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Fixed errors when data is duplicated on CS #148

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merged 1 commit into from
Apr 12, 2018
Merged

Fixed errors when data is duplicated on CS #148

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53 changes: 30 additions & 23 deletions R/chemspider.R
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Original file line number Diff line number Diff line change
Expand Up @@ -291,43 +291,46 @@ cs_prop <- function(csid, verbose = TRUE, ...){
ll <- sapply(ll, str_trim)
ll <- ll[!ll == '']

# Log Octanol-Water Partition Coef
prop <- 'Log Octanol-Water Partition Coef'
value_pred <- as.numeric(gsub('.* = \\s(.*)','\\1', ll[grepl('^Log Kow \\(KOWW', ll)]))
value_pred <- save_val(as.numeric(gsub('.* = \\s(.*)','\\1', ll[grepl('^Log Kow \\(KOWW', ll)])))
unit_pred <- NA
source_pred <- gsub('(.*) = \\s(.*)','\\1', ll[grepl('^Log Kow \\(KOWW', ll)])
source_pred <- save_val(gsub('(.*) = \\s(.*)','\\1', ll[grepl('^Log Kow \\(KOWW', ll)]))
value_exp <- save_val(as.numeric(gsub('.* = \\s(.*)',
'\\1', ll[grepl('^Log Kow \\(Exper.', ll)])))
unit_exp <- NA
source_exp <- save_val(gsub('^.*\\:\\s(.*)','\\1',
ll[which(grepl('^Log Kow \\(Exper.', ll)) + 1]))

# Boiling Point
prop <- c(prop, 'Boiling Point')
value_pred <- c(value_pred,
as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
ll[grepl('^Boiling Pt \\(deg C', ll)])))
ll[grepl('^Boiling Pt \\(deg C', ll)]))))
unit_pred <- c(unit_pred, 'deg C')
source_pred <- c(source_pred,
gsub('^.*\\((.*)\\)\\:$',
save_val(gsub('^.*\\((.*)\\)\\:$',
'\\1',
ll[grepl('^Boiling Pt, ', ll)]))
ll[grepl('^Boiling Pt, ', ll)])))

value_exp <- c(value_exp, save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
ll[grepl('^BP \\(exp database', ll)]))))
unit_exp <- c(unit_exp, 'deg C')
source_exp <- c(source_exp, NA)

# Melting Point
prop <- c(prop, 'Melting Point')
value_pred <- c(value_pred,
as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
ll[grepl('^Melting Pt \\(deg C', ll)])))
ll[grepl('^Melting Pt \\(deg C', ll)]))))
unit_pred <- c(unit_pred, 'deg C')
source_pred <- c(source_pred,
gsub('^.*\\((.*)\\)\\:$',
save_val(gsub('^.*\\((.*)\\)\\:$',
'\\1',
ll[grepl('^Boiling Pt, ', ll)]))
ll[grepl('^Boiling Pt, ', ll)])))
value_exp <- c(value_exp, save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+).*',
'\\1',
ll[grepl('^MP \\(exp database', ll)]))))
Expand All @@ -336,13 +339,14 @@ cs_prop <- function(csid, verbose = TRUE, ...){
# epi_mp_exp <- as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+).*','\\1', ll[grepl('^MP\\s+\\(exp', ll)]))
# epi_bp_exp <- as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+).*','\\1', ll[grepl('^BP\\s+\\(exp', ll)]))

# Water Solubility from KOW
prop <- c(prop, 'Water Solubility from KOW')
value_pred <- c(value_pred, as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
value_pred <- c(value_pred, save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
ll[grepl('^Water Solubility at 25 deg C', ll)])))
ll[grepl('^Water Solubility at 25 deg C', ll)]))))
unit_pred <- c(unit_pred, 'mg/L (25 deg C)')
source_pred <- c(source_pred, gsub('^.*\\((.*)\\)\\:$','\\1',
ll[grepl('^Water Solubility Estimate from Log Kow', ll)]))
source_pred <- c(source_pred, save_val(gsub('^.*\\((.*)\\)\\:$','\\1',
ll[grepl('^Water Solubility Estimate from Log Kow', ll)])))
value_exp <- c(value_exp,
save_val(as.numeric(gsub('.*=\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
Expand All @@ -356,41 +360,44 @@ cs_prop <- function(csid, verbose = TRUE, ...){
'\\1',
ll[which(grepl('^Water Sol \\(Exper. database match', ll)) + 1])))

# Water Solubility from Fragments
prop <- c(prop, 'Water Solubility from Fragments')
value_pred <- c(value_pred, as.numeric(gsub('.*=\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
value_pred <- c(value_pred, save_val(as.numeric(gsub('.*=\\s+([-+]?[0-9]*\\.?[0-9]+[eE]?[-+]?[0-9]*).*',
'\\1',
ll[grepl('^Wat Sol \\(v1.01', ll)])))
ll[grepl('^Wat Sol \\(v1.01', ll)]))))
unit_pred <- c(unit_pred, 'mg/L')
source_pred <- c(source_pred, NA)
value_exp <- c(value_exp, NA)
unit_exp <- c(unit_exp, NA)
source_exp <- c(source_exp, NA)

# Log Octanol-Air Partition Coefficient (25 deg C)
prop <- c(prop, 'Log Octanol-Air Partition Coefficient (25 deg C)')

value_pred_new <- as.numeric(gsub('.*:\\s(.*)', '\\1', ll[grepl('^Log Koa \\(KOAWIN', ll)]))
value_pred_new <- save_val(as.numeric(gsub('.*:\\s(.*)', '\\1', ll[grepl('^Log Koa \\(KOAWIN', ll)])))
value_pred <- c(value_pred, ifelse(length(value_pred_new)==0,NA,value_pred_new))

unit_pred <- c(unit_pred, NA)
source_pred <- c(source_pred, gsub('^.*\\[(.*)\\]\\:$',
source_pred <- c(source_pred, save_val(gsub('^.*\\[(.*)\\]\\:$',
'\\1',
ll[grepl('^Log Octanol-Air Partition Coefficient', ll)]))
ll[grepl('^Log Octanol-Air Partition Coefficient', ll)])))
value_exp <- c(value_exp,
save_val(suppressWarnings(as.numeric(gsub('^.*\\:(.*)',
'\\1',
ll[grepl('^Log Koa \\(experimental database\\).*', ll)])))))
unit_exp <- c(unit_exp, NA)
source_exp <- c(source_exp, NA)

# Log Soil Adsorption Coefficient
prop <- c(prop, 'Log Soil Adsorption Coefficient')
value_pred <- c(value_pred,
as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+).*',
save_val(as.numeric(gsub('.*:\\s+([-+]?[0-9]*\\.?[0-9]+).*',
'\\1',
ll[grepl('^Log Koc:', ll)])))
ll[grepl('^Log Koc:', ll)]))))
unit_pred <- c(unit_pred, NA)
source_pred <- c(source_pred, gsub('^.*\\((.*)\\)\\:$',
source_pred <- c(source_pred, save_val(gsub('^.*\\((.*)\\)\\:$',
'\\1',
ll[grepl('^Soil Adsorption Coefficient', ll)]))
ll[grepl('^Soil Adsorption Coefficient', ll)])))
value_exp <- c(value_exp, NA)
unit_exp <- c(unit_exp, NA)
source_exp <- c(source_exp, NA)
Expand Down