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Patch for get.trait.data.pft.R #2761

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merged 6 commits into from
Feb 9, 2021
Merged

Patch for get.trait.data.pft.R #2761

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b81dcbd
Condition reading in of species.csv or cultivars.csv for existing mem…
jessicaguo Jan 28, 2021
e25e197
Add PR #2761
jessicaguo Jan 28, 2021
514510a
Merge branch 'develop' into patch-cultivars-bug
dlebauer Feb 8, 2021
15262e4
Make colClasses if/then more compact
jessicaguo Feb 9, 2021
5430058
Updated with develop
jessicaguo Feb 9, 2021
67ee924
Merge branch 'develop' into patch-cultivars-bug
mdietze Feb 9, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -39,6 +39,7 @@ This is a major change:
- ensure Tleaf converted to K for temperature corrections in PEcAn.photosynthesis::fitA (#2726)
- fix bug in summarize.result to output stat, which is needed to turn on RE in the meta-analysis (#2753)
- ensure that control treatments always receives the random effect index of 1; rename madata.Rdata to jagged.data.Rdata and include database ids and names useful for calculating parameter estimates by treatment (#2756)
- ensure that existing meta-analysis results can be used for pfts with cultivars (#2761)

### Changed

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14 changes: 10 additions & 4 deletions base/db/R/get.trait.data.pft.R
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Expand Up @@ -136,20 +136,26 @@ get.trait.data.pft <- function(pft, modeltype, dbfiles, dbcon, trait.names,
} else {
# Check if PFT membership has changed
PEcAn.logger::logger.debug("Checking if PFT membership has changed.")
if (pfttype == "plant") {
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There seems to be a lot more duplicate code here than necessary. Could we just have the if be used to define the colClasses variable, and then use that variable in the existing_membership load?

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Okay, fixed to be much more compact. Thanks!

# Columns are: id, genus, species, scientificname
colClass = c("double", "character", "character", "character")
} else if (pfttype == "cultivar") {
# Columns are: id, specie_id, genus, species, scientificname, cultivar
colClass = c("double", "double", "character", "character", "character", "character")
}
existing_membership <- utils::read.csv(
need_paths[["pft_membership"]],
# Columns are: id, genus, species, scientificname
# Need this so NA values are formatted consistently
colClasses = c("double", "character", "character", "character"),
colClasses = colClass,
stringsAsFactors = FALSE,
na.strings = c("", "NA")
)
)
diff_membership <- symmetric_setdiff(
existing_membership,
pft_members,
xname = "existing",
yname = "current"
)
)
if (nrow(diff_membership) > 0) {
PEcAn.logger::logger.error(
"\n PFT membership has changed. \n",
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