case_study_comparisions.Rmd

[mle2718]

case_study_comparisons.Rmd does not knit for me. I get this error message:

Quitting from lines 221-319 [unnamed-chunk-7] (case_study_comparisons.Rmd)

Error:
! object 'scallop0322WindCloseSpatTable' not found
Backtrace:
 1. FishSET::zone_summary(...)
 2. FishSET::data_pull(spat, project)
Execution halted

This looks like it is missing a piece of code that loads in previously processed data from FishSET.

https://github.com/NEFSC/READ-SSB-CHAJI-Effort-Displacement---Scallop/blob/ab339b86577f4d0cc7866553a8cf9cf71c0e23cd/analysis_code/case_study_comparisons.Rmd#L221-L243

[mchaji]

I was able to get the case study comparison to knit all the way through. I noticed some of the aggregate values look suspicious so I'm going to look at that and compare the z-test and averages with the mock tables . I took a quick look at the averages and they look good so far.

[mle2718]

I was able to get the case study comparison to knit all the way through. I noticed some of the aggregate values look suspicious so I'm going to look at that and compare the z-test and averages with the mock tables . I took a quick look at the averages and they look good so far.

@mchaji: Can you share your steps on getting the case study comparison to knit? This is what I am doing:

1. Restart R.
2. Execute "knit_tiny_scallop_analysis_loop.R"
3. Restart R.
4. Knit "case_study_comparisions.Rmd"

[mchaji]

I just did this and it worked

1. Restarted R
2. knitted tiny report
3. knitted case study comparison

[mchaji]

I was able to get the case study comparison to knit all the way through. I noticed some of the aggregate values look suspicious so I'm going to look at that and compare the z-test and averages with the mock tables . I took a quick look at the averages and they look good so far.

@mchaji: Can you share your steps on getting the case study comparison to knit? This is what I am doing:

1. Restart R.
2. Execute "knit_tiny_scallop_analysis_loop.R"
3. Restart R.
4. Knit "case_study_comparisions.Rmd"

Are you getting an error?

[mchaji]

I just knitted the tiny report and it ran but I tried the loop and I'm getting the same summarise error

Quitting from lines 875-896 [unnamed-chunk-36] (scallop_analysis_0322.Rmd) Error in dplyr::summarise(): i In argument: dplyr::across(dplyr::all_of(value), .fns = match.fun(fun)). Caused by error in get(): ! object '%' of mode 'function' was not found Backtrace:

1. ... %>% ...
   14. base::match.fun(fun)
   15. base::get(as.character(FUN), mode = "function", envir = envir)

[mle2718]

I just knitted the tiny report and it ran but I tried the loop and I'm getting the same summarise error

Quitting from lines 875-896 [unnamed-chunk-36] (scallop_analysis_0322.Rmd) Error in dplyr::summarise(): i In argument: dplyr::across(dplyr::all_of(value), .fns = match.fun(fun)). Caused by error in get(): ! object '%' of mode 'function' was not found Backtrace:

1. ... %>% ...

2. base::match.fun(fun)

3. base::get(as.character(FUN), mode = "function", envir = envir)

This is the error message that I get when I run the "knit_scallop_analysis_loop.Rmd"

[mle2718]

I was able to get the case study comparison to knit all the way through. I noticed some of the aggregate values look suspicious so I'm going to look at that and compare the z-test and averages with the mock tables . I took a quick look at the averages and they look good so far.

@mchaji: Can you share your steps on getting the case study comparison to knit? This is what I am doing:

1. Restart R.
2. Execute "knit_tiny_scallop_analysis_loop.R"
3. Restart R.
4. Knit "case_study_comparisions.Rmd"

Are you getting an error?

Yes.

[mle2718]

I just did this and it worked

1. Restarted R

2. knitted tiny report

3. knitted case study comparison

This sequence of events produces the same error message as before (1st post).

Lets go over this tomorrow when we meet.

[mchaji]

I just did it again after clearing my work space but this time

1. Restarted R & Cleared Workspace
2. Ran chunks in tiny report until line 216 (last chunk is spatial data)
3. knitted case study comparison

[mle2718]

241 will tidy this up a bit