Add script that extracts Soilgrids SOC based on location of sites

[Qianyuxuan]

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

• Immediately
• Within one week
• When possible

Types of changes

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

Checklist:

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

[Qianyuxuan]

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 <#3040 (comment)>: > + 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. — Reply to this email directly, view it on GitHub <#3040 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFCCZ73TGII3OLAXHKGWLI3WAZR4DANCNFSM6AAAAAAQNCFL34>. You are receiving this because you were mentioned.

[serbinsh]

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]

@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]

@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]

@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]

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 :)