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Questions related to R

How to change tunit in VariogramST (R)?

Hi there, I am trying to use VariogramST function in R, for spatial-temporal kriging. The values I am working on, are monthly based; while in the function VariogramST, the predefined "tunit" is...

28 January 2020 6,234 3 View

What type of EDA one should do before starting modelling in a longitudinal study?

Hi everyone, I would like to know how do you conduct EDA on a longitudinal study. For example, If I want to study the impact of pred1 (categorical - 3 levels) and pred2 (continuous) on the...

22 January 2020 4,891 3 View

Any algorithm/R package for Bayesian network causal inference of binary data?

I have a dataset of 150 samples of 60 binary variables. The pcalg binCItest results are not impressive and i can not find a straightforward way to do this using bnlearn or catnet. I appreciate if...

17 January 2020 1,069 5 View

How to calculate True Skill Statistic (TSS) from ENMeval R package output?

I used ENMeval R package to produce my species distribution model with algorithm "maxent.jar". I hope to calculate TSS for my binary map output from generated from maxSSS. However, I am unsure...

13 January 2020 2,247 3 View

Interpretation of interaction in the mixed effect model?

Hi, I have categorized 3 my time points (ftime0, ftime1, ftime2) and treatment type (access_typeAVF, access_typeAVG). Treatment is given after time point 0 (or baseline). Serials (subject) are...

06 January 2020 7,827 5 View

R 3D plot with centered axis ?

I want to represent a series of results computed from y = f(x1, x2, x3), with x1, x2 and x3 being in the [-2, +2] range. For now, I use the "scatter3d" package, and an example of a resulting...

22 December 2019 5,162 4 View

What is Spatial auto-correlation in ecology, when it good to consider and when it should be avoided?

auto correlation is daunting for early career researcher, what is limit to say something is auto correlated [

17 December 2019 6,410 3 View

Variation partitioning - Is there a all -encompassing function/package in R?

I am a bit frustrated looking for a competent function doing variation partitioning (e.g. on linear model output) it should be able to tick the following boxes A) calculate all overlaps and "pure"...

05 December 2019 9,485 3 View

Interaction terms and singularity errors?

Hi, I am currently trying to produce a linear regression model. I have used hierarchial regression stechniques to produce a multivariable model. I have then looked for interaction terms and added...

04 December 2019 4,317 3 View

How To Convert Snp haplotype Data Into 0,1 Matrix? Which software or package is better?

Hi everybody I want to convert HapMap Snp haplotype Data Into 0,1 Matrix so that I can use it in other works. I appreciate your help. Best regards

03 December 2019 3,466 4 View

Is segmented beta regression possible in R?

Hi, I'm trying to apply segmented regression to a response variable that is bounded by 0 and 1, however I am struggling to interpret the error I have encountered. Reproducible example in R: data1

28 November 2019 3,297 12 View

Finding the rows that will divide the columns into the correct groups?

I have 200 samples, each one has measurements of the same 600 proteins. The samples are from 3 groups: before cancer, after cancer, no cancer. I want to find the right proteins, any combination of...

22 November 2019 3,660 3 View

How to plot a 3-way interaction (linear mixed model) in R?

Hi everyone, I am running a linear mixed model in R, using the lme-function. The following variables are used: Y ... Outcome (continuous) IV1 ... Time (categorical: 0, 1, 2, 3) IV2 ... Group...

14 November 2019 3,996 7 View

How to apply fuzzy K-means with spatial constraints in R?

Hello. I am looking for a solution in R to apply spatially-constrained clustering using fuzzy K-means (fuzzy c-means). I came across the spatialClust package, and was wondering whether anyone may...

31 October 2019 4,851 2 View

How to choose the right distance method ?

Hi everyone, I have some issues to determine how to pick correctly the right distance calculation method in R. I have two datasets : one containing habitat variables (worldclim data, so...

16 October 2019 7,686 5 View

How to test if a property of a sample is not statistically significantly different from a property of the population?

I am trying to check if my sample characteristics are similar to the population characteristics for the following 2 cases. 1. I have the information regarding the gender distribution of my...

13 October 2019 188 14 View

How to find differentially expressed genes from normalized counts with R?

A lot of the mRNA data that I get is already normalized and getting to the normalized counts is not trivial. While I'd prefer to use R packages like DeSeq2 or edgeR, they use raw counts. Is there...

10 October 2019 5,907 4 View

How to compare two groups with cofactors?

Hello People I have a set with two groups of snakes I want to compare, but there are also cofactors (e. g. sex, habitat ecc). Then I should use ANCOVA according to your answers. But I have also...

10 October 2019 8,761 5 View

How to calculate effect size in R with Metafor package?

Hi，everyone I have some problem when I calculate the mean effect size. Suppose that the A parameter has ten data from ten articles. How should I synthesize the data and calculate a total effect...

10 October 2019 3,971 4 View

How do you create a resistance map from a landcover map in R to be used for Circuitscape?

I am currently trying to edit the Corine Land Cover (CLC2018) raster map of Europe. I need to condense the landcover classes into a smaller number of different classes and then convert those...

10 October 2019 8,880 2 View

Is there a function to fit nonlinear mixed models (NLME) with the first-order (FO) and first-order conditional expectation(FOCE) methods?

Dear all, Can anyone tell me how to fit nonlinear mixed models by the first-order (FO) and first-order conditional expectation (FOCE) methods ? I only know that a Package called nlme can be used...

10 October 2019 1,222 3 View

How to choose the right distance method ?

Hi everyone, I have some issues to determine how to pick correctly the right distance calculation method in R. I have two datasets : one containing habitat variables (worldclim data, so...

10 October 2019 9,296 6 View

R and crude meteorological data processing tutorial?

Dear all, I have a huge database of crude hourly meteorological data, and I am looking for some tutorials for processing it, filling gaps, detect outliers, etc. preferably using R (but I could...

10 October 2019 9,038 6 View

Finding optimal cutoff point ?

Hello, everyone. I am studying the influence of one biomarker on multiple disease characteristics, and I would like to calculate its cutoff point. I created univariate ROC curves to investigate...

10 October 2019 9,649 4 View

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