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Questions tagged [rda]

Rda is a short name for RData.

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db-RDA in vegan package do not evaluate all explanatory variables

These days I am trying to develop a db-RDA analysis on the vegan package. I have 24 explanatory variables and 46 samples. The problem is that when developing the db-RDA I only get results for the first 7 environmental variables regardless of the…
Sergio Martinez Campos Gutirre
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Am I using dbRDA correctly with ordered variables? What are the *.L and *.Q arrows in the output?

When I apply an dbRDA to a distance matrix (in this case the Bray-Curtis distance) like this: dbrda(sqrt(dist) ~ ., site_vars) is it ok to include a column of ordered factors in the site_vars variable, which is a dataframe with values measured at…
Manuel Popp
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RDA non-significant RDA axes

I have looked online forums and through various papers and am a little stumped on the interpretation of my results for RDA analysis. I ran the full model with genetic cluster at the condition and came up with a significant model with a global test…
Kat Elizabeth
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Discriminant Analysis of Principal Components for Candidate SNPs

I just ran a redundancy analysis on my SNP dataset, and I have candidate SNPs from it. I would like to run a DAPC on this data, but the tutorial has left me a little confused. This is because I believe I already have my data in the clusters and I…
Daniel.Payter
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Colours not displaying on scatterplot points

I am trying to conduct a RDA analysis, and to do so I had to create a plot with my SNPs (the points on the scatterplot). I assigned colours to my points, but once I plotted them, they were not filled and instead were white circles outlined in…
Daniel.Payter
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error with rda test in vegan r package. Variable not being read correctly

I am trying to perform a simple RDA using the vegan package to test the effects of depth, basin and sector on genetic population structure using the following data frame. datafile. The "ALL" variable is the genetic population assignment…
Ella Bowles
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How to load a large .rda file selectively?

I have a large datafile in .rda and I can use load() into R studio. It takes 3 minutes. I would like to speed it up. Is there anyway to speed up the loading? Say somehow selectively. Thanks a lot.
jfz88
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RDA correlation triplot with vegan

I am trying to plot an RDA correlation triplot (using plot(rda_model)) using the vegan package in R, however I am confused about which 'scaling' to use. In Zuur (2007, Analysing Ecological Data), scaling refers to the power of the diagonal matrix…
Alex93
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Load a .rda file and iterate over its objects

I loaded a rda file which basically its a list of dataframes. How do I iterate over is objects? >load(data) >attach(data) The following objects are masked _by_ .GlobalEnv: GSE109597, GSE18897, GSE32575, GSE53232, GSE55205, GSE69039, GSE83223,…
fred
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RDA visualisation - plot Species abundance according to RDA1

I have sampled 87 plots and identified overall 9 earthworm species. My aim is to investigate changes in species richness and abundance across my site (sampled across 87 plots), which is known to be polluted (mainly by Cu, Zn, and Pb but I also…
user3016665
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How to rbind a list of rda files

I have a list of .rda data files with names all start with say AAA, and need to rbind all of them into one dataset I tried the following codes but it does not work files <- list.files(pattern="AAA") df <- do.call(`rbind`,lapply(files, load))
vera_kkk
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Is there a way to read in a sample of an Rda file?

I have a very large dataset in an Rda file that I want to use for a shiny app but since it's so large I'm thinking of just taking a sample of the file and read that in. Is there anyway to do that?
mjoy
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Conversion of RDA to CSV goes wrong

Since this morning, I am trying to convert the Smoothies table within the SensorMineR Dataset using R Studio, but when I do it, the CSV created file is not well tabulated. You can verify it yourself by running the following commands : smoothiesData…
YellowishLight
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Assign different names to models build during a loop

I made multiple models and stored them in separate names in a loop df <- data.frame(loc.id = rep(1000:1009,each = 20), y = rnorm(20*10), x = rnorm(20*10)) loc.vec <- c(1000:1009) for(l in seq_along(loc.vec)){ loc <- loc.vec[[l]] …
89_Simple
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Assigning unique names to objects created in for-loop

I am writing a loop where the output of each iteration has to be saved as .rda file Suppose I have a vector of 10 locations called 'location.id' dat <- data.frame(location.id = rep(c(00,11,22,33,44,55,66,77,88,99), each = 10), x =…
89_Simple
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