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Update 0_before_after_datmod_prep.R #5

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Update 0_before_after_datmod_prep.R #5

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4 changes: 2 additions & 2 deletions scripts/data_analysis/0_before_after_datmod_prep.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ temp.filename <- paste0(site, '_mod_dat.csv')
dat <- read.csv(file.path('data_cached', temp.filename))

# change infinite values to 365, representing a full year since application
dat<-do.call(data.frame,lapply(dat, function(x) replace(x, is.infinite(x),365)))
dat[,c("days_since_cultivation","days_since_fertilizer","days_since_planting")]<-do.call(data.frame,lapply(dat[,c("days_since_cultivation","days_since_fertilizer","days_since_planting")], function(x) replace(x, is.infinite(x),365)))

# change 'NaN' values to NA to omit during data processing
dat<-do.call(data.frame,lapply(dat, function(x) replace(x, "NaN",NA)))
Expand All @@ -27,7 +27,7 @@ drop.predictors <- caret::findCorrelation(predictors.cor, cutoff = 0.95, verbose
predictors.keep <- c(names.cor[-drop.predictors], 'frozen')

# Change all 0 values to 0.0000001, so we can take the log10 of those vlaues
dat.mod[dat.mod==0] <- 0.0000001
dat.mod[,responses][dat.mod[,responses]==0] <- 0.0000001

# log transform response vars
dat.mod[,responses] <- log10(dat.mod[,responses])
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