In JARS3N/PipeFish: pKa,outlier,pO2model,etc

Date: r as.Date(Sys.time())

Instrument: r A<-readxl::read_excel('FILE')[,1:2];A[which(A[,1]=="Instrument Serial"),2]

Filename: r basename('FILE')

knitr::opts_chunk$set(echo = FALSE)

library(readxl)
library(dplyr)
library(ggplot2)
x<-'FILE' #FilePath
XL.Level<-readxl::read_excel(x,sheet=PipeFish::fndLVLs(x)) %>% rename(.,O2=`O2 (mmHg)`)
XL.Rate<-readxl::read_excel(x,sheet='Rate')
grp<-XL.Level %>% 
  mutate(absO2=abs(152-O2)) %>%
  mutate(abspH=abs(pH-7.4)) %>%
  group_by(Well) %>%
  summarize(xpH=max(abspH),xO2=max(absO2))

Level Plots

library(ggplot2)
library(ggthemes)
XLev<-XL.Level %>% dplyr::select(.,Tick,O2,pH,Well)
ggplot(XLev,aes(Tick,O2,Well)) +geom_line(aes(col=Well))+theme_bw()+ggtitle("O2 Levels")
ggplot(XLev,aes(Tick,pH,Well)) +geom_line(aes(col=Well))+theme_bw()+ggtitle("pH Levels")

Outliers +/- 10 from 152 mmHg O2, spec < 3

spec1<-grp %>% filter(xO2 >10) %>% nrow()

n = r spec1, r c("Fail","Pass")[(spec1<3)+1]

Outliers +/- 20 from 152 mmHg O2, spec < 1

spec2<-grp %>% filter(xO2 >20) %>% nrow()

n = r spec2, r c("Fail","Pass")[(spec2<1)+1]

Outliers +/- 0.1 from 7.4 pH, spec < 1

spec3 <-grp %>% filter(.,xpH >0.1) %>% nrow(.)

n = r spec3, r c("Fail","Pass")[(spec3<1)+1]

pH rates are 0.0 +/- 10 mpH/minute

spec4<-XL.Rate %>% 
  mutate(abspR=abs(ECAR)) %>%
  group_by(Well) %>%
  summarize(W=max(abspR)) %>%
  filter(.,W > 10) %>%
  nrow(.)

n = r spec4, r c("Fail","Pass")[(spec4<1)+1]

JARS3N/PipeFish documentation built on May 7, 2019, 6:47 a.m.