07 March 2014

knitr, knitcitations, and unicode

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Friday notes


Testing integrate() and AUC to calculate area under curve of ‘Intermediate’ expressed transcripts.


Federico pointed out prinseq (Schmieder & Edwards, 2011) for filtering fastq files and deconseq to “automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets”. Both look useful for future work.

  • R. Schmieder, R. Edwards, (2011) Quality Control And Preprocessing of Metagenomic Datasets. Bioinformatics 27 863-864 10.1093/bioinformatics/btr026


After frustration, finally found how to type degree (and other symbols) from here. Had to enable Compose Key by going to System Settings –> Text Entry –> Keyboard Settings –> Compose Key. Choose right alt.

Degree symbol: Compose o o

Open science

Trying to update workflow on open lab notebook - using knitcitations to enter references in my notes and generate bibliography. Ran into error

inline R code fragments

Error in FUN(1L[[1L]], ...) : could not find function "is"

and filed issue that was quickly resolved by adding library(methods) which is apparently not loaded by Rscript but is interactively.


Gouveia, S.F., Hortal, J., Tejedo, M., Duarte, H., Cassemiro, F.A.S., Navas, C.A. & Diniz-Filho, J.A.F. (2014). Climatic niche at physiological and macroecological scales: the thermal tolerance–geographical range interface and niche dimensionality. Global Ecology and Biogeography, 23, 446–456

- sent by Aaron Ellison
- macrophysiology: "describe general properties of the interface between individual' endurance of environmental conditions and their geographical patterns of distribution of their species"
   - this description seems to ignore within-species differentiation
- CTmax for 47 species of anurans
- 'phylogenetic signal representation'
  - PSR curve at 45° line consistent with neutral evolution
  - PSR curve above line consistent with accelerated divergence
  - PSR curve below line implies "stronger phylogenetic signal"
- CTMax and macroecological niche accelerated evolutionary rates
- Tmax and Tvar slower evolutionary rates
- 'upper physiological limits alone may fail to characterize the macroecological (i.e. geographical) climatic boundaries of species' distributions'
- authors claim that realized variability is a better descriptor of CTmax than a *single* climatic parameter such as Tmax, but this masks that the differences in the P-values between these comparisons is not large: correlation between CTmax and Tmax (beta = -0.064, P = 0.095); correlation between CTmax and Tvar (beta = -0.079, P = 0.023). 
- position in 'hyperdimensional niche space' a better predictor of range limits than CTmax

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