#' @param use.loess Whether to use LOESS model or not?
#' @param use.loess Whether to use LOESS model or not?
#' @param smooth.param Smoothing parameter for LOESS model.
#' @param smooth.param Smoothing parameter for LOESS model.
#' @param add.constant A numeric constant that will be added to each curve before the log transform (defaults to 1)
#' @param add.constant A numeric constant that will be added to each curve before the log transform (defaults to 1)
#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well.
#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, assumes the first OD measurement of each well to be blank.
#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)
#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)
#' @param growth.cutoff Minimum threshold for curve growth.
#' @param growth.cutoff Minimum threshold for curve growth.
#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.
#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.
\item{add.constant}{A numeric constant that will be added to each curve before the log transform (defaults to 1)}
\item{add.constant}{A numeric constant that will be added to each curve before the log transform (defaults to 1)}
\item{blank.value}{User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well.}
\item{blank.value}{User can enter a blank OD measurement for uninoculated wells. if NULL, assumes the first OD measurement of each well to be blank.}
\item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
\item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
<h3><span data-tooltip="OD value for blank well read. As the default option <NULL>, GCAT will automatically take the first OD reading of each well to be the blank.">Media background</span></h3>
<h3><span data-tooltip="OD value for blank well read">Media background</span></h3>
<h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
<h3><span data-tooltip="GCAT transforms optical density (OD) to log(x+δ). x = OD – Media background. Specify a value for n or choose from the defaults. Note: 0 is not recommended unless all wells contain many repeated measurements for initial density that can be used to accurately estimate the baseline density. See the user manual for more details.">OD Transform</span></h3>
@ -84,8 +85,8 @@
<h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture.
<h3><span data-tooltip="Enter the index of the timepoint at which the wells were inoculated with the culture.
" >Inoculation timepoint</span></h3>
" >Inoculation timepoint</span></h3>
<div class="field">
<div class="field">
<%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 2. " %><br />
<%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 1. " %><br />