phiala / ecodist Goto Github PK

Hi Sarah, I've had troubles getting mgram to work in R due to R size limits (my dataset has 97,000 rows which obviusly grows with the distance matrix function). Have you come across this and if so, can you recommend a way to use mgram with bigger data sets? eg is there a way to break them down without losing the spatial integrity? Or another programme that works better? Thank you! Cate

distance(x, method = "mahalanobis", ...)

does not work unless icov is specified. The reason is clear. In the code

    if (missing(icov)) {
        icov <- solve(cov(x))
    }

should be

    if (missing(icov)) {
        icov <- solve(var(x))
    }

The function cov() computes only a block of the variance matrix (and requires 2 arguments); var(x) computes the entire variance matrix.

Hi,

I would like to report an issue when trying to use the MRM function (ecodist package 2.0.9 in RStudio 2022.02.3 Build 492 on MacOS Catalina) through the example provided in the package documentation.

data(graze)
MRM(dist(LOAR10) ~ dist(sitelocation) + dist(forestpct), data=graze, nperm=10)
Error in xj[i, , drop = FALSE] : incorrect number of dimensions

I also tried to apply this function on personal data, without success.

Thank you in advance for your help,

Best regards

Guillaume

Hello!

I made the unfortunate mistake of updating my version of R. Ever since the update, I have been unable to install ecodist from github using devtools. I'm trying to use logistic MRM and I don't think the CRAN version has the logistic regression bug fix yet, which is why I'd like to download and compile ecodist from here. Below is the error I am getting:

devtools::install_github("phiala/ecodist")
Downloading GitHub repo phiala/ecodist@master
✔ checking for file ‘/private/var/folders/p0/bxmttvw95r3bl3752w_ggcy00000gp/T/RtmpSlG8eE/remotes25e41a05c30/phiala-ecodist-77ad31a/DESCRIPTION’ ...
─ preparing ‘ecodist’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing source package ‘ecodist’ ...
** libs
gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ecodist.c -o ecodist.o
In file included from ecodist.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:55:11: fatal error: stdlib.h: No such file or directory
# include <stdlib.h> /* Not used by R itself, but widely assumed in packages */
^~~~~~~~~~
compilation terminated.
make: *** [ecodist.o] Error 1
ERROR: compilation failed for package ‘ecodist’
─ removing ‘/private/var/folders/p0/bxmttvw95r3bl3752w_ggcy00000gp/T/RtmpZyvR9t/Rinst2ab1ad7e356/ecodist’
-----------------------------------
ERROR: package installation failed
Error in run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error

Here is the sessionInfo(). I have xcode-select installed.
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1

Thanks for any help or suggestions!
Kelly