Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

95 update mc6_mthds with fval and fval_unit drops #102

Merged
merged 4 commits into from
Jul 31, 2023
Merged

95 update mc6_mthds with fval and fval_unit drops #102

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
2ce5a5b
95 update mc6_mthds with fval and fval_unit drops
cthunes Jul 25, 2023
4004b56
95 removed fval and fval_unit from tcplLoadData
cthunes Jul 26, 2023
345b6a2
Merge pull request #107 from USEPA/main
cthunes Jul 27, 2023
3b3255d
95 Removed fval columns references from new method
cthunes Jul 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
136 changes: 68 additions & 68 deletions R/mc6_mthds.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,9 +86,9 @@ mc6_mthds <- function() {

flag <- "Model directionality questionable"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(dr[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(dr[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(dr[ , coffsign := ifelse(top < 0, -1*coff, coff)])
e3 <- bquote(dr[ , gtabscoff := abs(resp) > abs(coffsign)])
e4 <- bquote(dr[ , nrsp_gtabscoff := sum(gtabscoff), by = m4id])
Expand All @@ -98,7 +98,7 @@ mc6_mthds <- function() {
e8 <- bquote(dr[ , nrsp_ltcoff := sum(ltcoff), by = m4id])
e9 <- bquote(dr[ , test := ifelse(coffsign > 0, nrsp_gtabscoff > 2*nrsp_gtcoff, nrsp_gtabscoff > 2*nrsp_ltcoff)])
e10 <- bquote(f[[.(mthd)]] <- unique(dr[which(test), .SD, .SDcols = .(out)], by = NULL))
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "coffsign", "gtabscoff", "nrsp_gtabscoff", "gtcoff", "ltcoff", "nrsp_gtcoff", "nrsp_ltcoff")
cr <- c("mc6_mthd_id", "flag", "test", "coffsign", "gtabscoff", "nrsp_gtabscoff", "gtcoff", "ltcoff", "nrsp_gtcoff", "nrsp_ltcoff")
e11 <- bquote(dr[ , .(cr) := NULL])
list(e1, e2, e3, e4, e5, e6, e7, e8, e9, e10, e11)

Expand All @@ -108,12 +108,12 @@ mc6_mthds <- function() {

flag <- "Average number of replicates per conc is less than 2"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := nrep < 2])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -123,12 +123,12 @@ mc6_mthds <- function() {

flag <- "Number of concentrations tested is less than 4"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := modl != "none" & nconc <= 4])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -138,13 +138,13 @@ mc6_mthds <- function() {

#flag <- "Bmd falling > 50% conc range tested, indicative of a steep curve"
#out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
#"flag", "fval", "fval_unit")
#init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
#e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
#"flag")
#init <- bquote(list(.(mthd), .(flag), FALSE))
#e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
#e2 <- bquote(ft[ , crng := 10^logc_max - 10^logc_min])
#e3 <- bquote(ft[ , test := bmd > 0.5*crng & hitc >= 0.9])
#e4 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
#cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "crng")
#cr <- c("mc6_mthd_id", "flag", "test", "crng")
#e5 <- bquote(ft[ , .(cr) := NULL])
#list(e1, e2, e3, e4, e5)

Expand All @@ -154,13 +154,13 @@ mc6_mthds <- function() {

#flag <- "Bmd falling < 50% conc range tested, indicative of a shallow curve"
#out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
#"flag", "fval", "fval_unit")
#init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
#e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
#"flag")
#init <- bquote(list(.(mthd), .(flag), FALSE))
#e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
#e2 <- bquote(ft[ , crng := 10^logc_max - 10^logc_min])
#e3 <- bquote(ft[ , test := bmd < 0.5*crng & hitc >= 0.9])
#e4 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
#cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "crng")
#cr <- c("mc6_mthd_id", "flag", "test", "crng")
#e5 <- bquote(ft[ , .(cr) := NULL])
#list(e1, e2, e3, e4, e5)

Expand All @@ -170,12 +170,12 @@ mc6_mthds <- function() {

flag <- "Bmd > ac50, indication of high baseline variability"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ifelse(all(c("ac50","bmd") %in% names(ft)),ft[ , test := bmd > ac50],ft))
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -185,13 +185,13 @@ mc6_mthds <- function() {

flag <- "Only highest conc above baseline, active"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , lstc := max_med_conc == logc_max])
e3 <- bquote(ft[ , test := nmed_gtbl == 1 & hitc >= 0.9 & lstc])
e4 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "lstc")
cr <- c("mc6_mthd_id", "flag", "test", "lstc")
e5 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4, e5)

Expand All @@ -201,13 +201,13 @@ mc6_mthds <- function() {

flag <- "Only one conc above baseline, active"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , lstc := max_med_conc == logc_max])
e3 <- bquote(ft[ , test := nmed_gtbl == 1 & hitc >= 0.9 & !lstc])
e4 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "lstc")
cr <- c("mc6_mthd_id", "flag", "test", "lstc")
e5 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4, e5)

Expand All @@ -217,12 +217,12 @@ mc6_mthds <- function() {

flag <- "Multiple points above baseline, inactive"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := nmed_gtbl > 1 & hitc < 0.9])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -232,16 +232,16 @@ mc6_mthds <- function() {

flag <- "Gain AC50 < lowest conc & loss AC50 < mean conc"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , c_min := 10^logc_min])
e3 <- bquote(ft[ , c_max := 10^logc_max])
conc_cols <- c("c_min", "c_max")
e4 <- bquote(ft[ , cmen := rowMeans(.SD), .SDcols = .(conc_cols)])
e5 <- bquote(ifelse("ac50_loss" %in% names(ft), ft[ , test := modl == "gnls" & ac50 < c_min & ac50_loss < cmen], ft))
e6 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test", "c_min", "c_max","cmen")
cr <- c("mc6_mthd_id", "flag", "test", "c_min", "c_max","cmen")
e7 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4, e5, e6, e7)

Expand All @@ -251,12 +251,12 @@ mc6_mthds <- function() {

flag <- "Noisy data"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := rmse > coff])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -266,12 +266,12 @@ mc6_mthds <- function() {

flag <- "Borderline"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := abs(top) <= 1.2*coff & abs(top) >= 0.8*coff])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -281,9 +281,9 @@ mc6_mthds <- function() {

#flag <- "Hit-call potentially confounded by overfitting"
#out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
#"flag", "fval", "fval_unit")
#init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
#e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
#"flag")
#init <- bquote(list(.(mthd), .(flag), FALSE))
#e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
#e2 <- bquote(ft[modl == "hill" & npts < 5 & hitc == 1, test := TRUE])
#e3 <- bquote(ft[modl == "gnls" & npts < 7 & hitc == 1, test := TRUE])
#e4 <- bquote(ft[npts > 1, cna := cnst_aic + 4/(npts - 2)])
Expand All @@ -300,7 +300,7 @@ mc6_mthds <- function() {
#nhc := TRUE])
#e14 <- bquote(ft[hitc == 1 & !nhc, test := TRUE])
#e15 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
#cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test",
#cr <- c("mc6_mthd_id", "flag", "test",
#"cna", "hna", "gna", "nma", "nmdl", "nhc")
#e16 <- bquote(ft[ , .(cr) := NULL])
#list(e1, e2, e3, e4, e5, e6, e7, e8, e9, e10,
Expand All @@ -312,15 +312,15 @@ mc6_mthds <- function() {

flag <- "Less than 50% efficacy"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[hitc >= 0.9 & coff >= 5,
test := top < 50 | max_med < 50])
e3 <- bquote(ft[hitc >= 0.9 & coff < 5,
test := top < log2(1.5) | max_med < log2(1.5)])
e4 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e5 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4, e5)

Expand All @@ -330,12 +330,12 @@ mc6_mthds <- function() {

flag <- "AC50 less than lowest concentration tested"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[hitc >= 0.9, test := ac50 < 10^logc_min])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -345,12 +345,12 @@ mc6_mthds <- function() {

flag <- "Cell viability assay fit with gnls winning model"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[hitc >= 0.9, test := modl=="gnls" & cell_viability_assay == 1])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand All @@ -360,12 +360,12 @@ mc6_mthds <- function() {

flag <- "Flag series where no median response values are greater than baseline as defined by 3 times the baseline median absolute deviation (bmad)"
out <- c("m5id", "m4id", "aeid", "mc6_mthd_id",
"flag", "fval", "fval_unit")
init <- bquote(list(.(mthd), .(flag), NA_real_, NA_character_, FALSE))
e1 <- bquote(ft[ , .(c(out[4:7], "test")) := .(init)])
"flag")
init <- bquote(list(.(mthd), .(flag), FALSE))
e1 <- bquote(ft[ , .(c(out[4:5], "test")) := .(init)])
e2 <- bquote(ft[ , test := nmed_gtbl == 0])
e3 <- bquote(f[[.(mthd)]] <- ft[which(test), .SD, .SDcols = .(out)])
cr <- c("mc6_mthd_id", "flag", "fval", "fval_unit", "test")
cr <- c("mc6_mthd_id", "flag", "test")
e4 <- bquote(ft[ , .(cr) := NULL])
list(e1, e2, e3, e4)

Expand Down
4 changes: 1 addition & 3 deletions R/tcplLoadData.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -686,9 +686,7 @@ tcplLoadData <- function(lvl, fld = NULL, val = NULL, type = "mc", add.fld = TRU
m5id,
spid,
mc6_mthd_id,
flag,
fval,
fval_unit
flag
FROM
mc4,
mc6
Expand Down