Error in [.default(DF, chr) : invalid subscript type 'list'

[Cheryl Lohr]

 

Hi folks

I'm trying to rerun some models through the package openCR. I know my code works just fine. At least it did last week, and I haven't changed it. But I'm suddenly getting this error with read.capthist

Error in [.default(DF, chr) : invalid subscript type 'list'

 

Previously, making sure I have the latest versions of R and Rstudio have fixed these kinds of issues. I currently have R4.0.2 and RStudio 1.3.1073. And I'm still getting the error. All packages have been updated.

Can anyone help me please?

 

Thanks,

Cheryl

 

 

Cheryl Lohr

Research Scientist, Animal Science Program

DBCA Biodiversity and Conservation Science

Location: 37 Wildlife Pl, Woodvale, WA 6026

Mail: Woodvale Wildlife Research Centre

Locked Bag 104 Bentley Delivery Centre

WA 6983

Ph: 94055150 (internal ext 5750)

Mob: 0407335004

 

 

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[Joanne Potts]

Hi Cheryl,

We had this trouble, as did Dev here: https://groups.google.com/g/secrgroup/c/6jc5ReLtoMQ/m/tD3DzAwLBwAJ

I have been meaning to follow this up.

For us, it was fixed by ensuring ‘verify=TRUE’ when making capture histories with multi session data. Maybe that will help you? Unsure if that will resolve the issue with Dev though.

Jo

On 14 Aug 2020, at 11:37 am, Cheryl Lohr <chery...@dbca.wa.gov.au> wrote:

 

Hi folks

I'm trying to rerun some models through the package openCR. I know my code works just fine. At least it did last week, and I haven't changed it. But I'm suddenly getting this error with read.capthist

Error in [.default(DF, chr) : invalid subscript type 'list'

 

Previously, making sure I have the latest versions of R and Rstudio have fixed these kinds of issues. I currently have R4.0.2 and RStudio 1.3.1073. And I'm still getting the error. All packages have been updated.

Can anyone help me please?

 

Thanks,

Cheryl

 

 

Cheryl Lohr

Research Scientist, Animal Science Program

DBCA Biodiversity and Conservation Science

Location: 37 Wildlife Pl, Woodvale, WA 6026

Mail: Woodvale Wildlife Research Centre

Locked Bag 104 Bentley Delivery Centre

WA 6983

Ph: 94055150 (internal ext 5750)

Mob: 0407335004

 

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[Cheryl Lohr]

Hi Jo,

Thanks for getting back to me. Unfortunately, that solution didn’t work. I presume I added in the verify=TRUE correctly (see below).

 

I don’t think my case supports the idea that the problem is with R4.0 as I didn’t download R4.0 until after this error appeared. I’ve also posted this problem to StackOverflow.

 

BL<-read.capthist(captfile="2010_2011_BL_SECR_capturedata.txt",

                  trapfile = list("2010MAR_BL_SECR_traplocs.txt",

                                  "2010APR_BL_SECR_traplocs.txt",

                                  "2010JUN_BL_SECR_traplocs.txt",

                                  "2010JUL_BL_SECR_traplocs.txt",

                                  "2010AUG_BL_SECR_traplocs.txt",

                                  "2010OCT_BL_SECR_traplocs.txt",

                                  "2010NOV_BL_SECR_traplocs.txt",

                                  "2011MAR_BL_SECR_traplocs.txt",

                                  "2011MAY_BL_SECR_traplocs.txt",

                                  "2011JUN_BL_SECR_traplocs.txt",

                                  "2011AUG_BL_SECR_traplocs.txt"),

                  detector = "multi",

                  fmt=c("trapID","XY"),

                  verify=TRUE)

 

Thanks,

Cheryl

 

Cheryl Lohr

Research Scientist, Animal Science Program

DBCA Biodiversity and Conservation Science

Location: 37 Wildlife Pl, Woodvale, WA 6026

Mail: Woodvale Wildlife Research Centre

Locked Bag 104 Bentley Delivery Centre

WA 6983

Ph: 94055150 (internal ext 5750)

Mob: 0407335004

 

 

From: Joanne Potts <joa...@theanalyticaledge.com>
Sent: Friday, 14 August 2020 9:41 AM
To: Cheryl Lohr <chery...@dbca.wa.gov.au>
Cc: secr <secr...@googlegroups.com>
Subject: Re: Error in [.default(DF, chr) : invalid subscript type 'list'

 

[External Email] This email was sent from outside the department – be cautious, particularly with links and attachments.

[Murray Efford]

Hi Cheryl

I assume you're using secr 4.3.0. I don't have a problem with this simple example, so I wonder if there's something odd in your data? I can't see that verify has anything to do with it, but I may be wrong.

If you want to shovel the data over to me offline I'll check it out.

Murray

[On the side - as a user you only need to provide fmt = 'trapID'.  fmt = c('trapID', 'XY') as it appears in the function definition is the odd way R remembers that there are just these two possibilities for this argument.]

> library(secr)
This is secr 4.3.0. For overview type ?secr
Warning message:
package ‘secr’ was built under R version 4.0.2 
> 
> # generate some text files
> write.capthist(ovenCH)
> 
> CH <- read.capthist(captfile = 'ovenCHcapt.txt', trapfile = 'ovenCHtrap.txt',
+     detector = 'multi')
No errors found :-)
> 
> CHtrapsbysession <- read.capthist(captfile = 'ovenCHcapt.txt', 
+     trapfile = list(
+         'ovenCHtrap.txt',
+         'ovenCHtrap.txt',
+         'ovenCHtrap.txt',
+         'ovenCHtrap.txt',
+         'ovenCHtrap.txt'),
+     fmt = "trapID",
+     detector = 'multi')
No errors found :-)
> 
> identical(summary(CH, terse = TRUE), summary(CHtrapsbysession, terse = TRUE))
[1] TRUE
> 
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_New Zealand.1252  LC_CTYPE=English_New Zealand.1252    LC_MONETARY=English_New Zealand.1252
[4] LC_NUMERIC=C                         LC_TIME=English_New Zealand.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] secr_4.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6        codetools_0.2-16    lattice_0.20-41     digest_0.6.25       MASS_7.3-51.6      
 [6] grid_4.0.0          nlme_3.1-147        magrittr_1.5        evaluate_0.14       RcppParallel_5.0.1 
[11] stringi_1.4.6       rlang_0.4.6         raster_3.1-5        sp_1.4-1            Matrix_1.2-18      
[16] rmarkdown_2.1       splines_4.0.0       tools_4.0.0         stringr_1.4.0       RcppNumerical_0.4-0
[21] xfun_0.15           yaml_2.2.1          abind_1.4-5         parallel_4.0.0      compiler_4.0.0     
[26] mgcv_1.8-31         htmltools_0.4.0     knitr_1.29 

[Matt Rees]

Yeah I'm also having this issue on secr 4.3.0, but not on 4.2.2. 

I'm combining multiple capthists into one with multiple sessions, and that works fine. 

However, the error message (same as Cheryl) pops up when I call secr.fit. 

Let me know if you want me to send more info. 

Matt. 

[Murray Efford]

I've looked at Cheryl's data and it's fine. The problem is in verify(). I think Jo meant to suggest verify = FALSE, which dodges the issue.

I introduced a bug when I adapted secr for R 4.0 (my function for coercing character variables to factors didn't allow for covariate dataframes with no columns). I think that explains the error

Until I get out the next release (possibly months away) I suggest dodging the routine verify step with verify = FALSE in read.capthist and secr.fit. I assume this also takes care of the issue in openCR. Let me know if this is not enough! My apologies.

Murray

[Matt Rees]

Ah brilliant - verify = FALSE does the trick for me. 

Thanks Murray & Jo. 

[Cheryl Lohr]

Hi Murray,

Thanks so much for your email. The verify=FALSE has worked.

Thanks,

Cheryl

 

Cheryl Lohr

Research Scientist, Animal Science Program

DBCA Biodiversity and Conservation Science

Location: 37 Wildlife Pl, Woodvale, WA 6026

Mail: Woodvale Wildlife Research Centre

Locked Bag 104 Bentley Delivery Centre

WA 6983

Ph: 94055150 (internal ext 5750)

Mob: 0407335004

 

 

From: secr...@googlegroups.com <secr...@googlegroups.com> On Behalf Of Murray Efford
Sent: Friday, 14 August 2020 1:47 PM
To: secr <secr...@googlegroups.com>
Subject: Re: Error in [.default(DF, chr) : invalid subscript type 'list'

 

[External Email] This email was sent from outside the department – be cautious, particularly with links and attachments.

I've looked at Cheryl's data and it's fine. The problem is in verify(). I think Jo meant to suggest verify = FALSE, which dodges the issue.

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