I am trying to run the following model:
mod1<- phylo_glmmTMB(response ~ sv1 + # sampling variables
sv2 + sv3 + sv4 + sv5 +
sv6 + sv7 +
(1|phylo) + (1|reference_id), #random effects
ziformula = ~ 0,
#ar1(pos + 0| group) # spatial autocorrelation structure; group is a dummy variable
phyloZ = supertreenew,
phylonm = "phylo",
family = "binomial",
data = data)
But I keep getting the error:
Error in Matrix::rankMatrix(TMBStruc$data.tmb[[whichX]]) :
length(d <- dim(x)) == 2 is not TRUE
This error is also occurring with other reproducible example (data) that I found.
Before I run the model, I just loaded my data (data and supertree) and computed a Z matrix from supertree:
#Compute Z matrix
#supertreenew <- vcv.phylo(supertreenew)
#or
supertreenew <- phylo.to.Z(supertreenew)
#enforced match between
supertreenew <- supertreenew[levels(factor(data$phylo)), ]
I have installed the development version via:
remotes::install_github("wzmli/phyloglmm/pkg")
But no success.
The dimension of my supertree are:
[[1]]
... [351]
[[2]]
... [645]
Any guess?
My session info:
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] phyloglmm_0.1.0.9001 brms_2.18.0 cpp_1.0.9 performance_0.10. DHARMa_0.4.6
[6] phytools_1.2-0 maps_3.4.0 ape_5.6-2 lme4_1.1-31 Matrix_1.5-1
[11] TMB_1.9.1 glmmTMB_1.1.5.9000 remotes_2.4.2
(First error, "Error in Matrix::rankMatrix") This is a consequence of the addition of a check of the rank of the fixed-effects matrix in recent versions of glmmTMB. For now, adding
control = glmmTMB::glmmTMBControl(rank_check = "skip")
to your phylo_glmmTMB call should work around the problem.
(Second error, "Error in getParameterOrder(data, parameters, new.env(), DLL = DLL) ...") I just updated the refactor branch to handle this problem [caused by internal changes in glmmTMB]. Use remotes::install_github("wzmli/phyloglmm/pkg#refactor") to install this version, then try your example again.
library(dplyr)
library(plotly)
# data frame
Title = c('Titanic', 'Avatar', 'Jurassic World')
Profit = c(458672302, 523505847, 502177271)
df = data.frame(Title, Profit)
Basically, I'm trying to color the bars according to the Profit column. And when it's not ordered, it works figure 1
# X axis not ordered (working)
plot_ly(df, x = ~Title,
y = ~Profit,
color = ~Profit,
type = 'bar')
But when I try to reorder the x axis (to look like this), it returns an error, probably because it's a factor:
# X axis reordered (not working)
plot_ly(df, x = ~reorder(Title, -Profit) %>% as.character(),
y = ~Profit,
color = ~Profit,
type = 'bar')
Error in Summary.factor(c(3L, 1L, 2L), na.rm = TRUE) :
‘range’ not meaningful for factors
In addition: Warning message:
textfont.color doesn't (yet) support data arrays
Does anyone have any tips?
Your code works fine for me:
library(dplyr)
library(plotly)
# data frame
Title = c('Titanic', 'Avatar', 'Jurassic World')
Profit = c(458672302, 523505847, 502177271)
df = data.frame(Title, Profit)
# X axis reordered (not working)
plot_ly(df, x = ~reorder(Title, -Profit) %>% as.character(),
y = ~Profit,
color = ~Profit,
type = 'bar')
Output:
This is my sessioninfo:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] nl_NL.UTF-8/nl_NL.UTF-8/nl_NL.UTF-8/C/nl_NL.UTF-8/nl_NL.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plotly_4.10.0 ggplot2_3.3.5 dplyr_1.0.8
So what you can do is check your session using sessioninfo() in your console and check if you packages are right.
I would really be grateful if you can help me out.
I'm not able to show french character, such as "é,è, œ", in plot made with ggplot, while using markdown document for word or html. The outcome plot shows "" or kind of, if I knit the document.
If I only run the chunk, it shows "..." instead of the "é", for instance.
If that can help you, that's my sessioninfo()
> sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.2
>
> Matrix products: default BLAS:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> locale: [1] C
> [...]
I've tried, unsuccessfully the following:
1.Sys.setlocale("LC_ALL","French")
2.Sys.setenv(LANG = "fr_FR.UTF-8")
3.Save with encoding "UTF-8"
4.Terminal: defaults write org.R-project.R force.LANG fr_FR.UTF-8
The sample of the code is the following:
plot.1E <- ggplot(energy_electrique,
aes(y = Energie_kWh, x = Month, fill = as.factor(Year)))+
geom_col(position = "dodge", width = 0.8) +
scale_fill_manual("Années de mesure",
values = c("firebrick1", "forestgreen", "mediumblue", "gold"),
labels = c("2015","2016","2017","2018"))
Below is the outcome of the code. As you can see, the x axis title has "Ann...es de mesures" instead of "Années de mesures":
With runjags, I am trying to monitor a very large number of values. The format for the monitor list is a string of values, In this case I am asking to moitor just 3, Y[14], Y[15], Y[3].
run.jags(model="model.MC.txt",data=list(Y=Y.NA.Rep,sizes=sizesB,cumul=cumul),
monitor=c("thetaj", "Y[14]", "Y[15]","Y[3]"))
Suppose I wanted to monitor hundreds of values. I can create this string, but it just returns to the prompt "+". and fails to run.
Is there some upper limit on the size of strings that can be created and passed in as arguments?
Is there a better way (non string) to pass this list into run.jags?
The only way I have been able to get it to run is to paste the string literal
into the function call, a variable containing the string does not work.
The longer run list looks something like this:
run.jags(model="model.MC.txt",data=list(Y=Y.NA.Rep,sizes=sizesB,cumul=cumul)
,monitor=c('Y[14]', 'Y[15]', 'Y[18]', 'Y[26]', 'Y[41]',
'Y[55]', 'Y[62]', 'Y[72]', 'Y[80]', 'Y[81]', 'Y[128]', 'Y[138]',
'Y[180]', 'Y[188]', 'Y[191]', 'Y[209]', 'Y[224]', 'Y[244]', '
'Y[255]', 'Y[263]', 'Y[282]', 'Y[292]', 'Y[303]', 'Y[324]',
'Y[349]', 'Y[358]', 'Y[359]', 'Y[365]', 'Y[384]',
... many lines deleted
'Y[1882]', 'Y[1895]', 'Y[1899]', 'Y[1903]', 'Y[1918]', 'Y[1922]',
'Y[1929]', 'Y[1942]', 'Y[1953]', 'Y[1990]'))
I'm not sure that this is a problem with runjags - the following code has 1002 monitors and runs just fine:
model <- "model {
for(i in 1 : N){ #data# N
Y[i] ~ dnorm(true.y[i], precision) #data# Y
true.y[i] <- (m * X[i]) + c #data# X
}
m ~ dnorm(0, 10^-3)
c ~ dnorm(0, 10^-3)
precision ~ dgamma(10^-3, 10^-3)
}"
X <- 1:1000
Y <- rnorm(length(X), 2*X + 10, 1)
N <- length(X)
monitors <- c('m','c',paste0('Y[',1:1000,']'))
results <- run.jags(model, n.chains=2, monitor=monitors, sample=100, method='rjags')
results <- run.jags(model, n.chains=2, monitor=monitors, sample=100, method='inter')
I have also tried writing the string directly into the function call by using:
cat('monitor = c("'); cat(monitors, sep='", "'); cat('")\n')
...and copy/pasting the resulting text as the monitor argument - that still works for me in R.app but when pasting into RStudio I get:
> results <- run.jags(model, n.chains=2, monitor = c("m", "c", "Y[1]", "Y[2]", "Y[3]", "Y[4]", "Y[5]", "Y[6]", "Y[7]", "Y[8]", "Y[9]", "Y[10]", "Y[11]", "Y[12]", "Y[13]", "Y[14]", "Y[15]", "Y[16]", "Y[17]", "Y[18]", "Y[19]", "Y[20]", "Y[21]", "Y[22]", "Y[23]", "Y[24]", "Y[25]", "Y[26]", "Y[27]", "Y[28]", "Y[29]", "Y[30]", "Y[31]", "Y[32]", "Y[33]", "Y[34]", "Y[35]", "Y[36]", "Y[37]", "Y[38]", "Y[39]", "Y[40]", "Y[41]", "Y[42]", "Y[43]", "Y[44]", "Y[45]", "Y[46]", "Y[47]", "Y[48]", "Y[49]", "Y[50]", "Y[51]", "Y[52]", "Y[53]", "Y[54]", "Y[55]", "Y[56]", "Y[57]", "Y[58]", "Y[59]", "Y[60]", "Y[61]", "Y[62]", "Y[63]", "Y[64]", "Y[65]", "Y[66]", "Y[67]", "Y[68]", "Y[69]", "Y[70]", "Y[71]", "Y[72]", "Y[73]", "Y[74]", "Y[75]", "Y[76]", "Y[77]", "Y[78]", "Y[79]", "Y[80]", "Y[81]", "Y[82]", "Y[83]", "Y[84]", "Y[85]", "Y[86]", "Y[87]", "Y[88]", "Y[89]", "Y[90]", "Y[91]", "Y[92]", "Y[93]", "Y[94]", "Y[95]", "Y[96]", "Y[97]", "Y[98]", "Y[99]", "Y[100]", "Y[101]", "Y[102]", "Y[103]", "Y[104]", "Y[105]... <truncated>
+
+
Which is somewhat similar to your description. So I'm guessing that you are using RStudio and that the problem is to do with the maximum length of a line of code that can be interpreted by RStudio.
If so, the fix is to simply hard wrap the command so it is broken over multiple lines - I tried this with 72 character width (100+ lines) and it works fine in RStudio. If my assumption is incorrect please modify your question to give more details of how you are running R, and your system using:
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] runjags_2.0.4-2
loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0 parallel_3.4.0 coda_0.19-1 grid_3.4.0 rjags_4-6 lattice_0.20-35
I am trying to plot a graph with price and a few technical indicators such as ADX, RSI, and OBV. I cannot figure out why addOBV is giving an error and why addADX not showing at all in the graph lines in the chart?
Here my code:
tmp <- read.csv(paste("ProcessedQuotes/",Nifty[x,],".csv", sep=""),
as.is=TRUE, header=TRUE, row.names=NULL)
tmp$Date<-as.Date(tmp$Date)
ydat = xts(tmp[,-1],tmp$Date)
lineChart(ydat, TA=NULL, name=paste(Nifty[x,]," Technical Graph"))
plot(addSMA(10))
plot(addEMA(10))
plot(addRSI())
plot(addADX())
plot(addOBV())
Error for addOBV is:
Error in try.xts(c(2038282, 1181844, -1114409, 1387404, 3522045, 4951254, :
Error in as.xts.double(x, ..., .RECLASS = TRUE) :
order.by must be either 'names()' or otherwise specified
Below you can see DIn is not shown fully in the graphs.
> class(ydat)
[1] "xts" "zoo"
> head(ydat)
Open High Low Close Volume Trades Sma20 Sma50 DIp DIn DX ADX aroonUp aroonDn oscillator macd signal RSI14
I don't know why that patch doesn't work for you, but you can just create a new function (or you could mask the one from quantmod). Let's just make a new, patched version called addOBV2 which is the code for addOBV except for the one patched line. (x <- as.matrix(lchob#xdata) is replaced with x <- try.xts(lchob#xdata, error=FALSE)).
addOBV2 <- function (..., on = NA, legend = "auto")
{
stopifnot("package:TTR" %in% search() || require("TTR", quietly = TRUE))
lchob <- quantmod:::get.current.chob()
x <- try.xts(lchob#xdata, error=FALSE)
#x <- as.matrix(lchob#xdata)
x <- OBV(price = Cl(x), volume = Vo(x))
yrange <- NULL
chobTA <- new("chobTA")
if (NCOL(x) == 1) {
chobTA#TA.values <- x[lchob#xsubset]
}
else chobTA#TA.values <- x[lchob#xsubset, ]
chobTA#name <- "chartTA"
if (any(is.na(on))) {
chobTA#new <- TRUE
}
else {
chobTA#new <- FALSE
chobTA#on <- on
}
chobTA#call <- match.call()
legend.name <- gsub("^.*[(]", " On Balance Volume (", deparse(match.call()))#,
#extended = TRUE)
gpars <- c(list(...), list(col=4))[unique(names(c(list(col=4), list(...))))]
chobTA#params <- list(xrange = lchob#xrange, yrange = yrange,
colors = lchob#colors, color.vol = lchob#color.vol, multi.col = lchob#multi.col,
spacing = lchob#spacing, width = lchob#width, bp = lchob#bp,
x.labels = lchob#x.labels, time.scale = lchob#time.scale,
isLogical = is.logical(x), legend = legend, legend.name = legend.name,
pars = list(gpars))
if (is.null(sys.call(-1))) {
TA <- lchob#passed.args$TA
lchob#passed.args$TA <- c(TA, chobTA)
lchob#windows <- lchob#windows + ifelse(chobTA#new, 1,
0)
chartSeries.chob <- quantmod:::chartSeries.chob
do.call("chartSeries.chob", list(lchob))
invisible(chobTA)
}
else {
return(chobTA)
}
}
Now it works.
# reproduce your data
ydat <- getSymbols("ZEEL.NS", src="yahoo", from="2012-09-11",
to="2013-01-18", auto.assign=FALSE)
lineChart(ydat, TA=NULL, name=paste("ZEEL Technical Graph"))
plot(addSMA(10))
plot(addEMA(10))
plot(addRSI())
plot(addADX())
plot(addOBV2())
This code reproduces the error:
library(quantmod)
getSymbols("AAPL")
lineChart(AAPL, 'last 6 months')
addOBV()
Session Info:
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] quantmod_0.3-17 TTR_0.21-1 xts_0.9-1 zoo_1.7-9 Defaults_1.1-1 rgeos_0.2-11
[7] sp_1.0-5 sos_1.3-5 brew_1.0-6
loaded via a namespace (and not attached):
[1] grid_2.15.0 lattice_0.20-6 tools_2.15.0
Googling around, the error seems to be related to the fact that addOBV converts the data into a matrix, which causes problems with TTR::OBV. A patch has been posted on RForge.