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Questions tagged [rda]

Rda is a short name for RData.

116 questions
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How can I change the font and font size of the RDA arrows - ggvegan?

I'm making an RDA, and I can not change the information it returns me, as font and font size. I would like to change the font of the arrows and the size of the letters is this possible? I marked the information I want to change with a red circle, to…
Hellen Kezia Silva Almada
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What is the difference between R vegan species-scores, and Primer Spearman rank correlation of species to axis?

In constrained ordination analysis, like CAP or dbRDA, researchers often want to know how much of the dissimilarity is attributed to specific species. In Primer PERMANOVA, Spearman rank or Pearson correlations of species to the axis is an option to…
Philip Haupt
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vegan dbrda species scores are empty despite community matrix provided

I have performed "Distance based redundancy analysis" (dbRDA) in R using the vegan community ecology package. I would like to show the relative contribution of (fish) trophic groups to the dissimilarity between samples (abundance data of trophic…
Philip Haupt
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Loading a file using R & plumber

I'm trying to use plumber to predict the value of a cost. For the prediction part, I saved my model in a .rda file. Idon't know how to load it in Plumber, Is it possible to load it just like in plane R ? I saw a similar question, but I don't get how…
nidabdella
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Append new lines to a .Rda file in R

Writing a fresh .Rda file to save a data.frame is easy: df <- data.frame(a=c(1,2,3,4), b=c(5,6,7,8)) save(df,file="data.Rda") But is it possible to write more data afterwards, there is no append=TRUE option using save. Similarly, writing new lines…
JohnBee
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Better way to save and load Linear model coefficients for prediction

I am working to make hourly coefficients for 50000 customers from one year data set. (365 rows*28 columns) I want to save these coefficients for prediction later in another R code file. Currently, I am saving a list of 24 hourly models using save…
Sripati
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R shiny upload a .rda file

I don't get to upload and display a rda file with the library shiny in R. Someone knows how to do it ? I use the R version 3.1.1. Here is the web site for using shiny : http://shiny.rstudio.com ** #ui.R library(shiny) shinyUI(navbarPage("MareyMap…
adrbessy
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How to open non .rda files in R

I am trying to do some work for my thesis which has me using the R programming language (and the R app on Mac OS Lion) for the first time. I had to download the files from here to work with but none of the files comes in .rda or .r they all come in…
Tsundoku
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dbRDA plot arrow vectors disappear when I plot in ggplot

I am doing a distanced based RDA plot for the first time and I'm not too familiar with the structure. I have quite a large dataset, which I have subsetted a portion below. > dput(pc) structure(list(Chlorophyll = c(1.457, 2.458, 1.89, 1.028, 1.202,…
no_frills_30
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How can I change the colour of my points on my db-RDA triplot in R?

QUESTION: I am building a triplot for the results of my distance-based RDA in R, library(vegan). I can get a triplot to build, but can't figure out how to make the colours of my sites different based on their location. Code below. #running the…
LeahF
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Why customizing the RDA plot makes arrows shorter and overlapped?

I used the Vegan package for RDA and got its plot but I want to customize the plot and make a better one for publication. The plot(rda) of vegan gave a plot and the arrows had normal size (the graph with blue arrows) but when I used the following…
Fereshteh Shahoveisi
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How to calculate length of loading vector and distance from given point in R?

I've run a standard RDA analysis for my data. I am struggling to find a formal analysis for some important insights (i.e. I need a way to report these statements in my paper) Consider the red x lying in between Shrub and WaterCont at ~(-0.5,-0.5). I…
Rspacer
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How to calculate R2 or contribution to RDA of each loading in a PCA in R?

I've run a standard RDA analysis for my data. I am struggling to find a formal analysis for some important insights (i.e. I need a way to report these statements in my paper) The R2 value + rank or order of importance of each environmental…
Rspacer
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How to plot an RDA with two matrix in ggplot

This is my first time trying to plot an RDA in R. My datas for the RDA are two matrix; one with environmental conditions such as pH, temperature, etc. and the other with different species (relative frequencies of every species at each station).…
Virginie Chalifoux
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Plotting a partial RDA in R results in a categorical variable being plotted as arrows, instead of centroids

I am studying whether environmental parameters affect the community composition of root fungi living in symbiosis with beeches in a forest. Therefore, I am performing a RDA with a presence-absence community dataset and an environmental dataset which…
Teun Everts
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