version 2.1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tcpl
 Title: ToxCast Data Analysis Pipeline
-Version: 2.0.2
+Version: 2.1.0
 Authors@R: c(
     person("Richard S", "Judson",role = c("cre","ths"), email = "Judson.Richard@epa.gov"),
     person("Dayne L", "Filer", role = "aut",email = "dayne.filer@gmail.com"),
@@ -17,16 +17,17 @@ Description: A set of tools for processing and modeling high-throughput and
     can be used for diverse chemical screening efforts.
 URL: https://github.com/USEPA/CompTox-ToxCast-tcpl
 Depends: R (>= 3.2.0)
-Imports: data.table (>= 1.9.4), DBI, RMySQL, numDeriv, RColorBrewer,
+Imports: data.table (>= 1.9.4), DBI, RMariaDB, numDeriv, RColorBrewer,
         utils, stats, methods, graphics, grDevices, sqldf
-Suggests: roxygen2, knitr, prettydoc, rmarkdown, htmlTable
+Suggests: roxygen2, knitr, prettydoc, rmarkdown, htmlTable, testthat
+        (>= 2.1.0)
 License: GPL-2
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2019-07-26 13:41:17 UTC; jbrown20
+Packaged: 2022-03-03 17:58:01 UTC; jbrown20
 Author: Richard S Judson [cre, ths],
   Dayne L Filer [aut],
   Jason Brown [ctb],
@@ -37,4 +38,4 @@ Author: Richard S Judson [cre, ths],
   Katie Paul Friedman [ctb]
 Maintainer: Richard S Judson <Judson.Richard@epa.gov>
 Repository: CRAN
-Date/Publication: 2019-07-26 14:50:02 UTC
+Date/Publication: 2022-03-03 19:10:02 UTC

NAMESPACE

@@ -39,6 +39,7 @@ export(tcplMultiplot)
 export(tcplObjCnst)
 export(tcplObjGnls)
 export(tcplObjHill)
+export(tcplPlot)
 export(tcplPlotFitc)
 export(tcplPlotFits)
 export(tcplPlotM4ID)
@@ -56,7 +57,7 @@ export(tcpldbStats)
 import(DBI)
 import(data.table)
 importFrom(RColorBrewer,brewer.pal)
-importFrom(RMySQL,MySQL)
+importFrom(RMariaDB,MariaDB)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,graphics.off)
@@ -99,6 +100,3 @@ importFrom(utils,read.table)
 importFrom(utils,tail)
 importFrom(utils,write.csv)
 importFrom(utils,write.table)
-importMethodsFrom(RMySQL,dbConnect)
-importMethodsFrom(RMySQL,dbDisconnect)
-importMethodsFrom(RMySQL,dbWriteTable)

NEWS

@@ -1,3 +1,17 @@
+tcpl v2.1.0
+==============
+*updated for release with toxcast invitrodb data
+*added option to allow change in single conc bmad calculation
+
+tcpl v2.0.3
+==============
+*Created tcplPlot a generic plotting function with call similar to tcplLoadData
+*added option for concentration units to be different during plotting.
+*fixed tcpllite bug for schema change
+*filtered gnls from tcplCytopt
+*updated to Rmariadb
+*various bugfixes
+
 tcpl v2.0.2
 ==============
 * Updated tcplLoadChem to return dsstox substance ids

R/blineShift.R

@@ -24,18 +24,17 @@
 
 blineShift <- function(resp, logc, wndw) {
 
-  wndw <- unique(wndw)[1]
+  if (any(is.na(resp))) return(resp)
+  if (length(unique(logc)) < 4) return(resp)
 
+  wndw <- unique(wndw)[1]
   ordr <- order(logc)
   resp <- resp[ordr]
   logc <- logc[ordr]
 
   uconc <- unique(logc)
   nconc <- length(uconc)
-
-  if (any(is.na(resp))) return(resp)
-  if (nconc < 4) return(resp)
-
+
   low <- 1:max(ceiling(nconc/4), 2)
   rsub <- resp[which(logc %in% uconc[low])]
   csub <- logc[which(logc %in% uconc[low])]

R/data.R

@@ -42,11 +42,14 @@
 #' Chemical library of tested chemicals in the example datasets with the corresponding sample IDs.
 #' 
 #'
-#' @format A data frame with 6 rows and 3 variables:
+#' @format A data frame with 6 rows and 6 variables:
 #' \describe{
 #'  \item{spid}{sample ID}
 #'   \item{casn}{Chemical Abstract Service(CAS) number}
 #'    \item{chnm}{chemical name}
+#'     \item{dsstox_substance_id}{chemical-specific DTXSID}
+#'      \item{code}{CAS number compressed into numeric string}
+#'       \item{chid}{unique chemical ID number for tcpl}
 #'
 #' }
 #' @source Toxcast database

R/mc3_mthds.R

@@ -581,6 +581,14 @@ mc3_mthds <- function() {
                        resp := 1-(cval/bval)])
       list(e1)
 
+    },
+
+    bval.aeid.nwlls.med = function(aeids) {
+      e1 <- bquote(dat[J(.(aeids)), 
+                       bval := median(cval[wllt == "n"], na.rm = TRUE), 
+                       by = list(aeid)])
+      list(e1)
+
     }
 
   )

R/mc5_mthds.R

@@ -151,6 +151,24 @@ mc5_mthds <- function(ae) {
       e1 <- bquote(coff <- c(coff, 0.3))
       list(e1)
 
+    },
+    pc25 = function() {
+
+      e1 <- bquote(coff <- c(coff, 25))
+      list(e1)
+    },
+
+	pc30 = function() {
+
+      e1 <- bquote(coff <- c(coff, 30))
+      list(e1)
+    },
+
+    bmad1 = function() {
+
+      e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)]))
+      list(e1)
+
     }
   )
 }

R/multiplotFit.R

@@ -106,10 +106,13 @@ multiPlotfit <- function(resp, logc, pars) {
 
   do.call(what = plot, args = c(resp[md] ~ logc[md], p), quote = TRUE)
 
+  if (is.null(pars$modl)) pars$modl <- "none"
+  if (is.na(pars$modl)) pars$modl <- "none"
+
   if(pars$modl == "hill") AC50 <- signif(10^pars$hill_ga,4) 
   if(pars$modl == "gnls") AC50 <- signif(10^pars$gnls_ga,4) 
   if(pars$modl == "cnst") AC50 <- NA
-
+  if(pars$modl == "none") AC50 <- NA
 
   legend("topleft", bty="n", text.font=2,
          legend = paste(paste0("AC50: ",AC50), 

R/plotFit.R

@@ -39,6 +39,27 @@
     ylab <- pars$resp_unit
     #y0 <- c(-50, 150)
   }
+
+  #new labels for x axis
+  xlab <- NULL
+  if (is.na(pars$conc_unit)) {
+    xlab <- expression(bold(paste("Concentration (",mu,"M)")))
+  }else{
+    if (pars$conc_unit == "uM") {
+      xlab <- expression(bold(paste("Concentration (",mu,"M)")))
+    }
+    if (pars$conc_unit == "mg/l") {
+      xlab <- "Concentration (mg/l)"
+    }
+    if (pars$conc_unit == "CF") {
+      xlab <- "Concentration (CF)"
+    }
+  }
+  if (is.null(xlab)) {
+    xlab <- paste0("Concentration (",pars$conc_unit,")")
+  }
+
+
   if(pars$bmad != 0){
     y0 <- c(signif(-10*pars$bmad,2), signif(20*pars$bmad,2))
   }else{
@@ -103,7 +124,7 @@
             font.lab = 2,
             col = "black",
             cex = 2,
-            xlab = expression(bold(paste("Concentration (",mu,"M)"))),
+            xlab = xlab,
             ylab = ylab,
             main = "",
             bty = "n",

R/sc2.R

@@ -74,6 +74,18 @@ sc2 <- function(ae, wr = FALSE) {
     warning("No level 5 methods for AEID", ae, " -- cutoff will be 0.")
   }
 
+  ## Extract methods that need to overwrite bmad
+  ms_overwrite <- ms[grepl("ow_",mthd),]
+  ## ignore any other methods
+  ms <- ms[!grepl("ow_",mthd),]
+
+  ## Apply bmad overwrite methods first if needed
+  if (nrow(ms_overwrite) > 0) {
+  exprs <- lapply(mthd_funcs[ms_overwrite$mthd], do.call, args = list())
+  fenv <- environment()
+  invisible(rapply(exprs, eval, envir = fenv))
+  }
+
   ## Apply cutoff methods
   exprs <- lapply(mthd_funcs[ms$mthd], do.call, args = list())
   fenv <- environment()

R/sc2_mthds.R

@@ -117,8 +117,32 @@ sc2_mthds <- function() {
       e1 <- bquote(coff <- c(coff, log2(1.5)))
       list(e1)
 
-    }
+    },
+
+    pc25 = function() {
+
+      e1 <- bquote(coff <- c(coff, 25))
+      list(e1)
+
+    },    
+
+    ow_bmad_nwells = function() {
+
+      e1 <- bquote(dat[ , bmad := mad(resp[wllt == "n"], na.rm = TRUE)])
+      list(e1)
+    },
+     bmad2 = function() {
+
+      e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)*2]))
+      list(e1)
+
+    },
 
+    log2_0.76 = function() {
+
+      e1 <- bquote(coff <- c(coff, 0.76))
+      list(e1)
+    }
   )
 }
 

R/tcplAppend.R

@@ -18,9 +18,8 @@
 #' 
 #' @import DBI
 #' @import data.table
-#' @importFrom RMySQL MySQL
+#' @importFrom RMariaDB MariaDB
 #' @importFrom utils read.csv read.table tail write.table
-#' @importMethodsFrom RMySQL dbConnect dbWriteTable dbDisconnect 
 
 tcplAppend <- function(dat, tbl, db, lvl=NULL) {
 
@@ -37,11 +36,12 @@ tcplAppend <- function(dat, tbl, db, lvl=NULL) {
            "?tcplConf for more details.")
     }
 
-    db_pars <- list(drv = RMySQL::MySQL(),
+    db_pars <- list(drv = RMariaDB::MariaDB(),
                     user = getOption("TCPL_USER"),
                     password = getOption("TCPL_PASS"),
                     host = getOption("TCPL_HOST"),
-                    dbname = db)
+                    dbname = db,
+                    bigint = "numeric")
 
     dbcon <- do.call(dbConnect, db_pars)
 

R/tcplCytoPt.R

@@ -79,9 +79,9 @@
 #' tcplConfDefault()
 #' 
 #' ## Can only calculate the cytotox burst if using the MySQL database and
-#' ## TCPL_DRVR == 'RMySQL'
+#' ## TCPL_DRVR == 'MySQL'
 #' 
-#' if (conf_store == 'RMySQL') {
+#' if (getOption("TCPL_DRVR") == "MySQL") {
 #' 
 #' ## Load the "burst" endpoints -- none are defined in the example dataset
 #' tcplLoadAeid(fld = "burst_assay", val = 1)
@@ -114,7 +114,7 @@ tcplCytoPt <- function(chid = NULL, aeid = NULL, flag = TRUE,
                        min.test = TRUE, default.pt = 3) {
 
   ## Variable-binding to pass R CMD Check
-  modl_ga <- hitc <- code <- chnm <- casn <- use_global_mad <- nhit <- NULL
+  modl_ga <- hitc <- code <- chnm <- casn <- use_global_mad <- nhit <- modl <- NULL
   ntst <- global_mad <- cyto_pt <- med <- cyto_pt_um <- lower_bnd_um <- burstpct <- NULL
 
   if (!is.null(aeid) & !is.vector(aeid)) {
@@ -160,6 +160,8 @@ tcplCytoPt <- function(chid = NULL, aeid = NULL, flag = TRUE,
   }
   print(8)
   zdat <- tcplSubsetChid(dat = zdat, flag = flag)
+  #filter out gnls curves
+  zdat <- zdat[modl != "gnls",]
   print(9)
   zdst <- zdat[, list(med = median(modl_ga[hitc == 1]), mad = mad(modl_ga[hitc == 
                                                                             1]), 

R/tcplLiteInit.R

@@ -8,6 +8,7 @@ tcplLiteInit <- function () {
                     'assay_component_map'= c('acid', 'acsn'),
                     'sample'= c('spid', 'chid', 'stkc', 'stkc_unit', 'tested_conc_unit', 'spid_legacy'),
                     'chemical_library'= c('chid', 'clib'),
+                    'chemical' = c('chid', 'casn', 'chnm', 'dsstox_substance_id', 'code'),
 
                     'mc0'= c('m0id', 'acid', 'spid', 'apid', 'rowi', 'coli', 'wllt', 'wllq', 'conc', 'rval', 'srcf', 'created_date', 'modified_date', 'modified_by'),
                     'mc1' = c('m1id', 'm0id', 'acid', 'cndx', 'repi', 'created_date', 'modified_date', 'modified_by'),
@@ -44,11 +45,10 @@ tcplLiteInit <- function () {
     }
   }
 
-  methods = c("mc2_methods", "mc3_methods","mc4_methods", "mc5_methods","mc5_fit_categories", "mc6_methods", "sc1_methods", "sc2_methods", "chemical")
+  methods = c("mc2_methods", "mc3_methods","mc4_methods", "mc5_methods","mc5_fit_categories", "mc6_methods", "sc1_methods", "sc2_methods")#, "chemical")
 
   for (m in methods) {
-    tcpl_path <- find.package('tcpl')
-    tcpl_fpath <- paste(tcpl_path,'csv',sep='/')
+    tcpl_fpath <- file.path(system.file(package = "tcpl"), "csv")
     tcpl_fpath <- paste(tcpl_fpath, m, sep='/')
     tcpl_fpath <- paste(tcpl_fpath, 'csv', sep='.')
     fpath <- paste(db, m, sep='/')

R/tcplLoadConcUnit.R

@@ -0,0 +1,51 @@
+#-------------------------------------------------------------------------------
+# tcplLoadConcUnit: Load concentration units for assay endpoints
+#-------------------------------------------------------------------------------
+
+#' @title Load concentration units for assay endpoints
+#' 
+#' @description 
+#' \code{tcplLoadUnit} queries the tcpl databases and returns a data.table
+#' with the concentration units for the given assay endpoint ids (spid).
+#' 
+#' @param spid Integer, assay endpoint ids 
+#' 
+#' @return A data.table containing level 3 correction methods for the given
+#' spids.
+#' 
+#' @seealso \code{\link{tcplQuery}}, \code{\link{data.table}}
+#' 
+#' @import data.table
+
+tcplLoadConcUnit <- function(spid) {
+
+  qformat <- 
+    "
+    SELECT
+      spid,
+      tested_conc_unit AS conc_unit
+    FROM
+      sample
+    WHERE
+      spid IN ('%s');
+    "
+
+  qstring <- sprintf(qformat, paste(spid, collapse = "','"))
+
+  dat <- tcplQuery(query = qstring, db = getOption("TCPL_DB"), tbl=c("sample"))
+
+  if (nrow(dat) == 0) {
+    #warning("The given spid(s) do not have concentration units.")
+    return(dat)
+  }
+
+  len_miss <- lw(!spid %in% dat$spid)
+  if (len_miss > 0) {
+    #warning(len_miss, " of the given spid(s) do not have concentration units.")
+  }
+
+  dat[]
+
+}
+
+#-------------------------------------------------------------------------------