- topography: MolEcol published
- modelling: explore
- growth: refs MolEcol submission
- thickness: Plant Biology submission
- functional: pred for pres
- thickness: MEE resubmission
- topography: MolEcol resubmission
- distribution: acceptance
- thickness: first review round
- growth: Ref New Phyto
- topography: Ref & SI Mol Ecol & SRA submission
- modelling: interaction2 figure
- distribution: Apocynaceae
- functional: weather data
- symcapture: check data for New Phyto
- modelling: manuscript and first share
- modelling: msc: intro begins
- modelling: msc fig & tab
- Defense is done !!
- distribution: review 2
- functional: prep defense
- thickness: in prep
- growth: ready to submit but switched to overleaf
- symcapture: split to going repository
- topography: review 1
- modelling: defense, msc begins
- thesis: title updated post defense
- growth: figures for PNAS
- parvicapture: Manaus
- symcapture: spatial structure
- modelling: metrics, sensitivity, virtual experiment
- thesis: title
- modelling: time steps & system metrics
- modelling: forest gap dynamics: timesteps
- modelling: forest gap dynamics: mortality
- modelling: forest gap dynamics: mixed distributions and spatial clustering
- distribution: Oecologia revision 1
- modelling: forest gap dynamics: trying to define gaps
- modelling: forest gap dynamics
- distribution: congenerics and conspecifics
- thickness manuscript
- topography: size effect
- modelling: ecoevosimulator and topography
- thesis: validation
- thickness: lognormal
- thickness: new models
- thickness: weather data, models, and msc begins
- thickness: init
- thesis: printing prep, list of manuscripts
- modelling: updating to ecoevosimulator
- thesis: remerciements
- thesis: introduction & discussion: last review
- thesis: introduction: Bruno's comments
- thesis: discussion: Bruno's comments
- thesis: abstract and résumé substantiel
- thesis: Ch4 update
- thesis: discussion: take home
- thesis: A1
- thesis: chapters polishing
- thesis: appenbdix polishing
- thesis: discussion: first draft and Myriam's review begins
- introduction: Myriam's review
- thesis: discussion: subpart 18/19 almost almost done!
- thesis: discussion: part 3/4 almost done
- growth:msc revision
- thesis: discussion: part 2/4
- thesis: discussion: part 1/4
- thesis: introduction reviwe by Niklas, chapters formatting, appendix, and discussion plan
- growth: Msc PNAS first draft
- topography: pre-submission
- growth: Msc PNAS first draft
- symcapture: forest gaps dynamics
- topography: msc review in progress
- introduction: Niklas review in progress
- growth: Christophe v2
- symcapture: forest gaps dynamcis
- topography: Bruno's comments begins
- modelling: simulators cpp
- topography: Myriam review in progress
- thesis: introduction review in progress
- modelling: literature and structure
- topography: newphytoversion & Myriam review in progress
- thesis: introduction review in progress
- modelling: begins
- growth:outlines v. Christophe share 1
- topography:msc
- file reordering for genomics manuscripts writing
- genomics:manuscripts:outlines3growth
- thesis:introduction:plan
- thesis:introduction:models
- thesis:introduction:context
- thesis:introduction:evolution
- thesis:introduction:ecology
- thesis:introduction: closely-related species
- thesis:introduction:biodiveristy amazon basin
- thesis: introduction plan
- thesis: introduction begins
- symcapture: manuscript: outlines 4 shared
- parvicapture: Fst & bayescan
- symcapture: envgenom RE
- symcapture: manuscript: biblio, outlines 3, outlines 4
- environment: TWI vs RE continue
- thesis: chapter 3 4 formatting w Orcid
- parvicapture: filtering, structure, envgeno, growthgeno v2
- environment: TWI vs RE
- parvicapture: filtering, structure, envgeno, growthgeno (wip)
- parvicapture: fighting with denovo
- thesis: Chapters 1 and 2
- functional: resubmission 20200603
- thesis: begins
- functional: sp autocorr & plot random effects following minor review
- symcapture: outlines version 2
- symcapture: take home message firs draft
- symcapture: fixed NCI mistake & New figure
- parvicapture: splitting reference for denovo
- symcapture: revised models
- symcapture: manuscript M&M and Res v3 + SupMat extended
- symcapture: all updated models
- variance removed
- symcapture: transcripto removed
- symcapture: Animal fix begin
- variance: begins & CLONAPIN
- symcapture: Msc growth M&M & Res v2 + introgression
- parvicapture: denovo test succeed, full data run
- distribution: oecologia presubmission
- symcapture:manuscript: M&M & Res v1
- symcapture: growth model gamxgeno gemaxgenoenv 1 & 2
- symcapture: FT geno
- symcapture: gmax model is good !
- distribution: new results
- functional: updated for review
- symcapture: growth models with lognormal
- distribution: R+ variables + cleaning
- lectures: rmarkdown
- symcapture: growth & animal models
- symcapture: Animal model validated with VCFtools kinship relatedness 2
- lectures: rmarkdwon for FOREN seminar @INPHB
- symcapture: new growth model with DBH
- symcapture: growth R2
- distribution: without logging & cleaning
- parvicapture: rtest to search label mix
- parvicapture: raw2vcf script & error search
- symcapture: msc growth begins
- symcapture: env & growth genomics v2
- symcapture: Animal in growth model
- parvicapture: SNP filtering
- symcapture: Animal with pop var
- parvicapture: sequences delivery, quality, trimming, mapping, and SNP calling
- symcapture: synonymy, TWI outlier
- symcapture: introgression chapter begin
- distribution: draft 1
- symcapture: introgress, corrected envgenom & growthgenom
- symcapture: homemade PVE in growth
- symcapture: growth GWAS LMM & BSLMM
- symcapture: growth & environment
- symcapture: post meeting Niklas & Myriam fixes, growth models begin
- parvicapture: capture 1
- symcapture: growth begins & co
- symcapture: SLA polygenic, BSLMM try in stan (fail)
- lecture: bayes EFT update
- symvapture: EnvGenom variables, methods, NCI, ANCR
- distribution: biblio intro syngameon
- symvapture: BSLMM TWI begin
- symcapture: polygenic signal with BSLMM Zhou 2013 Plos Genetics
- functional: Oikos submission
- symcapture: PopStr, Annotation, PopHist, PopGenom, EnvGenom +explanation, 1st results
- sampling: Sympho check 10.19
- distribution: NCI in time & ms
- functional: new model inter intra
- parvicapture: LARGESCALE + capture
- symcapture: PopStr, Annotation, PopHist, PopGenom, EnvGenom begin
- functional: manuscript v2
- parvicapture: LARGESCALE + capture
- symcapture: bayepass, introgress and SFS
- phdpages: distribution integration
- phdpages: functional integration
- phdpages: index & disqus
- parvicapture: pippin pools
- symcapture: introgressions test & bayescan
- distributions: complexes & introduction bib (tbc)
- parvicapture: repeats, reamplification, quantit & pools
- symcapture: introgressions test & phylogeny with migrations
- GWAS: Santi meeting
- symcapture: variant filtering v2 & population structure
- symcapture: missing data filtering test in VariantFiltering & PopulationGenomics
- functional: Ecuador
- distribution: Tiputini2
- genomics: GWAS biblio beginning
- symcapture: pre variant call repeat
- distributions: Tiputini 1st test, discussion 1st draft, intro biblio
- functional: review2 graphs
- parvicapture: library done, pre-repeat
- symcapture: variant call & filtering done, population genomics start
- symcapture: bed in mapping & variant filtering template with outputs
- symcapture: haplotype w sarray, genomicDB & genotyping test & template w sarray, template vcf result analysis
- distribution: draft discussion 1st paragraph
- symcapture: mapping2 after mapping issue, and variant call code test
- symcapture: mapping stat
- symcapture: variant call template
- symcapture: quality check & mapping
- parvicatpure: lib P1, P2, P5
- symcapture: seq delivery QualityCheck: QC, trimming, mapping
- functional: growth exploration: growth, TWI, suitability
- parvicapture: baits & extraction result, and libraries & capture planning
- functional: growth exploration
- parvicapture: post-extraction (extraction repetitions & tests)
- distribution: growth
- functional: SupMat typo
- functional: v2 submitted to all coauthor
- parvicapture: extractions
- growth: test & cluster
- distribution: reorganisation, model exploration, complex distribution, draft, & species distribution @genologin
- functional: v2 end
- parvicapture: targets final
- symcapture: capture end
- general: CST2
- parvicapture: targets v1
- functional: review integration and wihtinPCA
- symcapture: capture & BDgenet
- parvicapture: functional targets v2 & neutral target begin
- symcapture: pdf & size selection
- parvicapture: functional targets v1
- parvicapture: transdecoder
- parvicapture: funcitonal selection v1
- parvicapture: init & trscAlign on genologin
- symcapture: capture
- functional: rm bullets & growth
- performance: reorganisation and death
- symcapture: PicoGreen1
- symcapture: capture prep
- functional: growth test
- bidouille: regular expressions
- functional draft: abstract ATBC & Myriam review 1
- symcapture: (i) renaming probes > symcapture, (ii) library preparation update, (iii) capture begin
- general: updateSylvain rm
- functional analysis: growth test begin
- functional draft: abstract ATBC v1
- functional draft: introduction review in progress & coauthor share 1
- functional draft: M&M, Result, Discussion, Fig & Tab review 1 ; bullet points ; Supplementary Material
- functional draft: Ontogeny & TWI discussion
- functional draft: Ontogeny review
- functional draft: Introduction, Fig. 8 Bootstrap & Interpretations
- distribution: NCIcomplex & NCIspecies & Merge
- functional: Interaction betaNCI lognormal fixed and Interaction reduced
- functional: NCI change
- functional: result begin
- distribution: M&M, Results
- functional: draft begin w all results
- distribution: new complex delineation, draft begin
- functional: InteractionSpecies2
- distribution: All complexes and species with reduced outputs
- functional: Interaction, InteractionSpecies & Sensitivity
- distribution: All sent on cluster
- distribution: Complexes and Species Distribution test
- distribution: JointModel Dirichlet_Multinomial
- functional: interaction results
- distribution: categorical_logit
- functional: sensitivity analysis
- Std from stan to R
- Parrallel std interaction model for cluster
- Wood traits
- full models comparison and sensitivity start
- functional cluster reduce NCI for std betaComp
- functional cluster alert
- A06, A07 & A08 new models with NCIj formula fix @EvaPhilippe
- Report Anne : mat&met, results
- A06, A07 & A08 new models with lognormal posterior for sigmaBeta
- A06, A07 & A08 new models with pred and R2 to cluster
- A04 & A05 updated (un-centered, R2 & new predict)
- A06, A07 & A08 new models with non-centered parameters
- A08 & A08 Outputs first sampling
- A07 & A08 models cluster code
- A08-interaction to be compiled on cluster
- A06-Biotic to be compiled on cluster
- A06-Biotic & A07-FullModel Cluster files
- A04 Abiotic & A05 Ontogenic correction
- Biotic full sampling
- A04 Abiotic model & A05 Ontogenic Model
- A07 Additive model
- Competition matrix with edge effects
- A06 Biotic model in stan
- A04 Abiotic & AO6 invSLA & invLA
- A07 Full Model template
- AO5 Ontogenic Model
- A06 Biotic Model
- A04 AbioticModel without random nested effect
- A01-PCA sharing
- A02 & A03 Models @annebaranger comments
- A02 & A03 Models post-meeting correction
- A03 Models corr2 and presentation
- A03 Models corr1
- Outliers, PCA, and environment @GeraldineDerroire corr1
- Functional A02 environment v1
- A04 - models building
- Functional A02, LBA correction
- Functional A03, analysis of environmental descriptors over all individuals
- PCA discussion and v1
- dbh formula correction
- PCA intro, M&M, & results revision
- data_cleaning final v1 (pre-share)
- outlier final v1 (pre-share)
- report_Anne opening
- PCA correction & discussion
- Environment descriptors analysis
- single model ok
- joint model start
- Symphonia niche
- new extraction plates
- extra girth density
- A01 - PCA
- A02 - Environment, analysis of DBH versus Dawkins
- distribution models Bernoulli converged
- distribution models abiotic with bernoulli
- extra girth update
- outliers - spotting other abnormal individuals
- distribution models > Bernoulli
- functional analysis PCA analysis v1 & templates for environment, data exploration and models
- outliers > data cleaning
- competition > sampling/extra_girth
- Maho cleaning LeafArea & AllTraits
- Maho Outliers 1
- Maho cleaning AllMeasure
- Maho LeafFresh cleaning 1
- distribution
- Model form
- Symphonia abiotic
- Maho morphology
- gitignore .zip
- Data_cleaning > Sympho/Maho split
- Data_cleaning: test loading data
- distribution > beta regression working
- Repository cleaning
- online docs removal
- scripts removal (dbh_correction.R from Camilla)
- ToDo removal (moved to GitHub project)
- Soctropecol poster figures cleaning
- data exploration/Eschweilera.Rmd & Symphonia.Rmd removal (redundant to preliminary studies)
- FTH project (data cleaning moved to preliminary > data_cleaning)
- environment.Rmd > preliminary/environment
- preliminary.Rmd > preliminary/data
- sampling.Rmd > preliminary/sampling
- growth removal from preliminary_Symphonia.Rmd
- Bayes lecture for Msc EFT
- Species complexes distribution
- data cleaning (FTH.Rmd)
- Bayes lecture for Msc EFT
- Species complexes distribution
- Species complexes distribution
- FTH project (to be deleted ?)
- Competition with DeltaBA
- Symphonia functional SLA & LDMC full model
- FTH example
- competition P1 description and model
- TopoDerivate script
- Symphonia dsitribution begin
- Symphonia functional analysis
- Library prep
- competition and light environment
- Update ToDo
- Eschweilera sampling selection
- Symphonia plates design and library preparation protocol
- Probes design: capture & baits
- Eschweilera: preliminray, env, sampling
- Probes design: repetitive regin ckeck, waiting for probes desing, new plates & library preparation
- Probes design: func target done & final bwa check
- ToDo
- Probes design: func seq with blat aln
- ToDo
- Probes design: functional seq with enrichment analysis and genes structure
- Probes design
- neutral seq v1 done
- functional seq selection (annotation)
- CST
- bidouille
- Probes design
- Probes design + ToDo
- Probes design transcripto, genomic, and chloro seq choice
- CST v1
- CST
- ToDo +Probes -MOD
- SocTropEcol final revision
- gap in environment for @EmiDt
- Update ToDo
- SocTropEcol poster pre-revision
- subjet revision from @mheuertz on 21/03/2018
- probes: more text and GO enrichment
- Soctropecol poster init
- probes design bookdown document init
- growth models development in bookdown
- data_exploration following final data release by @EmiDt
- subject: Phenotype, IV within species and communities
- growth2 dev (No, Nio, Nso)
- growth2 to growth bookdown
- lecture stan log normal check with @GeraldineDerroire
- subject: Environment and Traits sections
- stan lecture
- Symphonia growth model v2
- environment
- subject ferbuary 2018 new structure
- growth version 2 with greta
- environment for analysis
- probes init
- new subject first version
- new subject second part writting
- new subject plan and main ideas
- subject cleaning (subject _old and _all to be also removed in the future only kept until now for convenience)
- setting growth model N1 for tabebuia
- data_check improved
- Automatic data check for data cleaning in data_exploration
- internship_subject last review with @GeraldineDerroire before submit
- sampling table save
- Subject v4 and growth2 new model
- subject 3 pre*meeting + growth + sampling
- subject 3 model description and more structure
- growth predictions and model interpretations
- sampling vf 1
- sampling maps
- growth models
- sampling
- Symphonia preliminary analysis growth model following Herault et al, 2010
- subject third version introduction v1
- subject third version model description begining
- subject third version litterature review begining
- Internship subject first draft
- subject third version begining, introducing individual general scheme
- Morphotype and Genotype association to environment Water table depth
- Gap effect on Symphonia growth with gap maps (preliminary.html)
- Functional variability intra vs inter individuals not available with BRIDGE
- Strange year effect on growth
- Clean Paracou growth data for Symphonia
- Data on other Guyafor plots than Paracou (Symphonia, environment and genetic)
- Functional variability intra vs inter individuals not available on BRIDGE
- Symphonia maps on Paracou with habitats and GbS for Paracou visit (10/10/17)
- Begining of the Subject document 2 (broader view with some litterature review)
- STRUCTURE results in preliminary anlaysis
- Introduction of BRIDGE data in preliminary analysis
- Need to join and relate Symphonia.Rmd and preliminary.Rmd
- preliminary analysis genetic STRUCTURE and distance matrix
- preleminary analysis first model
- subject revision for 25.09.17 meeting
- Repository structure initialization
- lexicon
- Initialization