fragframe_1's People
fragframe_1's Issues
Sampling designs for beta-diversity partitioning
I am not sure if the beta-diversity partitioning is appropriate for all three sampling designs. What do to?
Improve reproducibility of the results and analysis
ToDo's for all
- Only specify absolute paths once
- Remove all other absolute paths
- save intermediate and main results in GitHub repo and NOT in the DropBox
ToDo for Felix
- adjust preprocessing files (which do use data from DropBox accordingly)
- check if iNEXT is still needed and helper function in 0_-init script
- Finalize README
- archive on ZENODO
Relative statt absolute Pfade
Hallo @KatharinaGerstner, ich nutze das Repo gerade auf meinem neuen OS (Ubuntu) und muss dann die Pfade in 00_InitializeDirectories_LoadPackagesAndFunctions.R
umbenennen. Ich glaube Hadley Wickham empfiehlt auch nur relative Pfade statt absoluter zu benutzen R for Data Science. Dann muss das bei Computerwechsel nicht geändert werden und auch nicht unterschiedlich für uns beide sein.
Dateiendungen
Wir sollten konsistente Dateiendungen verwenden. Bei mir scheint es .R
und bei dir .r
zu sein.
Was sollen wir nehmen? Mein RStudio macht standardmäßig .R
. Darum bin ich natürlich dafür :o)
Das ist natürlich totaler Kleinkram
Threshold for richness extrapolation
We might want to define a quality check for the application of the Chao1 estimator. Either in terms of numbers of individuals or coverage.
Next steps and to dos
ToDo's Felix
-
Set up GitHub Repository and add me/you as collaborator
-
Data frame containing studies, fragment ranks (continuous = 9999), biodiversity metrics, exclude matrix entities, pool samples within the same fragment (those can be used to test changes in spatial aggregation)
-
Data table with meta-data
-
Calculate standardized N, take into account different sampling efforts for calculation of N
ToDo's Katharina
-
Calculate effect size Fishers’ z and variance for each study
-
Setting up analyses on effect sizes for BDmetrics separately
-
Think about a multivariate analysis including correlation of BDmetrics
-
Calculate log-ratio effect sizes for studies with just two fragment sizes (continuous vs. fragmented)
If abfragen zu einzelnen Dateien
In der Datei 01.1_CalculateBDFromAbundance.R
gibt es if Abfragen zu einzelnen Dateinamen. Das sieht gefährlich und komisch aus. Ich vermute, stattdessen sollte in den Dateien selber etwas geändert werden, damit das Datenformat konsistent ist.
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