Update functions docs and tests by gaoyu19920914 · Pull Request #34 · microbiome/miaSim

gaoyu19920914 · 2022-05-19T16:31:51Z

Co-Authored-By: Daniel Garza danielriosgarza@gmail.com

What's new

added `names_species` and `names_resources` in related functions

`randomA`

added parameter interactions and 5 interaction types to customize values and proportions of interspecies interactions
added scale_off_diagonal to avoid exponential growth in certain gLV modeling scenarios
added list_A to enable generating groups of species in simulation

`randomE`

added trophic levels and trophic preferences
added exact to switch the number of resources to consume/produce between a poisson distribution and the exact number

simulations

CRM, GLV, HubbellRates, and Logistic

added control of stochasticity, external events, migration from the metacommunity, and the extend of measurement errors to all these simulations
added microbial trophic levels (an implicit inter-species interaction) in simulateConsumerResource
put together result matrix and some parameters into a list (which might affect ConvertToSE, and I will check for that)

handy plot functions

added in utils.R: makePlot, makePlotRes for simulations, and makeHeatmap for matrix
(these could be a transient status if we prefer to use miaVis to make beautiful plots)

documentations for functions

other minor improvements

What's changed

names of parameters, see this form for a detailed table of variables
ways to customize the distribution in randomA and randomE
tests using previous data formats

What to expect for the next

an independent standard R package miaSimShiny with miaSim as a dependency
updates in other simulating functions
1. review Ricker and SOI model
2. review Hubbell (and replace it by HubbellRates if possible)
3. review powerlawA (and replace it by randomA if needed)
format codes using stylerand biocthis

Co-Authored-By: Daniel Garza <danielriosgarza@gmail.com>

antagomir

Awesome job.

II left a few comments, will like to review once more after those have been somehow responded (at least in comments).

Could you also update the NEWS file? See https://blog.r-hub.io/2020/05/08/pkg-news/

DESCRIPTION

R/randomE.R

R/simulateGLV.R

R/utils.R

vignettes/miaSim.Rmd

R/utils.R

gaoyu19920914 · 2022-05-20T07:46:50Z

Thanks @antagomir for all your comments, they are really helpful for develop a package of high quality 👍
I am going through them now, and will reply to your suggestions and comments one by one.

1. turn duplicated manuals to templates in \man-roxygen 2. remove ggplot plotting functions with miaViz::plotSeries 3. update NEWS 4. TODO: examples in miaSim.Rmd

generateSimulations getCommunity .replaceByZero createParamList estimateAFromSimulations to facilitate comparisons among models using estimated A which is generated from a series of simulations.

Ricker model updated (unifying variable names and return format), rdirichlet function added (to resolve dependency issue from gtools)

avoid ode solver "returning early" error in some cases

antagomir · 2022-07-23T15:23:19Z

Hello @gaoyu19920914 - can you check if this PR is still something to merge?

If so, we should finalize the few issues there are in automated checks, and resolve the conversation.

Or if these were already handled otherwise we should close this PR.

Just let me know where we are with this one.

gaoyu19920914 · 2022-07-24T09:23:22Z

Hello @antagomir , thanks for your remind.

I just checked what to do, and will make some minor changes in the returning formats, and change their corresponding examples in miaSim.Rmd

Then I will solve the fail in check.

antagomir · 2022-07-24T09:50:01Z

Great. THere have been some updates to the main branch, remember to pull those changes also before your push so that all is in sync.

to keep align with unified formats and variables

reduce notes from R CMD CHECK

antagomir · 2022-07-26T14:25:24Z

Note that the branch still has conflicts with the main branch.

gaoyu19920914 · 2022-07-26T14:38:11Z

Note that the branch still has conflicts with the main branch.

Thanks for reminding, I am resolving these conflicts.

R/convertToSE.R

R/simulateConsumerResource.R

R/simulateGLV.R

R/simulateStochasticLogistic.R

R/utils.R

vignettes/miaSim.Rmd

- uncomment examples of miaViz - replace :-sequences by seq() - miaSim.Rmd - input validation in Hubbell

gaoyu19920914 · 2022-07-26T22:44:19Z

Thanks for the detailed comments, and here's a summary for the latest changes.

I've uncommented all miaViz plot examples. The plots are good to visualize.
for (i in 2:n)-like for-loop changed for the BioC review.
Every simulateX function returns a list as their result, and this list is of specific format, with the first element named 'matrix' and of specific dimensions related to the number of species and length of time series to simulate, hence I take this kind of list as one specific type of object.
In miaSim.Rmd vignette, to be coherent with other examples, all results are named as Xmodel, and converted results are named as X_TSE after modification.
Input validation: mentioned changes has been made accordingly.

R/simulateStochasticLogistic.R

antagomir · 2022-07-27T07:29:11Z

Ok sounds good!

There are still some failing checks that should be resolved. We can discuss more in Slack/Gitter on the details if necessary.

remove link to SummarizedExperiment to solve R CMD CHECK failing

add TreeSummarizedExperiment to solve R CMD CHECK failing

antagomir · 2022-07-31T20:56:31Z

Are there pending issues? The system shows "Changes requested". If you can resolve all issues above that have been dealt with, we can see if everything is complete and this PR could be merged.

YagmurSimsekk · 2022-07-31T21:56:07Z

@antagomir As far as I know, it is ready to merge, @gaoyu19920914 can confirm. However, I will take a last look and solve the reviews.

YagmurSimsekk

It seems ready to me.

gaoyu19920914 · 2022-08-01T12:35:16Z

@antagomir As far as I know, it is ready to merge, @gaoyu19920914 can confirm. However, I will take a last look and solve the reviews.

Thanks @YagmurSimsekk for your updates. I confirm that all previously mentioned issues are solved.

antagomir

Yess, almost there. Some minor suggestions to add.

Next time, let us aim at smaller and more focused PRs.

Also remember to update the version number if not done yet.

NEWS

R/randomE.R

R/simulateGLV.R

antagomir · 2022-08-01T16:50:55Z

Just confirm when it is ready to merge.

gaoyu19920914 · 2022-08-01T18:14:54Z

I think we can merge all changes to main.

antagomir · 2022-08-01T18:31:08Z

Super!

Update functions docs and tests

661ba95

Co-Authored-By: Daniel Garza <danielriosgarza@gmail.com>

antagomir requested review from YagmurSimsekk and antagomir May 19, 2022 18:25

antagomir requested changes May 19, 2022

View reviewed changes

gaoyu19920914 added 5 commits May 30, 2022 11:47

update functions, docs and examples

be255be

1. turn duplicated manuals to templates in \man-roxygen 2. remove ggplot plotting functions with miaViz::plotSeries 3. update NEWS 4. TODO: examples in miaSim.Rmd

Update DESCRIPTION

59b9310

add functions

a3848e7

generateSimulations getCommunity .replaceByZero createParamList estimateAFromSimulations to facilitate comparisons among models using estimated A which is generated from a series of simulations.

update Ricker model

d9b501c

Ricker model updated (unifying variable names and return format), rdirichlet function added (to resolve dependency issue from gtools)

Update simulateConsumerResource.R

768d94e

avoid ode solver "returning early" error in some cases

gaoyu19920914 added 3 commits July 26, 2022 15:18

update SOI

1b809d0

to keep align with unified formats and variables

update documentation

1ef69dd

reduce notes from R CMD CHECK

Update utils.R

169f8d1

gaoyu19920914 added 2 commits July 26, 2022 22:24

modify convertToSE and related examples

01f9d92

Merge branch 'main' into devel

c825f31

antagomir reviewed Jul 26, 2022

View reviewed changes

minor changes

ceaffb1

- uncomment examples of miaViz - replace :-sequences by seq() - miaSim.Rmd - input validation in Hubbell

antagomir reviewed Jul 27, 2022

View reviewed changes

R/simulateStochasticLogistic.R Outdated Show resolved Hide resolved

gaoyu19920914 and others added 4 commits July 27, 2022 10:23

Update convertToSE.R

32f3613

remove link to SummarizedExperiment to solve R CMD CHECK failing

update dependencies

d2de50e

add TreeSummarizedExperiment to solve R CMD CHECK failing

dependency test

fda64c3

assay_name replaced

31f503b

YagmurSimsekk linked an issue Jul 30, 2022 that may be closed by this pull request

Argument abund_values deprecated and replaced with assay_name #40

Closed

YagmurSimsekk reviewed Jul 31, 2022

View reviewed changes

gaoyu19920914 requested a review from antagomir August 1, 2022 12:35

antagomir requested changes Aug 1, 2022

View reviewed changes

gaoyu19920914 added 2 commits August 1, 2022 18:29

update version, NEWS, and style

da26061

Merge branch 'main' into devel

aff20b9

gaoyu19920914 requested a review from antagomir August 1, 2022 18:12

antagomir merged commit e7af665 into main Aug 1, 2022

YagmurSimsekk deleted the devel branch August 20, 2022 20:46

Conversation

gaoyu19920914 commented May 19, 2022

What's new

added names_species and names_resources in related functions

randomA

randomE

simulations

handy plot functions

documentations for functions

other minor improvements

What's changed

What to expect for the next

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antagomir commented Aug 1, 2022

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gaoyu19920914 commented Aug 1, 2022

added `names_species` and `names_resources` in related functions

`randomA`

`randomE`

antagomir commented Jul 27, 2022 •

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