
• Submission to Nature Ecology & Evolution
• Olivier comments

Ecoevosimulator

Ecoevosimulator

Writing

• Literature
• Niklas kick-off (05/03)
• Co-authors kick-off (date?)
• External review of the simulator?
• Draft
• Second author review (who?)
• Co-authors approval
• Submit

Virtual experiment

• develop the topography generator
• develop the forest gap dynamics generator
• tune the dispersion with a uniform kernel including autofecondation and mother and father dispersal
• define response variables (genotypic structure, environmental distance or mean viability or fitness, gene flow)
• analyse response variables sensitivity to parameters one-by-one
• define and test an experimental design to explore the questions

TROLL JoE

• Reviewer comments
• English correction ?
• Coauthor comments
• Resubmission

Genetic data production

Symphonia geonmics

• Choose kit
• Select target sequence to be captured
• Design probes (target sequences to be sent to the company)
• Extract DNA
• Prepare libraries
  • Normalisation
  • Digestion
  • Adaptor ligation
  • Size selection (1 col remaining)
  • Tagging and amplification
  • Amplification check
  • Library repeat
  • Capture
• Sequencing
  • Quantify DNA
  • Build equimolar pools for lanes
• Raw data analysis
  • Quality check
  • Trimming
  • Targets mapping
  • Reference mapping
  • de novo assembly
  • de novo reference mapping
  • Genome by Sequencing (GbS)
  • SNP call
  • SNP filtering

Eschweilera geonmics

• Sampling
• Select target sequence to be captured
  • Functional targets (Oscar transcripts)
  • Neutral targets (ddRAD consensus sequences)
• Design probes (target sequences to be sent to the company)
• Extract DNA
• Prepare libraries
  • Purification
  • Dosage (NanoDrop adjusted Qubit)
  • Concentration (SpeedVac)
  • Normalization
  • Library test (2 samples)
  • Digestion (1')
  • Adaptor ligation
  • Tagging and amplification
  • Purification
  • Dosage (PicoGreen)
  • Equimolar pools preparation
  • Pools fragment size evaluation (Bioanalyzer)
  • Pools fragment size selection (Pippin)
  • Capture
• Sequencing
  • Quantify DNA (Qubit/qPCR)
  • Equimolar pools for lanes
• Raw data analysis
  • Quality check
  • Trimming
  • Targets mapping
  • Reference mapping
  • de novo assembly
  • de novo reference mapping
  • Genome by Sequencing (GbS)
  • SNP call
  • SNP filtering

Species distribution

Writing

• Rewrite & include comments
• Co-authors' comments
• Resubmit

Analysis

• Find bayesian niche model form
• Define species complex to be tested
• Explore graphically complex distribution with environment
• Define niche descriptors
• Infer Complexes niche
• Infer species niche within complexes
• Species distribution & growth

Genetic Variance Modelling

Unordered

• Santi's approval for CLONAPIN data
• reduce dataset (intelligent way for environmental variables, e.g. same region = same environment)
• develop simple model
• explore currently used methodology
• simulate data
• fit models on simulated and real data

Uppangala

Uppangala

• Manuscript new version
• Maxime, Valérie and François revisions
• Coauthor sharing (Ayappan, Bala, Ravi, and Chandra)
• Submission

FRB candidature

• CV
• Candidature
• Submission

Thesis Discussion

Thesis Discussion

• Syngameon modelling pre-results
• First draft
• Revision
• Supervisors' review
• Final version

Thesis Introduction

Thesis Introduction

• First draft
• Revision
• Supervisors' review
• Final version

27.07 Myriam's Skype

Main

• Introduction: review now or at the end?
• Ch1: mail to editors?
• Ch3 Topo
  • integrate review
  • submit?
• Ch4 Growth
  • choose journal
  • first draft
  • reviews => integrate PhD (need Bruno's availability)
  • etc post PhD if long process
• Discussion
  • Ch5 modelling:
    • Myriam's mind
    • Use external advises?
    • Next steps (TWI, NCI, which processes)?
  • Plan
  • Plan review?
  • final review

Others

• Niklas?
• Calendar
  • field
  • contract
  • quarantine
  • UB
• OFB candidature: wait 1st week Bordeaux?
• FEM review: accept?

LT & weather

LT & weather

short communication

• Explore weather and REW data with LT Symphonia (randomForest ?)
• Build a model to represent temporal variation (cf article Schmitt et al. 2020)
• Discuss the interpretation with Gérladine, Bruno and maybe more specialists of ecophysiology (Sabrina answer the 19/10)
• Write a short communication focused on the seasonal functional variation with a strong pattern but on different individuals advocating for more studies
• Santi review
• Sabrina review (12/03)
• Co-authors review
• Write Abstract
• Co-authors approval
• Submit

gap data transformation to d_gap

J'ai enfin pu faire tourner le script sur tabebuia et obtenir les données gap cependant il y a de nouveau un soucis cette fois-ci avec la fonction mask avec l'erreur : "Error in p@polygons[[i]] : indice hors limites"

Aussi ligne 163 c'est "subset" et pas "subest"

PhD comitee 15.05

PhD comittee

• Update participants
• Prepare CST2 Report
• Prepare CST2 presentation
• Obtain Richard and Sabrina signatures
• Send report to the doctoral school

Functional ecology

Review

• Rewrite including sp complex concept
• Include reviewers comments

Analysis

• Analyses traits co-variation (PCA)
• Explore FT-E interactions
• Build a first generic model
  • Ontogenetic/Light effect
  • TWI effect
  • Competition effect
• Infer models for every traits and complex

Writing

• Check analysis
• M&M and Results
• Introduction & Discussion draft
• Discuss results / interpretation with Sabrina & Geraldine (27/2)
• Submit ATBC (20/03)
• Myriam review
• Explore species coexistence explanation
• Rewrite discussion
• Coauthors revision
• Submission

Data production

• Eschweilera measures
• Eschweilera data cleaning and preparation from FT
• Prepare environmental data