Error projecting into new time

[Penelope Murphy]

Hi there!

I'm a teaching assistant for a course where students are encouraged to use Wallace as part of a climate change vulnerability assessment for a species of their choosing. As an introduction to Wallace, students were instructed to follow through the Wallace version 1 vignette using Tremarctos ornatus occurrence data. To preface, ecological niche modeling is kind of out my wheelhouse and I've got a pretty decent working knowledge in R. I worked through the vignette myself on a PC with little issue (after installing a new version of Java), but many students have been encountering the same issue. When they go to project suitability under future climate projections, they encounter an error and are unable to proceed (error attached). Students are following the vignette instructions to a tee: modeling with GBIF T. ornatus occurrence data, using WorldClim climate data, modeling niches with Maxent, and attempting to project to 2070 with RCP 8.5 projections and CCSM4 for the global circulation model. 

I've run through the vignette side by side with a student and we were unable to identify the source of the error on her computer. So far, I've checked that people are using the same version of Wallace (1.1.3) and I created an R script where people preemptively install and load most of the packages that Wallace uses (attached). 

Any ideas what the issue may be? Thanks for the help in advance!

Penelope

[Penelope Murphy]

Another bit of detail: this has been an issue for both Mac and PC users. 

Thanks!

Penelope

[Wallace Ecological Modeling App]

Hi Penelope,

First of all, great to hear about Wallace being used in your teaching! Please give us some feedback via our external curriculum survey. 

I also want to give you a heads up, we are very excited to announce v2 will be up on CRAN very soon! 

This error has already been fixed in our new version, so if you wish to try out Wallace v2, check out the new vignette (which includes installation instructions until Wallace is on CRAN) - https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html.

I can see why you might not want the students to have to completely start over, so I think I fixed the problem and you can download the corrected version of Wallace v1.1.3 from my Github for now.

library(devtools)
devtools::install_github("https://github.com/bjohnso005/wallace/tree/v1.1.3")
library(wallace)
run_wallace()

Thanks for letting us know! Please reach out if you are still having trouble, if you have any issues installing, and stay tuned for an update when the new version is officially released!

-Bethany

[Penelope Murphy]

Hi Bethany,

Thanks so much for looking into this. And yes, I did fill out the poll. I believe this worked for some students, but for others they are still encountering the same issue when using WorldClim data. I am now also experiencing an issue on my computer when I previously was not-- does it matter what version of raster you're running?? I really can't figure it out. It's the same error code regardless of what version is being use (v1.1.3 from CRAN, the v1.1.3 you sent or v2)

Thanks,

Penelope

[nolan...@gmail.com]

Hi Bethany and Penelope,

Just want to chime in- I am also experiencing this issue, regardless of whether I use v2 or the 1.3.1 install Bethany provided.

-N

[Wallace Ecological Modeling App]

Hi Nolan & Penelope,

Please try updating your `raster` and `terra` packages. I think it might be a problem with an outdated package- I just updated and it worked. Let me know if it is still not working for you.

-Bethany

[nolan...@gmail.com]

Hi Bethany,

Still nothing after updating raster and terra, getting the same error. "Error in .cmip5: resolution should be one of: 2.5, 5, 10".

Running terra 1.6-47, raster 3.6-11, wallace 1.9.4-5. Please let me know if there's any other information I can provide to help resolve this issue.

[Wallace Ecological Modeling App]

What are you choosing for:
time period
GCM
RCP
and threshold?

[nolan...@gmail.com]

Small follow up: I did a completely fresh install and still received the same errors.

Time period: 2050

GCM: CCSM4

RCP:2.6

Threshold: None

[nolan...@gmail.com]

Sorry for double-posting, I just varied everything (2070, another GCM, RCP 8.6, threshold as minimum training presence) and again received the.cmip5 error.

[Penelope Murphy]

Hi Bethany,

Thank you so much for the suggestion. I am also still encountering the error. I'm running R 4.2.2, raster v3.6-11, and terra v1.6-47. 

All the best,

Penelope

On Tue, Dec 6, 2022 at 4:10 PM Penelope Murphy <penw...@gmail.com> wrote:

Hi Bethany,

Thank you so much for the suggestion. I am also still encountering the error. I'm running R 4.2.2, raster v3.6-11, and terra v1.6-47. 

All the best,

Penelope

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[Wallace Ecological Modeling App]

We are trying to test out a way to fix this issue.

Would you mind trying to run a few lines of code (outside of Wallace) and seeing if you get an error? I expect r1 not to work, but let me know if r2, r3, and r4 don't work for you as well. Thanks!

library(raster)
n <- 0.1666667*60
r1 <- raster::getData('CMIP5', var = "bio", res = n,
                rcp = 60, model = "CC",
                year = 50)
r2 <- raster::getData('CMIP5', var = "bio", res = round(n, 1),
                      rcp = 60, model = "CC",
                      year = 70)
r3 <- raster::getData('CMIP5', var = "bio", res = as.integer(n),
                      rcp = 45, model = "CC",
                      year = 50)
r4 <- raster::getData('CMIP5', var = "bio", res = round(n * 10)/10,
                      rcp = 85, model = "CC",
                      year = 50)

[nolan...@gmail.com]

Hello,

Thanks for your efforts in trying to fix this, I really appreciate it! r1 was the only line of code that gave me an error, everything else flashed me a warning about getdata being phased out but was still able to run.

Best,
Nolan

[Bethany Johnson]

Nolan & Penelope,

This should be fixed in 1.9.4-6 now and on my branch of v1.1.3. Try updating wallace and let me know if it's fixed.

[nolan...@gmail.com]

Hey Bethany,

Confirmed working for me! Thanks so much!!

Best,
Nolan