Who knows how to make a Lindeman spine with R?

More Nathalie Niquil's questions See All

Results on Parameter-Dependent Pareto Front?

Dear community, I would like to request some references related to results on parameter-dependent Pareto Front, if there are any. I am interested in studying the behavior of the Pareto Front with...

08 May 2019 9,669 3 View

How do I quantify cells and fibers in tissues used in immunohistochemistry?

Hi all, I would need to compare the number of cells and fibers in different part of a tissue which was used in fluorescent immunohistochemistry. However, I am not sure how to proceed. I could use...

21 March 2019 8,043 3 View

What Big Data solution use for deep learning on clinical data purpose ?

Hello everyone, I would like to perform machine learning and deep learning in a near futur on clinical data, coming from different sources and technologies (Omics data, Imaging data, and so...

23 August 2017 3,551 5 View

NLP : Short text classification/categorization

Hello everyones, I'm looking for a way to classify really short pieces of text (max 18 words) into 9 different classes. As a learning set, I've got a dataframe with each sentence (one column)...

12 July 2017 2,965 10 View

Change of metric and uniform continuity?

Dear all, we know, owing to a result appearing in the book of R. M. Dudley (Real analysis and Probability - Theorem 2.8.2), that for any separable metric space (S, d), there is a metric e on S,...

19 April 2017 4,159 6 View

Weak convergence of signed measures?

Dear all, I am searching a result concerning the weak convergence of signed measures defined on the Borel algebra of a given metric space. The result that i find so far is established for weak...

10 February 2017 2,604 3 View

Relation between $\mu$-continuity sets and the Borel sigma-algebra?

Dear all, For any sigma-finite measure $\mu$ on the Borel subsets of a metric space X (separable if needed), we recall that a $\mu$-continuity set is any Borel set B such that $\mu(boundary of B)...

23 January 2017 3,301 4 View

What is the dual space of bounded continuous functions defined on a metric space (not necessarily compact)?

What is the dual space of bounded continuous functions defined on a metric space (not necessarily compact)? (i would appreciate to have a reference for the result too)

16 January 2017 6,534 8 View

Has anyone noticed high or uneven fluorescence background with iBlot PVDF membrane stacks?

I was wondering if anyone else has used the iBlot PVDF membrane stacks and noticed uneven and/or relatively high autofluorescence / background when used for fluorescence Western blotting? I am...

29 May 2016 8,048 2 View

ELISA from HUVEC cell culture supernatant

I want to do an ELISA on HUVEC cell culture supernatant to check for TNF alpha release. Can anybody recommend a suitable cell density/ml medium? I am thinking to culture my cells in a 6 well...

17 February 2016 5,274 2 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

How to normalise data on OPM package from R Studio ?

Good afternoon, I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups...

02 March 2021 3,584 1 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

Is There Any Feasible Method To Test The Efficiency Of Fluorescent Compounds Other Than UV Spectrometers ? Suggestions Would Be Appreciated !

02 March 2021 5,785 3 View

Andrew Sánchez Meador

If I understand correctly, a Lindeman spine is just a series of flow networks, so I'd start with the "enaR" (tools for ecological network analysis) or maybe go as primitive as the "networks" (relational data) package. Either of these should allow you to design and implement flow networks. Maybe even try the "foodwebs" package.. but I have no experience with it so maybe someone else can chime in...

Just suggestions. Hope they help!

Package links:

http://cran.r-project.org/web/packages/enaR

http://cran.r-project.org/web/packages/network/network

http://cran.r-project.org/web/packages/foodweb

Nathalie Niquil

Thank you Andrew, I will look closely at the 3 packages. The Lindeman spine is a linear chain, with integer levels, making a summary of a trophic network. Primary producers and detritus are level I, hebivorous in levelII and omnivores are split between integer levels. This shows you the efficiency of the different levels. Those dominating the respiration or the exports. Usually, I use Netwrk, the fortran program developped by Bob Ulanowicz, for the calculation of the flow and make the graphic representation by hand.

Robert E. Ulanowicz

Dear Nathalie! Stuart Borrett has translated NETWRK (which includes the calculation of the Lindeman Spine) into R. Please give him a shout. If he doesn't respond, let me know, and I will dig up the code for you. The best, Bob

Stuart R Borrett

All, unfortunately enaR does not yet have the Trophic Spine calculations in it. However, we hope to add it in the future.

We have added functions to the enaR package to calculate the Lindeman Spine. These functions are currently in the beta branch of our package development, which you can access from github at https://github.com/SEELab/enaR/tree/beta. enaTroAgg is the main function for this calculation, but enaCycle calculates the cycle basis following Ulanowicz's work as well. The enaTroAgg function should replicate the results returned by Dr. Ulanowicz's Netwrk 4.2 program.

The functions will be included in our next major enaR update to CRAN, but you can install the beta branch of the package in R from github using the devtools package if you want to get started using this feature now. Please let me know if you need more information.

https://github.com/SEELab/enaR

https://github.com/SEELab/enaR/tree/beta