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canaper: Categorical Analysis of Neo- And Paleo-Endemism in R #475

Closed joelnitta closed 2 years ago

joelnitta commented 2 years ago

Date accepted: 2022-09-14 Submitting Author: !--author1-->@joelnitta<!--end-author1-- Other Package Authors: (delete if none) Shawn Laffan (@shawnlaffan) Repository: https://github.com/joelnitta/canaper Version submitted: 0.0.1 Submission type: Stats Badge grade: silver Editor: @tdhock Reviewers: @KlausVigo, @luismurao

Due date for @KlausVigo: 2021-11-24 Due date for @luismurao: 2021-12-21

Archive: TBD Version accepted: TBD

Package: canaper
Title: Categorical Analysis of Neo- And Paleo-Endemism
Version: 0.0.1
Authors@R: 
    c(
    person(given = "Joel H.",
           family = "Nitta",
           role = c("aut", "cre"),
           email = "joelnitta@gmail.com",
           comment = c(ORCID = "0000-0003-4719-7472")),
    person(given = "Shawn W.",
           family = "Laffan",
           role = c("ctb", "dtc")),
    person(given = "Brent D.",
           family = "Mishler",
           role = c("ctb", "dtc")),
    person(given = "Wataru",
           family = "Iwasaki",
           role = c("ctb"),
           comment = c(ORCID = "0000-0002-9169-9245"))
           )
Description: Provides functions to conduct categorical analysis of neo- and paleo-endemism (CANAPE).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c ("collate", "namespace", "rd", "roxyglobals::global_roclet", "srr::srr_stats_roclet"))
RoxygenNote: 7.1.2
URL: https://github.com/joelnitta/canaper
BugReports: https://github.com/joelnitta/canaper/issues
Imports: 
    ape,
    assertr,
    assertthat,
    dplyr,
    future.apply,
    phyloregion,
    progressr,
    purrr,
    stats,
    tibble,
    vegan
Suggests: 
    rmarkdown,
    knitr,
    future,
    tictoc,
    patchwork,
    tidyverse,
    testthat (>= 3.0.0),
    roxyglobals (>= 0.2.1),
    stringr,
    magrittr,
    covr,
    picante
Config/testthat/edition: 3
Depends: 
    R (>= 3.5.0)
VignetteBuilder: knitr
Remotes: 
    anthonynorth/roxyglobals

Pre-submission Inquiry

General Information

Note also there is a package website available: https://joelnitta.github.io/canaper/

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Confirm each of the following by checking the box.

This package:

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ropensci-review-bot commented 2 years ago

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

ropensci-review-bot commented 2 years ago

:rocket:

The following problem was found in your submission template:

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ropensci-review-bot commented 2 years ago

Checks for canaper (v0.0.1)

git hash: 43a9f0a2

Package License: MIT + file LICENSE

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package

Click here to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has: - code in R (100% in 11 files) and - 1 authors - 3 vignettes - 8 internal data files - 11 imported packages - 4 exported functions (median 41 lines of code) - 30 non-exported functions in R (median 7 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 11| 59.3| | |files_vignettes | 2| 83.0| | |files_tests | 8| 85.7| | |loc_R | 650| 52.9| | |loc_vignettes | 162| 64.9| | |loc_tests | 939| 83.5| | |num_vignettes | 3| 93.1| | |data_size_total | 66301| 81.2| | |data_size_median | 509| 59.9| | |n_fns_r | 34| 35.6| | |n_fns_r_exported | 4| 15.6| | |n_fns_r_not_exported | 30| 42.6| | |n_fns_per_file_r | 3| 42.7| | |num_params_per_fn | 4| 67.6| | |loc_per_fn_r | 10| 40.0| | |loc_per_fn_r_exp | 41| 75.3| | |loc_per_fn_r_not_exp | 7| 29.9| | |rel_whitespace_R | 13| 43.9| | |rel_whitespace_vignettes | 0| 0.0|TRUE | |rel_whitespace_tests | 7| 84.7| | |doclines_per_fn_exp | 55| 68.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 9| 22.0| | ---

2a. Network visualisation

Interactive network visualisation of calls between objects in package can be viewed by clicking here

3. goodpractice and other checks

Details of goodpractice and other checks (click to open)

#### 3a. Continuous Integration Badges [![github](https://github.com/joelnitta/canaper/workflows/R-CMD-check/badge.svg)](https://github.com/joelnitta/canaper/actions) **GitHub Workflow Results** |name |conclusion |sha |date | |:---------------|:----------|:------|:----------| |pkgdown |success |43a9f0 |2021-10-26 | |R-CMD-check |success |43a9f0 |2021-10-26 | |Render codemeta |failure |43a9f0 |2021-10-26 | |test-coverage |success |43a9f0 |2021-10-26 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 100 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- cpr_rand_test | 29 calc_biodiv_random | 16 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 353 potential issues: message | number of times --- | --- Lines should not be more than 80 characters. | 353

Package Versions

|package |version | |:--------|:---------| |pkgstats |0.0.2.16 | |pkgcheck |0.0.2.86 | |srr |0.0.1.120 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

tdhock commented 2 years ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 2 years ago

I'm sorry @tdhock, I'm afraid I can't do that. That's something only editors are allowed to do.

noamross commented 2 years ago

@ropensci-review-bot assign @tdhock as editor

ropensci-review-bot commented 2 years ago

Assigned! @tdhock is now the editor

joelnitta commented 2 years ago

I forgot to mention, I plan to submit this as a paper to Methods in Ecology and Evolution after ROpenSci review (have also added this to the original description)

tdhock commented 2 years ago

@ropensci-review-bot assign @KlausVigo as reviewer

mpadge commented 2 years ago

@tdhock Only just realised the command there has the wrong syntax - should be add <@name> to reviewers, like this example. Could you please try again? Nevertheless good that you got this one wrong, because it made us realise we need the bot to tell you it didn't understand. Thanks!

tdhock commented 2 years ago

@ropensci-review-bot add @KlausVigo to reviewers by the way it would be more user friendly to have the add editor and add reviewer commands be consistent / analogous, I guess that is what you are doing in https://github.com/ropensci-org/buffy/pull/42 ?

mpadge commented 2 years ago

sorry @tdhock, another bot glitch there - bot commands have to be kept as just that, with no additional comments. And yes, the point of the above-linked issue is to aid consistency between analogous commands, so that will hopefully improve soon. In the meantime, could you please try again, again, with just the command? With due apologies and gratitude! :bowing_man:

tdhock commented 2 years ago

@ropensci-review-bot add @KlausVigo to reviewers

ropensci-review-bot commented 2 years ago

Can't assign reviewer because there is no editor assigned for this submission yet

maelle commented 2 years ago

@tdhock sorry for all the hiccups! The initial issue body had been edited after your username was added so your username was no longer in the string <!--editor--> @tdhock<!--end-editor--> I edited it again so you can try again. Thanks for your patience!

tdhock commented 2 years ago

@ropensci-review-bot add @KlausVigo to reviewers

ropensci-review-bot commented 2 years ago

@KlausVigo added to the reviewers list. Review due date is 2021-11-24. Thanks @KlausVigo for accepting to review! Please refer to our reviewer guide.

ropensci-review-bot commented 2 years ago

@KlausVigo: If you haven't done so, please fill this form for us to update our reviewers records.

tdhock commented 2 years ago

@ropensci-review-bot add @luismurao to reviewers

ropensci-review-bot commented 2 years ago

@luismurao added to the reviewers list. Review due date is 2021-12-21. Thanks @luismurao for accepting to review! Please refer to our reviewer guide.

ropensci-review-bot commented 2 years ago

@luismurao: If you haven't done so, please fill this form for us to update our reviewers records.

luismurao commented 2 years ago

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Functionality

Estimated hours spent reviewing:

Review Comments

Parallelization calls as in the current version of the package

library(canaper) # This package :)
library(future) # For parallel computing
library(tictoc) # For timing things
library(patchwork) # For composing mult-part plots
library(tidyverse) # For data-wrangling and plottin

data(acacia)

plan(multisession,workers=ncores)
set.seed(071421)
acacia_rand_res <- cpr_rand_test(
  acacia$comm, acacia$phy, 
  null_model = "curveball",
  n_reps = 100, n_iterations = 100000,
  tbl_out = TRUE)
plan(sequential)

I think this could be more appropriate and easy to use

acacia_rand_res <- cpr_rand_test(
  acacia$comm, acacia$phy, 
  null_model = "curveball",
  n_reps = 100, n_iterations = 100000,
  tbl_out = TRUE
  parallel = TRUE, # Logical var to run processes in parallel
  nworkes = 3, # Number of threads
  random_seed=071421) # Random seed

README

Installation

There is a potential conflict in package dependencies as canaper depends on R (>= 3.5.0), but it imports phangorn version 2.8.1, which depends on R (>= 4.1.0). Please change parameter Depends: R (>= 3.5.0) to Depends: R (>= 4.1.0) in the description file or provide a way to install an earlier version of phangorn (version 2.5.5 should work).

Automated test

────────────────────────────────────────────────────────────────────
Warning (test-utils.R:143:3): Functions copied from phyloregion work
rgeos: versions of GEOS runtime 3.10.1-CAPI-1.16.0
and GEOS at installation 3.9.1-CAPI-1.14.2differ
Backtrace:
  1. testthat::expect_equal(dense2sparse(biod_example$comm), phyloregion::dense2sparse(biod_example$comm)) test-utils.R:143:2
  4. base::loadNamespace(x)
  7. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
  8. base:::runHook(".onLoad", env, package.lib, package)
 13. rgeos:::fun(libname, pkgname)
────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════
Duration: 71.8 s

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 255 ]
signficance       canape.Rmd:132

Performance

When benchmarking, I found a strange behavior. After using more than four threads, the program takes more time to finish a randomization test. Here is the code I used (could you please check it? I might be missing something)

library(purrr)
library(tidyverse)
library(tictoc)
library(future)
library(ggplot2)
rm(list = ls())
data(acacia)
acom <- acacia$comm
acom[acom>0] <- 1
n_reps_vec <- c(100,500,1000,1500,2000)
nwokers <- 1:7
acom <- acacia$comm
acom[acom>0] <- 1

rand_times <- seq_along(n_reps_vec) %>% purrr::map_dfr(function(nrep){
  rand_t <- nwokers %>% purrr::map_dfr(function(nwork){
      if(nwork>1){
        plan(multisession,workers=nwork)
      }
      set.seed(071421)
      tictoc::tic() 
      # Run randomization test
      acacia_rand_res <- canaper::cpr_rand_test(
        acom, acacia$phy,
        null_model = "curveball",
        n_reps = n_reps_vec[nrep],
        n_iterations = 100000,
        tbl_out = TRUE)
      aa <- tictoc::toc()
      r1 <-data.frame(n_reps = n_reps_vec[nrep] ,
                      nworkers=nwork,
                      time_secs = aa$toc - aa$tic)
      plan(sequential)
      return(r1)
    })
  return(rand_t)
})

ggplot(rand_times, aes(x = ncores,y=time_secs,color=as.factor(n_reps))) +
  geom_line() + theme_classic()

Questions and comments

@joelnitta please do not hesitate to contact me if you have any questions. Thanks for developing canaper.

joelnitta commented 2 years ago

@luismurao thanks so much for your review! I will try to address your comments soon.

joelnitta commented 2 years ago

@KlausVigo it would be great to have your comments as well so I can make changes incorporating both sets of reviews.

joelnitta commented 2 years ago

@KlausVigo, do you still intend to review this package?

If not, @tdhock can you please assign a new reviewer, as it is now multiple months past the due date.

Thanks!

KlausVigo commented 2 years ago

Hi @joelnitta! I will finish it today.

KlausVigo commented 2 years ago

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Functionality

Estimated hours spent reviewing: 12

Review Comments

Specific comments

Profiling

In my opinion the main bottleneck for this kind of analysis is memory consumption and only minor part computing time. Dense community matrices are now frequently getting too large to be hold in memory (RAM). Luckily community matrices are usually extremely sparse and this allows efficient coding. For example the acacia data set, which comes with canaper, has less than 2% non-zero cells and a sparse representation takes only 1/20 of memory of the dense representation. 

> library(canaper)
> library(Matrix)
> data("acacia")
> dim(acacia$comm)
[1] 3037  506
> comm <- as.matrix(acacia$comm)
> sum(comm > 0) / prod(dim(comm))
[1] 0.01898522
> object.size(comm)
12597112 bytes
> object.size(Matrix(comm, sparse=TRUE))
656576 bytes

The functions to compute the biodiversity measures make use of the sparsity, but the functions to sample the matrices not. We developed the phyloregion using sparse matrices which resulted in a far lower memory consumption and as a benefit it turned out faster in many cases (https://phyloregion.com/articles/Benchmark.html). With larger data sets we get into a trade-off. We want to use more cores, but this means several copies of the community matrices in memory. Providing a swapping algorithm which can handle sparse matrices would be a huge improvement for the community.

I used the following code for profiling:

library(canaper)
data(acacia)
Rprof(tmp <- tempfile(), memory.profiling = TRUE)

acacia_rand_res <- cpr_rand_test(
    acacia$comm, acacia$phy,
    null_model = "curveball",
    n_reps = 100,
    n_iterations = 100000)

Rprof()
summaryRprof(tmp, memory="both")
unlink(tmp)

I just highlight a few lines of the output I find interesting: 

...
"calc_biodiv_random"              111.54     92.35   29477.9      0.02     0.02
"cpr_rand_comm"                    99.56     82.43   22420.0      1.30     1.08
"simulate.nullmodel"               83.18     68.87   11655.6      1.24     1.03
...
"phylo_community"                   5.72      4.74    2994.7      1.60     1.32
"phylo_endemism"                    5.14      4.26    2876.1      0.02     0.02
"assertthat::assert_that"           4.66      3.86    1867.0      0.10     0.08
...
"PD"                                2.56      2.12    1656.1      0.00     0.00 
...

For submitting to CRAN:

There are some instances where more than 2 cores are used, e.g. the vignette canape.Rmd, line 83:

plan(multisession, workers = 3)

This could fail on CRAN, when submitting. There the use of maximal 2 cores is allowed and I speak from experience, I got Ripleyed for this once! Again the CRAN Repository Policy is a useful resource and gives some background information: "Checking the package should take as little CPU time as possible, as the CRAN check farm is a very limited resource and there are thousands of packages. Long-running tests and vignette code can be made optional for checking, but do ensure that the checks that are left do exercise all the features of the package. If running a package uses multiple threads/cores it must never use more than two simultaneously: the check farm is a shared resource and will typically be running many checks simultaneously. Examples should run for no more than a few seconds each: they are intended to exemplify to the would-be user how to use the functions in the package."

joelnitta commented 2 years ago

@KlausVigo thank you very much for the extensive and helpful review!

I just wanted to address one thing first: the reason I copied functions from phyloregion instead of importing them is because of a dependency of phyloregion (betapart), which has a package in Suggests (snow) that was resetting the random number generator and thus cpr_rand_test() was failing to return identical results when using parallel computing, even when set.seed() was used. There is an issue describing the problem in canaper, and a related discussion in the future package.

In the end, I opted to copy the phyloregion functions under the AGPL-3 license, since that fixed the issue and resulted in fewer dependencies. As @HenrikBengtsson mentioned though, it seems another way to fix this (and import phyloregion normally) would be to use future.packages = "snow" with future.apply::future_lapply(). Would you prefer that?

(By the way, it is possible that this behavior of snow may cause reproducibility issues with phyloregion as well. I suggest you look into it if you haven't already).

tdhock commented 2 years ago

hi @KlausVigo thanks for your detailed review. can you please tell us approximately how many hours you spent on reviewing? (you left that field blank in your review comment)

tdhock commented 2 years ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/475#issuecomment-1002754119 time 9

ropensci-review-bot commented 2 years ago

Logged review for luismurao (hours: 9)

KlausVigo commented 2 years ago

Hi @joelnitta,

I just made a commit to phyloregion cb819fb. This might solves the problem, at least sessionInfo() suggests that snow is not loaded via a namespace any more.

Regards, Klaus

@KlausVigo thank you very much for the extensive and helpful review!

I just wanted to address one thing first: the reason I copied functions from phyloregion instead of importing them is because of a dependency of phyloregion (betapart), which has a package in Suggests (snow) that was resetting the random number generator and thus cpr_rand_test() was failing to return identical results when using parallel computing, even when set.seed() was used. There is an issue describing the problem in canaper, and a related discussion in the future package.

In the end, I opted to copy the phyloregion functions under the AGPL-3 license, since that fixed the issue and resulted in fewer dependencies. As @HenrikBengtsson mentioned though, it seems another way to fix this (and import phyloregion normally) would be to use future.packages = "snow" with future.apply::future_lapply(). Would you prefer that?

(By the way, it is possible that this behavior of snow may cause reproducibility issues with phyloregion as well. I suggest you look into it if you haven't already).

joelnitta commented 2 years ago

@KlausVigo thanks for making that change: I switched back to importing phyloregion, and it passes the tests for consistent results using the same seed in parallel.

I just have one request: would you consider bumping the phyloregion version so that I can require the version with this fix in Imports? That will prevent this bug popping up for others.

Hi @joelnitta,

I just made a commit to phyloregion cb819fb. This might solves the problem, at least sessionInfo() suggests that snow is not loaded via a namespace any more.

KlausVigo commented 2 years ago

@joelnitta nice that this works and it seems to simplify things. I wasn't aware that ImportFrom(betapart, beta.pair) and betaprt::beta.pair made such a large difference with the NAMESPACE. I naively assumed it is about the same and the documentation about these issues does not tell you otherwise. @darunabas is the maintainer of phyloregion and has to submit it to CRAN. We probably need a week or so to clean up all changes and get the error messages sorted out as we haven't updated the package for a while.

@KlausVigo thanks for making that change: I switched back to importing phyloregion, and it passes the tests for consistent results using the same seed in parallel.

I just have one request: would you consider bumping the phyloregion version so that I can require the version with this fix in Imports? That will prevent this bug popping up for others.

joelnitta commented 2 years ago

@KlausVigo no problem: it is a very subtle error, and one that I would never have resolved without the help of @HenrikBengtsson. As he has mentioned this is likely a much wider problem across many packages on CRAN.

If you and @darunabas are able to release a new version of phyloregion in a reasonable amount of time on CRAN that would be great.

shawnlaffan commented 2 years ago

@KlausVigo - if you are updating phyloregion then it would be good to also address https://github.com/darunabas/phyloregion/issues/3

tdhock commented 2 years ago

I am wondering if we can move forward on this submission? @KlausVigo @luismurao have the comments/suggestions in your reviews been addressed?

joelnitta commented 2 years ago

@tdhock Sorry, I am the cause for the delay! Since the reviews came back I've gotten busy with other projects, and haven't been able to get back to this yet. I anticipate being occupied by other projects for another week or two. Please remind me again if you don't hear something soon after that.

emilyriederer commented 2 years ago

Hi @joelnitta and @tdhock ! I'm currently the rotating editor in chief for rOpenSci submissions. I wanted to check in and see if you expect to have time to revisit the review feedback soon? Otherwise, we may want to put this review on hold status

joelnitta commented 2 years ago

Thanks for checking in @emilyriederer. Sorry for falling behind on this. I am still occupied with other things at the moment, but I should be able to respond to the reviews by the end of August if not sooner.

joelnitta commented 2 years ago

Response to reviews

I am sorry for taking so long to respond to the reviewers. Thanks again to both reviewers for their helpful comments. Below I respond to each comment as appropriate.

Response to @luismurao

README

Installation

Automated test

Performance

Questions and comments

Response to @KlausVigo

Specific comments

Profiling

For submitting to CRAN

General comments

joelnitta commented 2 years ago

Update to response to reviewers

The longest running test is "Parallelization decreases calculation time". To make this test robust, I have to include a relatively high number of replicates, otherwise by random chance sometimes running in parallel won't be faster than running sequentially.

I have decided to follow 6.1.5.4 Extended tests of rOpenSci Statistical Software Peer Review and treat this as an extended test that can be optionally skipped (it is now skipped by default).

I have documented this in a comment as follows:

  # This test is skipped by default because of its long run time.
  # To include the test locally, first run
  # withr::local_envvar(CANAPER_EXTENDED_TESTS = "true") # nolint
  # To include the test in CI (github actions), include the phrase
  # 'run-extended' in the commit

devtools::test() on my computer now finishes in 36 s skipping the extended test, and 181 s when including it.

@tdhock, @emilyriederer sorry again for the long delay, but this should be ready to move forward. Please let me know if there is anything you need from my end.

emilyriederer commented 2 years ago

Also tagging @KlausVigo @luismurao . I know this review was a bit delayed and your availability may have changed. At your convenience, if you could please review @joelnitta 's responses and share whether these address your feedback (template available here) , that would be fantastic.

joelnitta commented 2 years ago

@emilyriederer If the reviewers have no further comments, can we proceed with this at your discretion as an editor?

emilyriederer commented 2 years ago

Hi @joelnitta - let me follow up with @tdhock since he's the managing editor on this one

tdhock commented 2 years ago

hi! Since the reviewers have been tagged two weeks ago and gave no feedback, I think it is OK to move ahead with this submission (the reviewer response is very complete/convincing).

tdhock commented 2 years ago

@ropensci-review-bot approve canaper

ropensci-review-bot commented 2 years ago

Approved! Thanks @joelnitta for submitting and @KlausVigo, @luismurao for your reviews! :grin:

To-dos:

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joelnitta commented 2 years ago

Thanks @tdhock!

joelnitta commented 2 years ago

@ropensci-review-bot finalize transfer of canaper