Error in MSI #81

Engine-Wu · 2022-07-13T12:21:07Z

I run the example code and finally received the error information like that “Error in log(index): non-numeric argument to mathematical function”. I don't know how to fix this problem. @AugustT

AugustT · 2022-07-13T13:50:52Z

I'm not able to reproduce this issue. The below code works for me. Are you able to share a reproducible example?

devtools::install_github('biologicalrecordscentre/brcindicators')

library(BRCindicators)

set.seed(123)

# Create some example data in the format required
nyr = 20
species = rep(letters, each = nyr)
year = rev(rep(1:nyr, length(letters)))

# Create an index value that increases with time
index = rep(seq(50, 100, length.out = nyr), length(letters))
# Add randomness to species
index = index * runif(n = length(index), 0.7, 1.3)
# Add correlated randomness acrosss species, to years
index = index * rep(runif(0.8, 1.2, n = nyr), length(letters))

se = runif(n = nyr * length(letters), min = 10, max = 20)

data <- data.frame(species, year, index, se)

# Our species are decreasing
plot(data$year, data$index)

# Species index values need to be 100 in the base year. Here I use
# the first year as my base year and rescale to 100. The standard error
# in the base year should be 0.
min_year <- min(data$year)

for(sp in unique(data$species)){
  
  subset_data <- data[data$species == sp, ]
  multi_factor <- 100 / subset_data$index[subset_data$year == min_year]
  data$index[data$species == sp] <- data$index[data$species == sp] * multi_factor
  data$se[data$species == sp] <- data$se[data$species == sp] * multi_factor
  data$se[data$species == sp][1] <- 0
  
}

# Run the MSI function
msi_out <- msi(data, plot = FALSE)

# Plot the resulting indicator
plot(msi_out)

AugustT · 2022-07-13T13:51:51Z

Your error suggests that somewhere R is trying to log something like a NULL or logical

Engine-Wu · 2022-07-13T14:08:20Z

I copy your code and run , but receive the same error information.

Engine-Wu · 2022-07-13T14:11:52Z

I'm not able to reproduce this issue. The below code works for me. Are you able to share a reproducible example?

devtools::install_github('biologicalrecordscentre/brcindicators')

library(BRCindicators)

set.seed(123)

# Create some example data in the format required
nyr = 20
species = rep(letters, each = nyr)
year = rev(rep(1:nyr, length(letters)))

# Create an index value that increases with time
index = rep(seq(50, 100, length.out = nyr), length(letters))
# Add randomness to species
index = index * runif(n = length(index), 0.7, 1.3)
# Add correlated randomness acrosss species, to years
index = index * rep(runif(0.8, 1.2, n = nyr), length(letters))

se = runif(n = nyr * length(letters), min = 10, max = 20)

data <- data.frame(species, year, index, se)

# Our species are decreasing
plot(data$year, data$index)

# Species index values need to be 100 in the base year. Here I use
# the first year as my base year and rescale to 100. The standard error
# in the base year should be 0.
min_year <- min(data$year)

for(sp in unique(data$species)){
  
  subset_data <- data[data$species == sp, ]
  multi_factor <- 100 / subset_data$index[subset_data$year == min_year]
  data$index[data$species == sp] <- data$index[data$species == sp] * multi_factor
  data$se[data$species == sp] <- data$se[data$species == sp] * multi_factor
  data$se[data$species == sp][1] <- 0
  
}

# Run the MSI function
msi_out <- msi(data, plot = FALSE)

# Plot the resulting indicator
plot(msi_out)

I just run the example code for MSI in the help in the help documentation. Here are the example code.
`# Create some example data in the format required
nyr = 20
species = rep(letters, each = nyr)
year = rev(rep(1:nyr, length(letters)))

Create an index value that increases with time

index = rep(seq(50, 100, length.out = nyr), length(letters))

Add randomness to species

index = index * runif(n = length(index), 0.7, 1.3)

Add correlated randomness acrosss species, to years

index = index * rep(runif(0.8, 1.2, n = nyr), length(letters))

se = runif(n = nyr * length(letters), min = 10, max = 20)

data <- data.frame(species, year, index, se)

Our species are decreasing

plot(data$year, data$index)

Species index values need to be 100 in the base year. Here I use

the first year as my base year and rescale to 100. The standard error

in the base year should be 0.

min_year <- min(data$year)

for(sp in unique(data$species)){

subset_data <- data[data$species == sp, ]
multi_factor <- 100 / subset_data$index[subset_data$year == min_year]
data$index[data$species == sp] <- data$index[data$species == sp] * multi_factor
data$se[data$species == sp] <- data$se[data$species == sp] * multi_factor
data$se[data$species == sp][1] <- 0

}

Run the MSI function

msi_out <- msi(data, plot = FALSE)

Plot the resulting indicator

plot(msi_out)`

Engine-Wu · 2022-07-13T18:35:24Z

I test the package. The result is below. "Error in log(index): non-numeric argument to mathematical function" is in the MSI.

`==> devtools::test()

ℹ Loading BRCindicators
ℹ Testing BRCindicators
✔ | F W S OK | Context
✖ | 4 0 | Test bma [0.3s]
────────────────────────────────────────────────────────────────────────────────────────────────
Error (testbma.R:16:3): simple run
Error: Package 'jagsUI' is needed for the 'bma' function to work. Please insatll this from CRAN. You will also be required to install JAGS, which you can download from https://sourceforge.net/projects/mcmc-jags/files/JAGS/
Backtrace:

BRCindicators::bma(...)
at testbma.R:16:2

Error (testbma.R:84:3): degraded data
Error: Package 'jagsUI' is needed for the 'bma' function to work. Please insatll this from CRAN. You will also be required to install JAGS, which you can download from https://sourceforge.net/projects/mcmc-jags/files/JAGS/
Backtrace:

BRCindicators::bma(...)
at testbma.R:84:2

Error (testbma.R:112:3): model options
Error: Package 'jagsUI' is needed for the 'bma' function to work. Please insatll this from CRAN. You will also be required to install JAGS, which you can download from https://sourceforge.net/projects/mcmc-jags/files/JAGS/
Backtrace:

BRCindicators::bma(...)
at testbma.R:112:2

Error (testbma.R:175:3): different parameters
Error: Package 'jagsUI' is needed for the 'bma' function to work. Please insatll this from CRAN. You will also be required to install JAGS, which you can download from https://sourceforge.net/projects/mcmc-jags/files/JAGS/
Backtrace:

BRCindicators::bma(...)
at testbma.R:175:2
────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 2 | Test lambda_indicator [7.6s]
✖ | 1 0 | Test msi
────────────────────────────────────────────────────────────────────────────────────────────────
Error (testmsi.R:39:3): runs without error
Error in log(index): non-numeric argument to mathematical function
Backtrace:
BRCindicators::msi(data, plot = FALSE)
at testmsi.R:39:2
BRCindicators::msi_tool(...)
at BRCindicators-master/R/msi.R:102:2
base::as.vector(log(index))
at BRCindicators-master/R/msi_tool.R:141:2
────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 1 | Test simulate_indicator
✔ | 6 | Test trend_summary_helper_functions

══ Results ═════════════════════════════════════════════════════════════════════════════════════
Duration: 8.0 s

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 9 ]`

drnickisaac · 2022-10-14T12:14:08Z

I too have explored this and I do not get the error. Perhaps it is a versioning issue. Would you please send us your sessionInfo()

larspett · 2022-10-14T14:02:09Z

Here it is: R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Swedish_Sweden.utf8 LC_CTYPE=Swedish_Sweden.utf8 LC_MONETARY=Swedish_Sweden.utf8
[4] LC_NUMERIC=C LC_TIME=Swedish_Sweden.utf8

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

other attached packages:
[1] BRCindicators_1.3.7

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 plyr_1.8.7 pillar_1.8.1 compiler_4.2.1 later_1.3.0
[6] RColorBrewer_1.1-3 tools_4.2.1 boot_1.3-28 lifecycle_1.0.3 tibble_3.1.8
[11] gtable_0.3.1 nlme_3.1-157 lattice_0.20-45 mgcv_1.8-40 pkgconfig_2.0.3
[16] rlang_1.0.6 Matrix_1.5-1 DBI_1.1.3 cli_3.4.1 rstudioapi_0.14
[21] RPostgreSQL_0.7-4 coda_0.19-4 stringr_1.4.1 dplyr_1.0.10 generics_0.1.3
[26] vctrs_0.4.2 grid_4.2.1 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1
[31] fansi_1.0.3 pool_0.1.6 carData_3.0-5 ggplot2_3.3.6 reshape2_1.4.4
[36] car_3.1-0 magrittr_2.0.3 scales_1.2.1 splines_4.2.1 abind_1.4-5
[41] assertthat_0.2.1 colorspace_2.0-3 utf8_1.2.2 stringi_1.7.8 munsell_0.5.0

larspett · 2022-10-14T14:03:35Z

I ran the example code for msi and keep getting

Run the MSI function

msi_out <- msi(data, plot = FALSE)
Error in log(index) : non-numeric argument to mathematical function

larspett · 2022-10-14T14:48:57Z

And here is the code snippet (from the help) that produced that error on my system
msi.txt

larspett · 2022-10-14T14:49:59Z

JAGS is 4.3.0

larspett · 2022-10-16T20:06:55Z

Could it be that either a required library was not brought over to the new directory during a main R upgrade or that the JAGS (or something else that is required) has an incorrect path in R after an upgrade? BRCindicators worked quite recently on this win10 computer but since then R had a major upgrade and I ported the libraries to the new directory.

larspett · 2022-10-17T09:35:57Z

Ping @AugustT @drnickisaac The demo code runs just fine on R i386 4.1.3 but not on R 4.2.1 on my machine. Can't test i386 4.1.3 on RStudio since RStudio crashes then (not happy with i386 when 4.2.1 x64 is installed)

AugustT · 2022-10-17T12:30:51Z

@larspett Thanks for pining down the cause. I'm travelling for the next 2 weeks so it is unlikely I will have the time to dig into it

@drnickisaac The error is from here:

BRCindicators/R/msi_tool.R

Line 141 in 31b7dc6

LNindex <- as.vector(log(index))

This function should be debugged and the values in index need to be checked throughout the function. I suspect a change to something in base R somewhere is changing some behaviour that results in a logical NA or NULL appearing in the index vector. Quite where the behaviour change has come from I can't say, but it could be as fa back as reading in the csv right at the beginning.

Looking at the R change logs has not given me any greater insight, but it does look like they made a lot of changes to the Windows version on this release. I think start with tracing back index through the function.

Engine-Wu · 2022-10-18T01:44:53Z

@AugustT @drnickisaac @drnickisaac I run the demo code in MAC and Linux system. I get the same error information.

MichelleJudge · 2023-09-12T11:49:17Z

Hi, I am wondering if there was a workaround for this issue? I tried today using R4.2.2 and I receiving the same error as mentioned above:

Error: "Error in log(index): non-numeric argument to mathematical function" is in the MSI.
Error occurs after running the line: LNindex <- as.vector(log(index))

Any advice would be appreciated.
Thanks!

larspett · 2023-12-11T14:59:47Z

Hi, did you get this working @AugustT @drnickisaac ? It works on my OSX machines but still fails on the Win10 machine JAGS. Tried installing from the repo now and running the example code but still get the same error

AugustT · 2023-12-11T15:25:43Z

@DylanCarbone can you have a look into this and we can discuss at out next meeting?

DylanCarbone · 2023-12-13T09:50:37Z

Hi Tom and Lars,

The error occurs because of the step that Tom flagged:

LNindex <- as.vector(log(index))

It attempts to log transform index, which is already a vector, but fails because the vector contains element names. Using the base R function, unlist() with parameter use.names set to FALSE fixes this log transformation step.

The function then incorrectly indexes the log transformed vector, treating it as if it was a matrix.

Therefore, to fix this error, change the following lines:

BRCindicators/R/msi_tool.R

Lines 133 to 151 in 31b7dc6

    
           index <- as.vector(INP5["index"]) 
        
           se <- as.vector(INP5["se"]) 
        
           nobs <- NROW(INP5) 
        
           uspecies <- sort(unique(INP5$species)) 
        
           nspecies <- length(uspecies) 
        
           year <- rep(uyear, nspecies) 
        
           # Transform indices and standard deviations to log scale (Delta method) 
        
           LNindex <- as.vector(log(index)) 
        
           LNse <- as.vector(se/index) 
        
           # Monte Carlo simulations of species indices 
        
           MC <- matrix(NA, nobs, nsim) 
        
           for (s in 1:nsim) {  
        
             for (o in 1:nobs) { 
        
               MC[o,s] <- rnorm(1, LNindex[o,1], LNse[o,1]) 
        
             }  
        
           } 
        
           MC[MC < log(TRUNC)] <- log(TRUNC)

To this:

 # reset parameters
  index <- unlist(INP5["index"], use.names = F)
  se <- unlist(INP5["se"], use.names = F)
  nobs <- NROW(INP5)
  uspecies <- sort(unique(INP5$species))
  nspecies <- length(uspecies)
  year <- rep(uyear, nspecies)
  
  # Transform indices and standard deviations to log scale (Delta method)
  LNindex <- log(index)
  LNse <- se/index
  
  # Monte Carlo simulations of species indices
  MC <- matrix(NA, nobs, nsim)
  for (s in 1:nsim) { 
    for (o in 1:nobs) {
      
      MC[o,s] <- rnorm(1, LNindex[o], LNse[o])
    } 
  }
  MC[MC < log(TRUNC)] <- log(TRUNC)

I'm unsure why some users are able to run the original function whilst others are not. There must have been some changes to the as.vector() function that affects the indexing of named vectors, but I cannot find articles on this.

larspett · 2023-12-13T10:06:39Z

Ok, will you update the repo with this? 13 dec. 2023 kl. 10:50 skrev DylanCarbone ***@***.***>: Hi Tom and Lars, The error occurs because of the step that Tom flagged: LNindex <- as.vector(log(index)) It attempts to log transform index, which is already a vector, but fails because the vector contains element names. Using the base R function, unlist() with parameter use.names set to FALSE fixes this log transformation step. The function then incorrectly indexes the log transformed vector, treating it as if it was a matrix. Therefore, to fix this error, change the following lines: https://github.com/BiologicalRecordsCentre/BRCindicators/blob/31b7dc69a1fe88719e0c26f4a94a6de3f0dbfcbe/R/msi_tool.R#L133-L151 To this: # reset parameters index <- unlist(INP5["index"], use.names = F) se <- unlist(INP5["se"], use.names = F) nobs <- NROW(INP5) uspecies <- sort(unique(INP5$species)) nspecies <- length(uspecies) year <- rep(uyear, nspecies) # Transform indices and standard deviations to log scale (Delta method) LNindex <- log(index) LNse <- se/index # Monte Carlo simulations of species indices MC <- matrix(NA, nobs, nsim) for (s in 1:nsim) { for (o in 1:nobs) { MC[o,s] <- rnorm(1, LNindex[o], LNse[o]) } } MC[MC < log(TRUNC)] <- log(TRUNC) I'm unsure why some users are able to run the original function whilst others are not. There must have been some changes to the as.vector() function that affects the indexing of named vectors, but I cannot find articles on this. — Reply to this email directly, view it on GitHub<#81 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AEVQXZHBFYZDZ6Y3UVATKVLYJF27RAVCNFSM53OQ3XZ2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBVGM2TSMRQGE3A>. You are receiving this because you were mentioned.Message ID: ***@***.***>

AugustT · 2023-12-13T10:36:21Z

@larspett of course. @DylanCarbone is learning how to manage R packages and he and I will run through this at our next meeting

…s and indexing BiologicalRecordsCentre#81

DylanCarbone · 2023-12-14T17:42:58Z

Hi @larspett, we have just updated the repo. When you have the time, please reinstall the package and let us know if you encounter any further issues. Thanks

larspett · 2023-12-14T17:50:10Z

Hi @DylanCarbone I did right away and it works just fine! Many thanks!

DylanCarbone added a commit to DylanCarbone/BRCindicators that referenced this issue Dec 14, 2023

Fixed error caused by attempting to log transforming vector with name…

927254e

…s and indexing BiologicalRecordsCentre#81

DylanCarbone mentioned this issue Dec 14, 2023

Fixed error caused by attempting to log transforming vector with name… #84

Merged

DylanCarbone closed this as completed Apr 26, 2024

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Error in MSI #81

Error in MSI #81

Engine-Wu commented Jul 13, 2022

AugustT commented Jul 13, 2022

AugustT commented Jul 13, 2022

Engine-Wu commented Jul 13, 2022

Engine-Wu commented Jul 13, 2022

Engine-Wu commented Jul 13, 2022

drnickisaac commented Oct 14, 2022

larspett commented Oct 14, 2022

larspett commented Oct 14, 2022

Run the MSI function

larspett commented Oct 14, 2022

larspett commented Oct 14, 2022

larspett commented Oct 16, 2022

larspett commented Oct 17, 2022

AugustT commented Oct 17, 2022

Engine-Wu commented Oct 18, 2022

MichelleJudge commented Sep 12, 2023

larspett commented Dec 11, 2023

AugustT commented Dec 11, 2023

DylanCarbone commented Dec 13, 2023

larspett commented Dec 13, 2023 via email

AugustT commented Dec 13, 2023

DylanCarbone commented Dec 14, 2023

larspett commented Dec 14, 2023

Error in MSI #81

Error in MSI #81

Comments

Engine-Wu commented Jul 13, 2022

AugustT commented Jul 13, 2022

AugustT commented Jul 13, 2022

Engine-Wu commented Jul 13, 2022

Engine-Wu commented Jul 13, 2022

Create an index value that increases with time

Add randomness to species

Add correlated randomness acrosss species, to years

Our species are decreasing

Species index values need to be 100 in the base year. Here I use

the first year as my base year and rescale to 100. The standard error

in the base year should be 0.

Run the MSI function

Plot the resulting indicator

Engine-Wu commented Jul 13, 2022

drnickisaac commented Oct 14, 2022

larspett commented Oct 14, 2022

larspett commented Oct 14, 2022

Run the MSI function

larspett commented Oct 14, 2022

larspett commented Oct 14, 2022

larspett commented Oct 16, 2022

larspett commented Oct 17, 2022

AugustT commented Oct 17, 2022

Engine-Wu commented Oct 18, 2022

MichelleJudge commented Sep 12, 2023

larspett commented Dec 11, 2023

AugustT commented Dec 11, 2023

DylanCarbone commented Dec 13, 2023

larspett commented Dec 13, 2023 via email

AugustT commented Dec 13, 2023

DylanCarbone commented Dec 14, 2023

larspett commented Dec 14, 2023