Error: subscript out of bounds - what does this mean?
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Ias S
Oct 21, 2016, 8:47:32 AM10/21/16
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HI,
I am using data that has been put into a unmarkedFrameGDS.
However, when I try a simple null model is get the following error?
Any help would be appreciated.
Thanks
Ian
db <- c(0, 10, 25, 50, 100, 200)
#numPrimary=nVisits
#load separate table with covariates at observer level ##in correst
obsCovs1 <- read.csv("covs_obs_level_ing.csv", header=T)
y <- as.matrix(yDat)
wt<- data.frame(covs)
str(wt)
siteCovs <- wt[,c("standage", "cov.tree")]
bird.obsCovs<- list(date=obsCovs1[,c("Day.1", "Day.2", "Day.3", "Day.4", "Day.5")], time=obsCovs1[,c("Time.1", "Time.2", "Time.3", "Time.4", "Time.5")])
umf <- unmarkedFrameGDS(y=y, siteCovs=siteCovs, yearlySiteCovs = bird.obsCovs, survey="point", dist.breaks=db, numPrimary=5, unitsIn="m")
head(umf)
summary(umf)
# Fit the model
m1 <- gdistsamp(~1, ~1, ~1, umf, output="density")
summary(m1)
I am using data that has been put into a unmarkedFrameGDS.
However, when I try a simple null model is get the following error?
Any help would be appreciated.
Thanks
Ian
db <- c(0, 10, 25, 50, 100, 200)
#numPrimary=nVisits
#load separate table with covariates at observer level ##in correst
obsCovs1 <- read.csv("covs_obs_level_ing.csv", header=T)
y <- as.matrix(yDat)
wt<- data.frame(covs)
str(wt)
siteCovs <- wt[,c("standage", "cov.tree")]
bird.obsCovs<- list(date=obsCovs1[,c("Day.1", "Day.2", "Day.3", "Day.4", "Day.5")], time=obsCovs1[,c("Time.1", "Time.2", "Time.3", "Time.4", "Time.5")])
umf <- unmarkedFrameGDS(y=y, siteCovs=siteCovs, yearlySiteCovs = bird.obsCovs, survey="point", dist.breaks=db, numPrimary=5, unitsIn="m")
head(umf)
summary(umf)
# Fit the model
m1 <- gdistsamp(~1, ~1, ~1, umf, output="density")
summary(m1)
Ias S
Oct 21, 2016, 8:48:15 AM10/21/16
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This was the error:
> m1 <- gdistsamp(~1, ~1, ~1, umf, output="density")
Error in `[<-`(`*tmp*`, i, j, value = 1649.33614313464) :
subscript out of bounds
Florent Bled
Oct 21, 2016, 10:51:39 PM10/21/16
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Hello Ias,
This issue usually appears when you try to access a column or a row in a dataframe that does not exist. You should double-check the structure of your data. Without a look at your actual data, it will be difficult to pin point exactly where the problem is coming from. If you want to, you can post here a subset of the data that reproduces the error. If you don't want to publicly do that, you can send me directly some data to take a look at it.
Cheers,
Florent
This issue usually appears when you try to access a column or a row in a dataframe that does not exist. You should double-check the structure of your data. Without a look at your actual data, it will be difficult to pin point exactly where the problem is coming from. If you want to, you can post here a subset of the data that reproduces the error. If you don't want to publicly do that, you can send me directly some data to take a look at it.
Cheers,
Florent
priyanka ratnakar
May 7, 2018, 6:44:54 AM5/7/18
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Hi Florent,
I a getting the same error.Can you please suggest a solution
for(i in 1:dim(dataset)[1]){
hitlist=trainmy2[trainmy2$VisitNumber==dataset[i,2],]
dayofweek=names(hitlist)[3:9][hitlist[1,3:9]>0]
dataset[i,dayofweek]=1
hitlist2=Copy_Walmart[Copy_Walmart$VisitNumber==dataset[i,2],]
agg=aggregate(ScanCount~DepartmentDescription,data=hitlist2,sum)
sub1<-gsub("", ".",paste0(names(agg)[1],".",agg[,1]))
sub2<-gsub("-", ".",sub1)
sub3<-gsub("&", ".",sub2)
sub4<-gsub("/", ".",sub3)
sub5<-gsub(",", ".",sub4)
dataset[i,sub5]=agg[,2]
print(i)
}
Error:- Error in `*tmp*`[[j]] : subscript out of bounds
Florent Bled
May 7, 2018, 10:54:26 PM5/7/18
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Hello priyanka!
Without an actual piece of the dataset from which to reproduce the error, it is difficult to figure out exactly what's happening. If you can't share a reproducible example, the way I would go about identifying where the issue is coming from is to first check where in the loop you're stopping (as easy as simply typing "i" and enter, that will print the latest value of i). Then, I'd run each line in the loop individually, one after the other, using this value of i. This way, you'd be able to identify which instruction is causing the error. From there, you'll be able to look at each element, and make sure that everything is indexed properly / has the correct format.
I hope it helps!
Florent
Without an actual piece of the dataset from which to reproduce the error, it is difficult to figure out exactly what's happening. If you can't share a reproducible example, the way I would go about identifying where the issue is coming from is to first check where in the loop you're stopping (as easy as simply typing "i" and enter, that will print the latest value of i). Then, I'd run each line in the loop individually, one after the other, using this value of i. This way, you'd be able to identify which instruction is causing the error. From there, you'll be able to look at each element, and make sure that everything is indexed properly / has the correct format.
I hope it helps!
Florent
priyanka ratnakar
May 8, 2018, 12:17:12 AM5/8/18
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Thanks Florent it did helped.
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Ian F
Jul 12, 2018, 7:43:25 PM7/12/18
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I am having a similar issue and have no idea whats wrong. any suggestions? I am trying to alter this script to fit my data set which has 4 rows and 10 columns. i keep getting the error code Error in `[<-`(`*tmp*`, j, 1, value = sub.data[1, 1]) :
subscript out of bounds. can anyone help?
data <- read.table(chr, header=TRUE)
len <- length(data$X)
overall.table <- matrix(nrow=len/4, ncol=(5*2)+0)
overall.length <- len/4
for(j in c(1:overall.length)) {
print(j) #displays entire object j
sub.data <- as.matrix(data[ (1+4*(j-1)):((1+4*(j-1))+11), 2:4])
overall.table[j,1] <- sub.data[1, 1]
overall.table[j,2:3] <- sub.data[1, 2:3]
overall.table[j,4:5] <- sub.data[2, 2:3]
overall.table[j,6:7] <- sub.data[3, 2:3]
overall.table[j,8:9] <- sub.data[4, 2:3]
overall.table[j,10:11] <- sub.data[5, 2:3]
overall.table[j,12:13] <- sub.data[6, 2:3]
overall.table[j,14:15] <- sub.data[7, 2:3]
overall.table[j,16:17] <- sub.data[8, 2:3]
overall.table[j,18:19] <- sub.data[9, 2:3]
overall.table[j,20:21] <- sub.data[10, 2:3]
overall.table[j,22:23] <- sub.data[11, 2:3]
overall.table[j,24:25] <- sub.data[12, 2:3]
overall.table[j,26:27] <- sub.data[13, 2:3]
overall.table[j,28:29] <- sub.data[14, 2:3]
overall.table[j,30:31] <- sub.data[15, 2:3]
overall.table[j,32:33] <- sub.data[16, 2:3]
overall.table[j,34:35] <- sub.data[17, 2:3]
Ian F
Jul 12, 2018, 7:43:25 PM7/12/18
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This is the data set im working with.
order label x y
1 rafalt.JPG 764 884
2 rafalt.JPG 2080 724
3 rafalt.JPG 3480 936
4 rafalt.JPG 2036 2720
1 rafnas.JPG 1552 1140
2 rafnas.JPG 2156 1020
3 rafnas.JPG 2788 1104
4 rafnas.JPG 2172 2048
1 Rafsp.JPG 1324 1008
2 Rafsp.JPG 2092 840
3 Rafsp.JPG 2964 924
4 Rafsp.JPG 2132 2356
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Jim Baldwin
Jul 13, 2018, 2:08:40 AM7/13/18
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IanF,
Your problem seems to be set of R problems rather than anything to do with unmarked. Case matters: You use
len <- length(data$X) when the data supplied uses a lowercase x.
But the main problem is that you're attempting to reference rows and columns that don't exist. sub.data is a 12 x 3 matrix and overall.table is a 3 x 10 matrix. Therefore, you can't request
overall.table[j,12:13] or sub.data[13, 2:3].
Jim
Ian F
Jul 14, 2018, 1:05:53 PM7/14/18
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Thank you very much for your help Jim it finally worked.
Linh Phạm
Aug 14, 2019, 11:46:38 AM8/14/19
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Hello,
I am also having problem with this error
> library(stringr)
> text <- list()
> htemp <- list()
> htags <- data.frame()
> data <- read.csv("0908 clean csv.csv", sep = ";")
> data <- as.matrix(data[-1])
>
> maxrows <- nrow(data)
> for(i in 1:maxrows){
+ text[i] <- as.character(data[i,5])
+ htemp <- str_extract_all(text[i], "#\\S+", TRUE)
+
+ if(ncol(htemp) != 0){
+ for(j in 1:ncol(htemp)){
+ htags[i,j] <- htemp[1,j]
+ }
+ }
+ }
Error in data[i, 5] : subscript out of bounds
>
> #Save Hashtags as csv for Excel
> write.csv(htags, "ht_unsort_danang.csv", fileEncoding = "UTF-8")
>
If anyone of you see when is the reason, please help me to solve it. Thank a lots
Here is a part of my data
Charles Afful
Mar 2, 2020, 7:23:30 PM3/2/20
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i have an inflation data and am trying to find the transition matrix if it and am having problem with the code am using this is the code i used
tm=matrix(c(rep(0,54)),3,3);tm
tpm=matrix(c(rep(0,54)),3,3);tpm
for(i in 1:length(data)-1)
tm[da[i],da[i+1]]=(tm[da[i],da[i+1]]+1)
tm
for (j in 1:3)
tpm[j,]=(tm[j,]/sum(tm[j,]))
tpm
and then also what the codes to find transition frequency
Audace ADANTODE
Jun 4, 2020, 3:54:00 PM6/4/20
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Hello Florent
I am facing the same problem. Here is my data and the code I used.
rm(list=ls())
library(raster)
library(ncdf4)
library(ncdf.tools)
library(ncdfgeom)
library(rgdal)
library(gdata)
setwd("C:/Users/USER/Desktop/spmo/Précipitation/2018")
getwd()
MergeBIL2NC<- function(variable,year){
pattern <- paste("PRISM_",variable,"_stable_4kmD1_",year,".*.bil$",sep="")
cat(paste("pattern, ", pattern,"!\n",sep="",collapse=""))
files <- list.files(path=".",pattern=pattern,recursive=TRUE,full.names=TRUE)
cat(paste("filelist, ", files,"!\n",sep="",collapse=""))
t <- stack(files)
filename <- paste(variable,"_",year,".nc",sep="")
cat(paste("filename, ", filename,"!\n",sep="",collapse=""))
t_nc <- writeRaster(t,filename=filename,bandorder="BIL",overwrite=TRUE,format="CDF",varname=variable)}
MergeBIL2NC("ppt",2018)
May you help me?
Poorvaja Ganesan
Jul 27, 2020, 11:03:26 AM7/27/20
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Hi
I am new to r programming and I dunno exactly where is my data set. I have pasted the code I tried and the error I got. Please help me out.
I am new to r programming and I dunno exactly where is my data set. I have pasted the code I tried and the error I got. Please help me out.
install.packages("Seurat")
library(Seurat)
library(ggplot2)
library(sctransform)
Read10X(data.dir = NULL, gene.column = 2, unique.features = TRUE, strip.suffix = FALSE)
pbmc_data <- Read10X(data.dir = "../data/pbmc3k/filtered_gene_bc_matrices/hg19/")
pbmc <- CreateSeuratObject(counts = pbmc_data)
# Lets examine a few genes in the first thirty cells
pbmc.data[c("CD3D", "TCL1A", "MS4A1"), 1:30]
On Friday, October 21, 2016 at 8:47:32 AM UTC-4, Ias S wrote:
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