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leitemfa adalardo e3bo nicolaycunha laurajanegraham yaccos javirudolph kkougiou sastoudt pandengwang theoreticalecology a-stupid-fish varbiroghmsc's Issues
Error in Rsquared() for poisson model
If the model is of family = poisson or family = overPoisson, the call to Rsquared() will result in the following error:
Error in Rsquared(model, averageSp = FALSE) : object 'R2' not found
I realise from the documentation now that it is not intended to calculate R2 for these models (and I think it also makes sense not to include this).
A more informative error message here would be really helpful though, for example:
Rsquared <- function (hmsc, newdata = NULL, averageSp = TRUE)
{
if (is.null(newdata)) {
Y <- hmsc$data$Y
}
if (!is.null(newdata)) {
Y <- newdata$Y
}
nsp <- ncol(Y)
Ypred <- predict(hmsc, newdata = newdata)
if (any(class(hmsc) == "probit")) {
Y0 <- Y == 0
Y1 <- Y == 1
R2 <- numeric()
for (i in 1:nsp) {
R2[i] <- mean(Ypred[Y1[, i], i]) - mean(Ypred[Y0[,
i], i])
}
}
if (any(class(hmsc) == "gaussian")) {
ssY <- colSums(scale(Y, scale = FALSE)^2)
ssRes <- colSums((Y - predict(hmsc))^2)
R2 <- 1 - ssRes/ssY
}
if (any(class(hmsc) %in% c("poisson", "overPoisson"))) {
stop("R2 may only be calculated for probit and gaussian models!")
}
if (averageSp) {
R2 <- mean(R2)
}
return(R2)
}
error in sampleCondPred when family="gaussian"
It keeps happening when I try to use conditional prediction for Gaussian model.
error message: error:
''element-wise multiplication: incompatible matrix dimensions: 30x32 and 1920000x1
Error in sampleCondPred(Y, EstModel, residVar, nsite, nsp, nsample, family = class(object)[2]) :
element-wise multiplication: incompatible matrix dimensions: 30x32 and 1920000x1''
It seems the function “sampleCondPred” does not work well for gaussian model, but it is fine for model specified with other families.
Where can I download the FINNISH BIRDS dataset?
Hi Guillaume,
I appreciate the method and I want to download the FINNISH BIRDS dataset to reproduce the results (Joint species distribution modelling with the r‐package Hmsc). Can you help me?
Expect for your reply!
species association and random variables
Hello,
I am not sure if I am making an error somewhere. But from what I understand, HMSCdata can accept both 'Random' and 'Auto' arguments (I have both in my dataset. Auto= spatial coordinates and Random= effort for each sampling plot). The model runs with both arguments specified but I have troubles in the corRandomEff function which creates two different arrays, one each for Random and Auto.
- How do I use/interpret these separate correlation matrices for my study site to generate a single one?
- Am I not supposed to use both arguments in a single model?
Error in matrix(1, nrow = nsite, ncol = 1) : non-numeric matrix extent
I am trying to use HMSC for some very simple analyses (more to get a grasp of what is possible for now - I have a dataset with the Y matrix, as well as the species phylogeny and geographic coordinates of the sampled locations)
Problem is, I stumbled upon a possible bug in the as.HMSCdata function.
In the latest commit in this function (2718725), some code was added to calculate the number of sites from the number of rows in Auto. However, the function turns Auto into a list before applying this, so that nrow(Auto) returns NULL. I'm not sure how to fix it without breaking other things, given the amount of conditionals in this function.
Fix bug in predict.hmsc
Hi,
I think there's another minor fix needed in this line:
https://github.com/guiblanchet/HMSC/blob/master/R/predict.hmsc.R#L166
It should be
niter<-dim(object$results$estimation$paramLatent)[1]
because we may have multiple columns in this matrix, so the length may not be equal to the number of iterations.
Best,
Miguel
Recreating species association plots
Hi
When I run the waterbirds example to try to recreate the species association plot for the influence of the previous year (Figure 7c in Ovaskainen et al, 2017), I do not get the same plot as the one presented in the paper. I have not edited the birds.R file in any way, nor have I changed anything in the data.
For some reason I end up with a plot where all associations are large and positive, rather than the range presented in the paper.
Ultimately I want to produce a similar plot for my own data, however I get the similar all positive results for associations. Do you have any suggestions about what might be happening here?
Cheers
Jay
Error rWishart(1, paramX + 1, diag(nparamX)) in hmsc()
Dear all,
I am writing to you because when fitting hmsc to my data I get the
following error:
"Error in rWishart(1, paramX + 1, diag(nparamX)) : inconsistent degrees of freedom and dimension"
I guess it is related to the prior of the sigma matrix of the
multivariate normal of thetas. I have checked the dimensions of my matrices and there does not seem to be any problem.
My data consists of a Ymatrix of community cover data, my X matrix has
three dummy variables (1/0), and my trait matrix has dummy variables as
well.
I ran a model with matrices Y and X, and it worked. However, when I
included the Tr matrix, the model returned the above-mentioned error.
I have tried different strategies like, reducing the number of traits
and including a phylogenetic matrix. However, the error continued.
I would be very thankful for any help,
Sincerely,
Agostina Torres
CONICET-Argentina
Rsquared for higher hierarchical levels
The Rsquared function apparently only works for the sampling unit level. I've been trying to calculate R2 for higher hierarchical levels by hand, using the instructions on page 12 of the HMSC manual (summing sampling-unit level predictions, comparing them with observed abundances etc, still trying) but it would be cool if there was a function with arguments allowing to choose hierarchical level.
hmsc.OverPoisson.R model output can't be used with VariPart
While using abundance or density data, we use an overdispersad Poisson for hmsc model:
protist_model <- hmsc(protist_hmsc, family = "overPoisson", niter = 10000, nburn = 2000, thin = 5)
Using the "overPoisson" will not give the structural output as a "probit".
The output structure is not correct and will not work with the VariPart()
Error while runing hmsc in a overPoisson family
Runing a hmsc in a overPoisson family gives the following error:
Error in glm.fit(x = c(26.3, 24.6, 18.9, 21.6, 35.2, 29.4, 42.2, 25.3, :
NA/NaN/Inf in 'x'
runing a parameter estimation based on a prior estimation in a overPoisson family gives the following error:
Error in rgamma(1, priors$param$shrinkOverall[1], priors$param$shrinkOverall[2]) :
invalid arguments
In addition: Warning messages:
1: In rgamma(nsp * nLatent[i], priors$param$shrinkLocal/2, priors$param$shrinkLocal/2) :
NAs produced
2: In rgamma(nsp * nLatent[i], priors$param$shrinkLocal/2, priors$param$shrinkLocal/2) :
NAs produced
as.HMSCdata not allowing Random=NULL
Hi again,
I think these lines here should be enclosed in
if(!is.null(Random)){ ... }
...otherwise we can't specify a model without Random (but with Auto). Or am I thinking wrong?
In any case, an explicit test should be included, to avoid a cryptic error message.
Best,
Miguel
error in calculation of mean on response scale?
When calculating the mean on the response scale the code here has:
exp(apply(res,1:2, mean)),
(for poisson)
Shouldn't it instead be:
apply(exp(res),1:2, mean)?
DID you have R-scripts about how to make the geographical distance to the HMSC model ?
If you have, It could be very thankful, I want to put the samples coordinates to compare their responses to environmental parameters, I think I would be very interesting for my data?
All the best,
Liyan
as.HMSCdata: non-numeric value in Y
When I read a species occurrences matrix (Y-matrix) from a .csv file, the as.HMSCdata function throws an error: “There is at least one non-numeric value in Y”. For instance:
Y <- read.csv("data/Y.csv", header = T)
dta <- as.HMSCdata(Y=Y, X=X)
Seems to be a problem of the data check performed on line 169 of the as.HMSCdata.R code: if(!is.numeric(Y)). This call returns FALSE when applied on Y as a data frame. Transforming Y to a data.matrix() solves the issue. The ‘Simulated example 1’ in the HMSC Manual (p18) describes that reading a .csv file should work, though.
Error in mcmcOverPoissonXLatent
Hello!
I tried to run the hmsc function for a overdispersed Poisson family "overPoisson", however the function throws the following error:
Error in mcmcOverPoissonXLatent(Y, Ylatent, X, Random, param$param$paramX, :
chol(): decomposition failed
What does it means?
Unexpected result with simulated data?
Hello,
I feel like this is an unexpected result given the simulated data I'm trying. Here's a totally reproducible example. Please see the comments within the script.
# Generate a species matrix where sp1 and sp2 are highly correlated, whereas sp3 is
# independent from the others
nsamples = 1000
sp1 = runif(nsamples, 0, 1)
sp = data.frame(cbind(
"sp1" = ifelse(sp1>0.7, 1, 0)
, "sp2" = ifelse(sp1 + rnorm(nsamples, 0, 0.05) > 0.7, 1, 0))
, "sp3" = ifelse(runif(nsamples, 0, 1)>0.7, 1, 0))
cor(sp)
# sp1 and sp2 are highly correlated (~0.90)
# sp3 is independent from the others
table(sp[,1], sp[,2])
# Again confirm association between sp1 and sp2
# Make a unit-level random effect
random = data.frame(uni = factor(paste0("P",1:nsamples)))
rownames(random) = random[,1]
rownames(sp) = random[,1]
# Model data
md = as.HMSCdata(Y = as.matrix(sp), Random = random)
# Fit model
m = hmsc(md, family="probit", niter=5000, nburn=1000, thin=10)
# Plot mixing object
mix = as.mcmc(m, parameters = "paramLatent")
plot(mix)
# Huh? All the latent parameters are centered on zero...
# I would expect that sp1 and sp2, because of being highly correlated, would show similar
# latent parameters, different from zero.
apply(corRandomEff(m, cor = TRUE)[, , , 1], 1:2, mean)
# This confirms the unexpected result: the high correlation of sp1 and sp2 is not captured
# in the random effect! (or very slightly captured)
# It seems the model wasn't able to extract the latent factor to which sp1 and sp2
# respond in consonance...
# Moreover, these mean correlations considerably fluctuate between runs with the same
# data; e.g. sp1 x sp2 varied between 0.24 and 0.35 correlation
Am I doing something wrong in model fitting so that it's actually not converging?
Pardon if this is not the right place to post this question...
Thanks, all the best,
Miguel
Error while installing the
Hello Guillaume,
While installing the package, this error came out (I included the whole output of the R console, error at the bottom, just before sessinInfo)
**> library(devtools)**
Warning messages:
1: le package ‘devtools’ a été compilé avec la version R 3.5.3
2: le package ‘usethis’ a été compilé avec la version R 3.5.3
**> install_github('guiblanchet/HMSC')**
Downloading GitHub repo guiblanchet/HMSC@master
checking for file 'C:\Users\alexandre.villers\AppData\Local\Temp\Rtmp020z31\remotes162014583434\guiblanchet-HMSC-8b39bf4/DESCRIPTION' ...
checking for file 'C:\Users\alexandre.villers\AppData\Local\Temp\Rtmp020z31\remotes162014583434\guiblanchet-HMSC-8b39bf4/DESCRIPTION' ...
√ checking for file 'C:\Users\alexandre.villers\AppData\Local\Temp\Rtmp020z31\remotes162014583434\guiblanchet-HMSC-8b39bf4/DESCRIPTION' (437ms)
- preparing 'HMSC': (464ms)
checking DESCRIPTION meta-information ...
checking DESCRIPTION meta-information ...
√ checking DESCRIPTION meta-information
- cleaning src
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories (428ms)
- looking to see if a 'data/datalist' file should be added
- building 'HMSC_2.2-0.tar.gz'
* installing *source* package 'HMSC' ...
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c adaptVar.cpp -o adaptVar.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c adaptVarAdd.cpp -o adaptVarAdd.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitX.cpp -o mcmcBinomialLogitX.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXPhyloLatent.cpp -o mcmcBinomialLogitXPhyloLatent.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrAuto.cpp -o mcmcBinomialLogitXTrAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrAutoLatent.cpp -o mcmcBinomialLogitXTrAutoLatent.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhylo.cpp -o mcmcBinomialLogitXTrPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhyloAuto.cpp -o mcmcBinomialLogitXTrPhyloAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhyloAutoLatent.cpp -o mcmcBinomialLogitXTrPhyloAutoLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhyloLatent.cpp -o mcmcBinomialLogitXTrPhyloLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalAuto.cpp -o mcmcNormalAuto.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalLatent.cpp -o mcmcNormalLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalNAAuto.cpp -o mcmcNormalNAAuto.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalNAXTrPhyloAuto.cpp -o mcmcNormalNAXTrPhyloAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalNAXTrPhyloAutoLatent.cpp -o mcmcNormalNAXTrPhyloAutoLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalNAXTrPhyloLatent.cpp -o mcmcNormalNAXTrPhyloLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalX.cpp -o mcmcNormalX.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcNormalXAuto.cpp -o mcmcNormalXAuto.o
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c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrLatent.cpp -o mcmcProbitXTrLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhylo.cpp -o mcmcProbitXTrPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloAuto.cpp -o mcmcProbitXTrPhyloAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloAutoLatent.cpp -o mcmcProbitXTrPhyloAutoLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloLatent.cpp -o mcmcProbitXTrPhyloLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rmvnorm.cpp -o rmvnorm.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm.cpp -o rtnorm.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm_1.cpp -o rtnorm_1.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm_slice.cpp -o rtnorm_slice.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rwishart.cpp -o rwishart.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleCondPred.cpp -o sampleCondPred.o
sampleCondPred.cpp: In function 'arma::cube sampleCondPred(arma::mat&, arma::mat&, arma::vec, int, double, int, std::string)':
sampleCondPred.cpp:42:12: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(family == "poisson" | family == "overPoisson"){
^
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleNum.cpp -o sampleNum.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentBinomialLogit.cpp -o sampleYlatentBinomialLogit.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentNormal.cpp -o sampleYlatentNormal.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentPoisson.cpp -o sampleYlatentPoisson.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentProbit.cpp -o sampleYlatentProbit.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateLatent.cpp -o updateLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateLatentAuto.cpp -o updateLatentAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamX.cpp -o updateMeansParamX.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamXBase.cpp -o updateMeansParamXBase.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamXPhylo.cpp -o updateMeansParamXPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamAuto.cpp -o updateParamAuto.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamLatent.cpp -o updateParamLatent.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamPhylo.cpp -o updateParamPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamShrinkGlobal.cpp -o updateParamShrinkGlobal.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamTr.cpp -o updateParamTr.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamTrPhylo.cpp -o updateParamTrPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamX.cpp -o updateParamX.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamX1.cpp -o updateParamX1.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamXPhylo.cpp -o updateParamXPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecX.cpp -o updatePrecX.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecXPhylo.cpp -o updatePrecXPhylo.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecXTr.cpp -o updatePrecXTr.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateResidVar.cpp -o updateResidVar.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateShrinkLocal.cpp -o updateShrinkLocal.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateVarDist.cpp -o updateVarDist.o
c:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o HMSC.dll tmp.def RcppExports.o adaptVar.o adaptVarAdd.o adaptVarAuto.o adaptVarAutoAdd.o adaptVarAutoRemove.o adaptVarRemove.o euclDist.o fixParamAuto.o fixParamPhylo.o mcmcBinomialLogitAuto.o mcmcBinomialLogitAutoLatent.o mcmcBinomialLogitLatent.o mcmcBinomialLogitX.o mcmcBinomialLogitXAuto.o mcmcBinomialLogitXAutoLatent.o mcmcBinomialLogitXLatent.o mcmcBinomialLogitXPhylo.o mcmcBinomialLogitXPhyloAuto.o mcmcBinomialLogitXPhyloAutoLatent.o mcmcBinomialLogitXPhyloLatent.o mcmcBinomialLogitXTr.o mcmcBinomialLogitXTrAuto.o mcmcBinomialLogitXTrAutoLatent.o mcmcBinomialLogitXTrLatent.o mcmcBinomialLogitXTrPhylo.o mcmcBinomialLogitXTrPhyloAuto.o mcmcBinomialLogitXTrPhyloAutoLatent.o mcmcBinomialLogitXTrPhyloLatent.o mcmcNormalAuto.o mcmcNormalAutoLatent.o mcmcNormalLatent.o mcmcNormalNAAuto.o mcmcNormalNAAutoLatent.o mcmcNormalNALatent.o mcmcNormalNAX.o mcmcNormalNAXAuto.o mcmcNormalNAXAutoLatent.o mcmcNormalNAXLatent.o mcmcNormalNAXPhylo.o mcmcNormalNAXPhyloAuto.o mcmcNormalNAXPhyloAutoLatent.o mcmcNormalNAXPhyloLatent.o mcmcNormalNAXTr.o mcmcNormalNAXTrAuto.o mcmcNormalNAXTrAutoLatent.o mcmcNormalNAXTrLatent.o mcmcNormalNAXTrPhylo.o mcmcNormalNAXTrPhyloAuto.o mcmcNormalNAXTrPhyloAutoLatent.o mcmcNormalNAXTrPhyloLatent.o mcmcNormalX.o mcmcNormalXAuto.o mcmcNormalXAutoLatent.o mcmcNormalXLatent.o mcmcNormalXPhylo.o mcmcNormalXPhyloAuto.o mcmcNormalXPhyloAutoLatent.o mcmcNormalXPhyloLatent.o mcmcNormalXTr.o mcmcNormalXTrAuto.o mcmcNormalXTrAutoLatent.o mcmcNormalXTrLatent.o mcmcNormalXTrPhylo.o mcmcNormalXTrPhyloAuto.o mcmcNormalXTrPhyloAutoLatent.o mcmcNormalXTrPhyloLatent.o mcmcOverPoissonAuto.o mcmcOverPoissonAutoLatent.o mcmcOverPoissonLatent.o mcmcOverPoissonX.o mcmcOverPoissonXAuto.o mcmcOverPoissonXAutoLatent.o mcmcOverPoissonXLatent.o mcmcOverPoissonXPhylo.o mcmcOverPoissonXPhyloAuto.o mcmcOverPoissonXPhyloAutoLatent.o mcmcOverPoissonXPhyloLatent.o mcmcOverPoissonXTr.o mcmcOverPoissonXTrAuto.o mcmcOverPoissonXTrAutoLatent.o mcmcOverPoissonXTrLatent.o mcmcOverPoissonXTrPhylo.o mcmcOverPoissonXTrPhyloAuto.o mcmcOverPoissonXTrPhyloAutoLatent.o mcmcOverPoissonXTrPhyloLatent.o mcmcPoissonAuto.o mcmcPoissonAutoLatent.o mcmcPoissonLatent.o mcmcPoissonX.o mcmcPoissonXAuto.o mcmcPoissonXAutoLatent.o mcmcPoissonXLatent.o mcmcPoissonXPhylo.o mcmcPoissonXPhyloAuto.o mcmcPoissonXPhyloAutoLatent.o mcmcPoissonXPhyloLatent.o mcmcPoissonXTr.o mcmcPoissonXTrAuto.o mcmcPoissonXTrAutoLatent.o mcmcPoissonXTrLatent.o mcmcPoissonXTrPhylo.o mcmcPoissonXTrPhyloAuto.o mcmcPoissonXTrPhyloAutoLatent.o mcmcPoissonXTrPhyloLatent.o mcmcProbitAuto.o mcmcProbitAutoLatent.o mcmcProbitLatent.o mcmcProbitX.o mcmcProbitXAuto.o mcmcProbitXAutoLatent.o mcmcProbitXLatent.o mcmcProbitXPhylo.o mcmcProbitXPhyloAuto.o mcmcProbitXPhyloAutoLatent.o mcmcProbitXPhyloLatent.o mcmcProbitXTr.o mcmcProbitXTrAuto.o mcmcProbitXTrAutoLatent.o mcmcProbitXTrLatent.o mcmcProbitXTrPhylo.o mcmcProbitXTrPhyloAuto.o mcmcProbitXTrPhyloAutoLatent.o mcmcProbitXTrPhyloLatent.o rmvnorm.o rtnorm.o rtnorm_1.o rtnorm_slice.o rwishart.o sampleCondPred.o sampleNum.o sampleYlatentBinomialLogit.o sampleYlatentNormal.o sampleYlatentPoisson.o sampleYlatentProbit.o updateLatent.o updateLatentAuto.o updateMeansParamX.o updateMeansParamXBase.o updateMeansParamXPhylo.o updateParamAuto.o updateParamLatent.o updateParamPhylo.o updateParamShrinkGlobal.o updateParamTr.o updateParamTrPhylo.o updateParamX.o updateParamX1.o updateParamXPhylo.o updatePrecX.o updatePrecXPhylo.o updatePrecXTr.o updateResidVar.o updateShrinkLocal.o updateVarDist.o -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/i386 -lRlapack -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/i386 -lR
installing to C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/HMSC/libs/i386
*** arch - x64
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c adaptVar.cpp -o adaptVar.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c adaptVarAdd.cpp -o adaptVarAdd.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c adaptVarAuto.cpp -o adaptVarAuto.o
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c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhylo.cpp -o mcmcBinomialLogitXTrPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcBinomialLogitXTrPhyloAuto.cpp -o mcmcBinomialLogitXTrPhyloAuto.o
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c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTr.cpp -o mcmcPoissonXTr.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrAuto.cpp -o mcmcPoissonXTrAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrAutoLatent.cpp -o mcmcPoissonXTrAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrLatent.cpp -o mcmcPoissonXTrLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrPhylo.cpp -o mcmcPoissonXTrPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrPhyloAuto.cpp -o mcmcPoissonXTrPhyloAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrPhyloAutoLatent.cpp -o mcmcPoissonXTrPhyloAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcPoissonXTrPhyloLatent.cpp -o mcmcPoissonXTrPhyloLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitAuto.cpp -o mcmcProbitAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitAutoLatent.cpp -o mcmcProbitAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitLatent.cpp -o mcmcProbitLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitX.cpp -o mcmcProbitX.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXAuto.cpp -o mcmcProbitXAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXAutoLatent.cpp -o mcmcProbitXAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXLatent.cpp -o mcmcProbitXLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXPhylo.cpp -o mcmcProbitXPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXPhyloAuto.cpp -o mcmcProbitXPhyloAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXPhyloAutoLatent.cpp -o mcmcProbitXPhyloAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXPhyloLatent.cpp -o mcmcProbitXPhyloLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTr.cpp -o mcmcProbitXTr.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrAuto.cpp -o mcmcProbitXTrAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrAutoLatent.cpp -o mcmcProbitXTrAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrLatent.cpp -o mcmcProbitXTrLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhylo.cpp -o mcmcProbitXTrPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloAuto.cpp -o mcmcProbitXTrPhyloAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloAutoLatent.cpp -o mcmcProbitXTrPhyloAutoLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c mcmcProbitXTrPhyloLatent.cpp -o mcmcProbitXTrPhyloLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rmvnorm.cpp -o rmvnorm.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm.cpp -o rtnorm.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm_1.cpp -o rtnorm_1.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rtnorm_slice.cpp -o rtnorm_slice.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c rwishart.cpp -o rwishart.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleCondPred.cpp -o sampleCondPred.o
sampleCondPred.cpp: In function 'arma::cube sampleCondPred(arma::mat&, arma::mat&, arma::vec, int, double, int, std::string)':
sampleCondPred.cpp:42:12: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(family == "poisson" | family == "overPoisson"){
^
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleNum.cpp -o sampleNum.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentBinomialLogit.cpp -o sampleYlatentBinomialLogit.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentNormal.cpp -o sampleYlatentNormal.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentPoisson.cpp -o sampleYlatentPoisson.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c sampleYlatentProbit.cpp -o sampleYlatentProbit.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateLatent.cpp -o updateLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateLatentAuto.cpp -o updateLatentAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamX.cpp -o updateMeansParamX.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamXBase.cpp -o updateMeansParamXBase.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateMeansParamXPhylo.cpp -o updateMeansParamXPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamAuto.cpp -o updateParamAuto.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamLatent.cpp -o updateParamLatent.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamPhylo.cpp -o updateParamPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamShrinkGlobal.cpp -o updateParamShrinkGlobal.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamTr.cpp -o updateParamTr.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamTrPhylo.cpp -o updateParamTrPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamX.cpp -o updateParamX.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamX1.cpp -o updateParamX1.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateParamXPhylo.cpp -o updateParamXPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecX.cpp -o updatePrecX.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecXPhylo.cpp -o updatePrecXPhylo.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updatePrecXTr.cpp -o updatePrecXTr.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateResidVar.cpp -o updateResidVar.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateShrinkLocal.cpp -o updateShrinkLocal.o
c:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/include" -DNDEBUG -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/Rcpp/include" -I"C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c updateVarDist.cpp -o updateVarDist.o
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o HMSC.dll tmp.def RcppExports.o adaptVar.o adaptVarAdd.o adaptVarAuto.o adaptVarAutoAdd.o adaptVarAutoRemove.o adaptVarRemove.o euclDist.o fixParamAuto.o fixParamPhylo.o mcmcBinomialLogitAuto.o mcmcBinomialLogitAutoLatent.o mcmcBinomialLogitLatent.o mcmcBinomialLogitX.o mcmcBinomialLogitXAuto.o mcmcBinomialLogitXAutoLatent.o mcmcBinomialLogitXLatent.o mcmcBinomialLogitXPhylo.o mcmcBinomialLogitXPhyloAuto.o mcmcBinomialLogitXPhyloAutoLatent.o mcmcBinomialLogitXPhyloLatent.o mcmcBinomialLogitXTr.o mcmcBinomialLogitXTrAuto.o mcmcBinomialLogitXTrAutoLatent.o mcmcBinomialLogitXTrLatent.o mcmcBinomialLogitXTrPhylo.o mcmcBinomialLogitXTrPhyloAuto.o mcmcBinomialLogitXTrPhyloAutoLatent.o mcmcBinomialLogitXTrPhyloLatent.o mcmcNormalAuto.o mcmcNormalAutoLatent.o mcmcNormalLatent.o mcmcNormalNAAuto.o mcmcNormalNAAutoLatent.o mcmcNormalNALatent.o mcmcNormalNAX.o mcmcNormalNAXAuto.o mcmcNormalNAXAutoLatent.o mcmcNormalNAXLatent.o mcmcNormalNAXPhylo.o mcmcNormalNAXPhyloAuto.o mcmcNormalNAXPhyloAutoLatent.o mcmcNormalNAXPhyloLatent.o mcmcNormalNAXTr.o mcmcNormalNAXTrAuto.o mcmcNormalNAXTrAutoLatent.o mcmcNormalNAXTrLatent.o mcmcNormalNAXTrPhylo.o mcmcNormalNAXTrPhyloAuto.o mcmcNormalNAXTrPhyloAutoLatent.o mcmcNormalNAXTrPhyloLatent.o mcmcNormalX.o mcmcNormalXAuto.o mcmcNormalXAutoLatent.o mcmcNormalXLatent.o mcmcNormalXPhylo.o mcmcNormalXPhyloAuto.o mcmcNormalXPhyloAutoLatent.o mcmcNormalXPhyloLatent.o mcmcNormalXTr.o mcmcNormalXTrAuto.o mcmcNormalXTrAutoLatent.o mcmcNormalXTrLatent.o mcmcNormalXTrPhylo.o mcmcNormalXTrPhyloAuto.o mcmcNormalXTrPhyloAutoLatent.o mcmcNormalXTrPhyloLatent.o mcmcOverPoissonAuto.o mcmcOverPoissonAutoLatent.o mcmcOverPoissonLatent.o mcmcOverPoissonX.o mcmcOverPoissonXAuto.o mcmcOverPoissonXAutoLatent.o mcmcOverPoissonXLatent.o mcmcOverPoissonXPhylo.o mcmcOverPoissonXPhyloAuto.o mcmcOverPoissonXPhyloAutoLatent.o mcmcOverPoissonXPhyloLatent.o mcmcOverPoissonXTr.o mcmcOverPoissonXTrAuto.o mcmcOverPoissonXTrAutoLatent.o mcmcOverPoissonXTrLatent.o mcmcOverPoissonXTrPhylo.o mcmcOverPoissonXTrPhyloAuto.o mcmcOverPoissonXTrPhyloAutoLatent.o mcmcOverPoissonXTrPhyloLatent.o mcmcPoissonAuto.o mcmcPoissonAutoLatent.o mcmcPoissonLatent.o mcmcPoissonX.o mcmcPoissonXAuto.o mcmcPoissonXAutoLatent.o mcmcPoissonXLatent.o mcmcPoissonXPhylo.o mcmcPoissonXPhyloAuto.o mcmcPoissonXPhyloAutoLatent.o mcmcPoissonXPhyloLatent.o mcmcPoissonXTr.o mcmcPoissonXTrAuto.o mcmcPoissonXTrAutoLatent.o mcmcPoissonXTrLatent.o mcmcPoissonXTrPhylo.o mcmcPoissonXTrPhyloAuto.o mcmcPoissonXTrPhyloAutoLatent.o mcmcPoissonXTrPhyloLatent.o mcmcProbitAuto.o mcmcProbitAutoLatent.o mcmcProbitLatent.o mcmcProbitX.o mcmcProbitXAuto.o mcmcProbitXAutoLatent.o mcmcProbitXLatent.o mcmcProbitXPhylo.o mcmcProbitXPhyloAuto.o mcmcProbitXPhyloAutoLatent.o mcmcProbitXPhyloLatent.o mcmcProbitXTr.o mcmcProbitXTrAuto.o mcmcProbitXTrAutoLatent.o mcmcProbitXTrLatent.o mcmcProbitXTrPhylo.o mcmcProbitXTrPhyloAuto.o mcmcProbitXTrPhyloAutoLatent.o mcmcProbitXTrPhyloLatent.o rmvnorm.o rtnorm.o rtnorm_1.o rtnorm_slice.o rwishart.o sampleCondPred.o sampleNum.o sampleYlatentBinomialLogit.o sampleYlatentNormal.o sampleYlatentPoisson.o sampleYlatentProbit.o updateLatent.o updateLatentAuto.o updateMeansParamX.o updateMeansParamXBase.o updateMeansParamXPhylo.o updateParamAuto.o updateParamLatent.o updateParamPhylo.o updateParamShrinkGlobal.o updateParamTr.o updateParamTrPhylo.o updateParamX.o updateParamX1.o updateParamXPhylo.o updatePrecX.o updatePrecXPhylo.o updatePrecXTr.o updateResidVar.o updateShrinkLocal.o updateVarDist.o -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/x64 -lRlapack -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/Users/ALEXAN~1.VIL/DOCUME~1/R/R-35~1.2/bin/x64 -lR
installing to C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/HMSC/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
Error : (converti depuis l'avis) package 'coda' was built under R version 3.5.3
ERROR: lazy loading failed for package 'HMSC'
* removing 'C:/Users/alexandre.villers/Documents/R/R-3.5.2/library/HMSC'
In R CMD INSTALL
Error in i.p(...) :
(converti depuis l'avis) installation of package ‘C:/Users/ALEXAN~1.VIL/AppData/Local/Temp/Rtmp020z31/file16206b024eff/HMSC_2.2-0.tar.gz’ had non-zero exit status
**> sessionInfo()**
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] usethis_1.4.0 devtools_2.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 ps_1.3.0 prettyunits_1.0.2 rprojroot_1.3-2 digest_0.6.18 crayon_1.3.4
[7] withr_2.1.2 assertthat_0.2.0 R6_2.3.0 backports_1.1.3 magrittr_1.5 rlang_0.3.1
[13] cli_1.0.1 curl_3.3 fs_1.2.7 remotes_2.0.2 callr_3.1.1 desc_1.2.0
[19] tools_3.5.2 glue_1.3.0 pkgload_1.0.2 compiler_3.5.2 processx_3.2.1 pkgbuild_1.0.2
[25] sessioninfo_1.1.1 memoise_1.1.0
Any idea ?
Thanks in advance
Installing HMSC
Hello,
I am having trouble installing HMSC through Rstudio (Version 1.0.136).
Initially, just using install.packages(), I receive the error "Warning in install.packages :
package ‘HMSC’ is not available (for R version 3.3.2)".
My standard workaround for this, is to install directly from github, which is how I found your repository:
library(devtools)
install_github("guiblanchet/HMSC")
This installs for quite a while, but ends with the error:
"ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [HMSC.so] Error 1
ERROR: compilation failed for package ‘HMSC’
- removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/HMSC’
Error: Command failed (1)
When looking into this error, I also tried installing "Rcpp" and "RcppArmadillo" before installing via "guiblanchet/HMSC", with the same result.
Then I found this article http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/
which seemed promising, but neither running
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
...through Terminal, nor following this help comment:
"Could you close out all R sessions (including RStudio), open Terminal and type:
xcode-select --install
This ensures that you have development command line tools (e. g. gcc, git, et cetera) on your system.
Please run:
git --version
To make sure the license agreements have been approved.
From there, I'd like you to try to install the gfortran binaries by again repeating:
curl -O http://r.research.att.com/l...
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
...got me any closer. I apologize for bothering you with such a mundane issue, but I believe I have a great data set to use with this package and I am excited to try it out.
Thanks!
Problem using single records with predict.HMSC
Hello,
We've been attempting to perform Leave one out Cross Validation to tune parameters and have had some issues getting the predict.HMSC function to accept only a single row of data for X and Y. It appears that the main issue that cannot be fixed by altering the settings or the way the initial data are formatted is an error at line 126:
dimnames(res)[[1]]<-rownames(data$Y)
With only a single row in Y this line returns the error:
Error in dimnames(res)[[1]] <- rownames(data$Y) : 'dimnames' must be a list
I was able to circumvent this issue with the following slight change:
dimnames(res)[[1]]<-list(rownames(data$Y))
Assuming that this does not mess with anything else this change in the package could ease use for those attempting LOO-CV with HMSC.
Thanks so much for all your work,
Robbie
Bug in iniParam
available from CRAN?
As far as I can tell, HMSC isn't available from CRAN. Package installation and management with packrat or conda would be facilitated by having HMSC available on CRAN. For instance, managing the dependency hierarchy of any packages that use HMSC as a dependency (at some possible point in the future) is going to be easier to deal with if your package is on CRAN.
Are you planning (or currently working on) submitting HMSC to CRAN?
Questions about put the phylogeny to the HMSC-R model
Hello, everyone
I want to put the phylogenetic tree matrix to the HMSC model in addition to the Pi, X, Y, the manual only provide the parameters Pi, X, Y and I don't know how to run the as.HMSCdata(), when add the phylogenetic tree, when I try the code: formdata <- as.HMSCdata(Y = Y, X = X, Random = Pi, interceptX = FALSE,Phylo=phy, scaleX=FALSE)
It got an error:
Error in apply(Phylo, 1, as.character) :
dim(X) must have a positive length
I don't know where the problem is, I have input the Phy<- read.csv("phy.dist.csv") before, the form of phylogenetic tree is as the same of Simulated Example 2, Can anyone help me?
All the best,
Liyan
Error when family="gaussian" in hmsc()
When running the hmsc() function with familly="gaussian"
data("bryophytes")
bryophytes <- as.HMSCdata(Y=bryophytes$Y, X = bryophytes$X, Tr = bryophytes$Tr, scaleX = TRUE, scaleTr = FALSE, interceptX = FALSE, interceptTr = FALSE)
model<-hmsc(bryophytes,family="gaussian",niter=10000,nburn=1000,thin=10)
I get the following error:
error: matrix multiplication: incompatible matrix dimensions: 5x5 and 60x1 Error in mcmcNormalXTr(Ylatent, X, Tr, param$param$paramX, param$param$paramTr, : matrix multiplication: incompatible matrix dimensions: 5x5 and 60x1
However, if I remove the trait matrix, it works
bryophytes <- as.HMSCdata(Y=bryophytes$Y, X = bryophytes$X, scaleX = TRUE, scaleTr = FALSE, interceptX = FALSE, interceptTr = FALSE)
as.mcmc() burning error
I get the error:
Error in rbind(paramBurnMCMCMat, paramMCMCMat) :
object 'paramBurnMCMCMat' not found
I am running the as.mcmc() with parameters = "meansParamX"
The error stems from line 154 in the as.mcmc.hmsc() source file
where object paramBurnMCMCMat does not exist and instead it should bind paramBurnMCMC
Some problem with conditional prediction and nsample
Hello,
The example of conditional predictions in the manual on page 46 does not run in this line
predValCond[,i,j] <- predict(model, newdata=fungiValTmp,
conditional=condSp, nsample=nsamp)[,i]
because the predictions come in a 3 dimensional array. The third dimension has the predictions for each sample of nsample. However, this somewhat confuses me because in the help of the function, the returning value is said to be
A matrix with the predicted values for each species at the sites in ‘newdata’ or a matrix of the same dimension as the fitted values.
This does not mention that predictions will be returned for each sample in nsample. On the other hand, the example of page 46 is written assuming that only one set of predictions is returned, regardless of nsample.
So, afterall, where is the problem, is it in function predict.hmsc() or in the example of page 46?
EDIT: (note that the example in help(predict.hmsc) does not run for the same reason)
All the best,
Miguel
Return credible intervals from predict.hmsc
Hi Guillaume,
I see that predict.hmsc() returns only the mean prediction via the lines apply(res,1:2, mean). Could you add quantile as well so we can retrieve the 95% credible intervals too? Thanks in advance!!!
Hao Ran
Misplaced '!'
Hi,
this '!' should not be there:
as.HMSCdata
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