Add script that extracts Soilgrids SOC based on location of sites

Qianyuxuan commented 1 year ago

Description

Add a script that extracts total soil organic carbon and its standard deviation based on user-defined site location from SoilGrids250m version 2.0: https://soilgrids.org

Motivation and Context

To provide SOC observations for SDA

Review Time Estimate

[x] Immediately
[ ] Within one week
[ ] When possible

Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

[x] My change requires a change to the documentation.
[ ] My name is in the list of CITATION.cff
[x] I have updated the CHANGELOG.md.
[x] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

Qianyuxuan commented 1 year ago

Thanks Chris @infotroph ! Great suggestion! I did test and found out "dplyr::pivot_longer" works well to replace "reshape2::melt". I will update my PR soon.

On Sep 29, 2022, at 9:10 PM, Chris Black @.***> wrote:

@infotroph commented on this pull request.

In modules/data.land/R/soilgrids_soc_extraction.R https://github.com/PecanProject/pecan/pull/3040#discussion_r984191186:

rownames(ocdquant) <- depths

colnames(ocdquant) <- c(rep("Mean", length(internal_site_info$site_info.lon)),

rep("0.05", length(internal_site_info$site_info.lon)),

rep("0.5", length(internal_site_info$site_info.lon)),

rep("0.95", length(internal_site_info$site_info.lon)))

rownames(siteid) <- depths

colnames(siteid) <- c(rep("Mean", length(internal_site_info$site_info.lon)),

rep("0.05", length(internal_site_info$site_info.lon)),

rep("0.5", length(internal_site_info$site_info.lon)),

rep("0.95", length(internal_site_info$site_info.lon)))

if (verbose) {

close(pb)

}

parse extracted data and prepare for output

ocd_fit <- reshape2::melt(ocdquant, id.vars = c("Mean")) Low priority: How difficult would it be to rewrite these manipulations to use something like dplyr::pivot_longer instead of adding reshape2 to the dependency list? data.land has a beastly number of dependencies already, so when there's a choice I recommend preferring solutions that use existing imports rather than add new ones.

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serbinsh commented 1 year ago

Looks like reshape2 is indeed no longer a depends

[sserbin@modex data.land]$ grep -ri "reshape" .
./inst/FIA_allometry/README.Rmd:# Note: the "reshape" package is currently required, although this may
./inst/FIA_allometry/README.Rmd:library(reshape)
./inst/FIA_allometry/allometry.r:# Note: the "reshape" package is currently required, although this may
./inst/FIA_allometry/allometry.r:  #install.packages("reshape")
./inst/FIA_allometry/allometry.r:library(reshape)
./inst/FIA_allometry/biomass.r:# Note: the "reshape" package is currently required, although this may
./inst/FIA_allometry/biomass.r:library(reshape)
./DESCRIPTION:    reshape2,

but we still have some reshape requirements that could be updated at some point

mdietze commented 1 year ago

@Qianyuxuan here are the most recent build errors.

 checking package dependencies ... NOTE: Imports includes 33 non-default packages.
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract: no visible binding for global variable 'name'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : cgamma: no visible global function definition for 'qgamma'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : fitQ: no visible global function definition for 'optim'

serbinsh commented 1 year ago

@Qianyuxuan here are the most recent build errors.

 checking package dependencies ... NOTE: Imports includes 33 non-default packages.
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract: no visible binding for global variable 'name'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : cgamma: no visible global function definition for 'qgamma'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : fitQ: no visible global function definition for 'optim'

@Qianyuxuan here are the most recent build errors.

 checking package dependencies ... NOTE: Imports includes 33 non-default packages.
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract: no visible binding for global variable 'name'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : cgamma: no visible global function definition for 'qgamma'
  checking R code for possible problems ... NOTE: soilgrids_soilC_extract : fitQ: no visible global function definition for 'optim'

So "qgamma" is an R base function yes, same with optim yes (well its stats::optim). Not sure what "name" is referring too

serbinsh commented 1 year ago

@mdietze in the current errors, I dont understand what check is referring to with

NOTE: soilgrids_soilC_extract: no visible binding for global variable 'name'

All I could find was in the docs

' @name soilgrids_soilC_extract

Is that what its referring too?

infotroph commented 1 year ago

Thanks! When I made the suggestion I may possibly have been forgetting that pivot_longer lived in tidyr instead of dplyr and therefore still meant adding a new dependency, but I like this change anyway :)

PecanProject / pecan