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lizzieinvancouver / egret

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get study spp and paper numbers for different treatment combos #32

Open lizzieinvancouver opened 4 months ago

lizzieinvancouver commented 4 months ago

And then do it by dormancy class!

So, basically, get the EGRET data where a row has only germination temperature (and duration), then cold (and duration) and germination temp are filled in ... then split (reshape) on treatment and start going though those combos.

And, again, then do it by dormancy class!

lizzieinvancouver commented 4 months ago

Reshaping treatment col

# reshaping
newdf <- reshape(alldat, idvar=c("lat", "lon", "year", "sp"), timevar="metric", direction = "wide")
# where time is the thing that gives names you want to become column names, idvar is columns to keep and ...
# the column missing here will be spread across new columns (in this case it was called 'value')
christophe-rd commented 4 months ago

First 30 rows of the treatment column and the number of datasetID that have them:

    datasetID                 treatment
225       208                   control
177       113       cold stratification
140        49                  chilling
388        48            moist chilling
101        38                  chemical
567        31                   storage
162        30                      cold
581        30            stratification
511        22             scarification
170        21                cold strat
678        19       warm stratification
105        16 chemical + moist chilling
286        16                       GA3
615        16               temperature
178        14       Cold stratification
226        14                   Control
259        13               dry storage
238        11                      dark
442        11            non-stratified
165         9 cold moist stratification
196         9 cold stratification, dark
197         9 cold stratification,light
513         9            scarification 
519         9    scarification+chilling
661         9           untreated, dark
662         9         untreated, light 
202         8 cold-moist stratification
351         7                     light
370         7           low temperature
410         7              NA (control)
lizzieinvancouver commented 4 months ago

We did some things vaguely similar in OSPREE, here some of the code: here and here