1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
drdata <- function(substances, experimentator = "%", db = "cytotox",
celltype = "IPC-81", enzymetype = "AChE",
organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1",
ok = "'ok','no fit'")
{
if (requireNamespace("RODBC")) {
channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
slist <- paste(substances,collapse="','")
if (db == "cytotox") {
experimenttype <- "plate"
responsetype <- "viability"
testtype <- "celltype"
type <- celltype
} else {
if (db == "enzymes") {
experimenttype <- "plate"
responsetype <- "activity"
testtype <- "enzyme"
type <- enzymetype
} else {
experimenttype <- "experiment"
responsetype <- "response"
testtype <- "organism"
type <- organism
}
}
query <- paste("SELECT conc,",responsetype,", unit, experimentator, ",
experimenttype, ", substance, ", testtype,
", ok FROM ", db, " WHERE substance IN ('",
slist,"') AND experimentator LIKE '",
experimentator,"' AND ",testtype," LIKE '",
type,"' AND ",
whereClause," AND ok in (",
ok,")",sep="")
if (db == "ecotox") query <- paste(query," AND type LIKE '",endpoint,"'",sep="")
data <- RODBC::sqlQuery(channel,query)
RODBC::odbcClose(channel)
names(data)[[1]] <- "dose"
names(data)[[2]] <- "response"
data$substance <- factor(data$substance,levels=substances)
return(data)
} else {
stop("For this function, the RODBC package has to be installed and configured.")
}
}
|
