first commit

README

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+Files and code for our studies on effects of deuterium on living organisms.
+Steven J. Koch stevekochscience@gmail.com
+Anthony L. Salvagno
+Alex Haddad
+
+Anthony's open notebook: http://research.iheartanthony.com/
+Alex's open notebook: http://alexhaddadnm.wordpress.com/
+
+Public Github repository: git@github.com:stevekochscience/Deuterium-in-life-science.git

Repeating Crumley/.Rhistory

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+require(RCurl)
+myCsV <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB5&output=html")
+myCsV <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB5&output=html")
+myCsv <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB6&output=csv")
+getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB6&output=csv")
+getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB6&output=csv", ssl.verifypeer=FALSE)
+myCsv <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB6&output=csv", ssl.verify=FALSE)
+myCsv <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdDNLeEtuc2pqa2JybjdGX21EUjd6Wmc&single=true&gid=0&range=A1%3AB6&output=csv", ssl.verifypeer=FALSE)
+read.csv(textConnection(myCSV))
+read.csv(textConnection(myCsv))
+mymatrix <- read.csv(textConnection(myCsv))
+mymatrix
+mymatrix[,1]
+mymatrix[,0]
+mymatrix[0,0]
+mymatrix[1,1]
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+mymatrix
+mymatrix
+source("RC Graph manual.r")
+mymatrix
+mymatrix[1,1]
+mymatrix[,1]
+mymatrix[,2]
+mymatrix[,3]
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+help(legend)
+help(legend)
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+source("RC Graph manual.r")
+break

Repeating Crumley/RC Graph manual.r

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+# Code is public domain--Steven J. Koch
+# This program is an example of how to obtain data from a Google spreadsheet and make an XY plot
+
+# RCurl library required to access public google spreadsheet.  Use "publish as Webpage" and choose CSV file, sheet 1, whatever range such as A1:B6
+# to get the https:// URL from Google that you pass to this
+# The following is based on instructions at: http://blog.revolutionanalytics.com/2009/09/how-to-use-a-google-spreadsheet-as-data-in-r.html#
+require(RCurl)
+
+myCsv <- getURL("https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhLNnjMk2r_qdFJRNGNaN0RNM0RucHE5dUY4Q3BNTFE&single=true&gid=0&range=A1%3AAC12&output=csv", ssl.verifypeer=FALSE)  #ssl.verifypeer=FALSE gets around certificate issues I don't understand.
+
+fullmatrix <- read.csv(textConnection(myCsv))
+
+# The example spreadsheet can be viewed at https://docs.google.com/spreadsheet/ccc?key=0AhLNnjMk2r_qdFJRNGNaN0RNM0RucHE5dUY4Q3BNTFE
+# For the test file using Repeating Crumley Trial 3, the first day column is 4 (all days are the same), 
+# the first y column is 3, and each subsequent y is 4 columns after the preceding.   
+daynumber <- fullmatrix[,4]
+yDIwater <- fullmatrix[,3]
+y33D <- fullmatrix[,7]
+y66D <- fullmatrix[,11]
+y99D <- fullmatrix[,15]
+y33DpDDW <- fullmatrix[,19]
+y66DpDDW <- fullmatrix[,23]
+yDDW <- fullmatrix[,27]
+
+# The following is a basic plot and legend.  Help from help(legend) and http://www.statmethods.net/advgraphs/axes.html and
+# http://www.harding.edu/fmccown/R/ ... I am doing a lot of things manually, such as naming colors twice, that maybe could be more concise
+
+# Save the graph to a PNG file
+# png("Repeating Crumley 3.png")
+
+#set up the plot, but add lines/points individually (type="n" turns off first plot)
+plot(daynumber, yDIwater, type="n", main="Repeating Crumley Trial 3", xlab="days", ylab="percent germinated")  
+lines(daynumber,yDIwater, type="o", pch=22, lty=1, col="black")
+lines(daynumber,y33D, type="o", pch=22, lty=1, col="red")
+lines(daynumber,y66D, type="o", pch=22, lty=1, col="blue")
+lines(daynumber,y99D, type="o", pch=22, lty=1, col="green")
+lines(daynumber,y33DpDDW, type="o", pch=22, lty=1, col="cyan")
+lines(daynumber,y66DpDDW, type="o", pch=22, lty=1, col="magenta")
+lines(daynumber,yDDW, type="o", pch=22, lty=1, col="yellow")
+legend("bottomright", c("DI Water", "33% D2O", "66%D2O", "99.9% D2O", "DDW + 33%D2O", "DDW + 66%D2O", "DDW"), col=c("black", "red", "blue", "green", "cyan", "magenta", "yellow"), lty=1, inset=.1)
+
+# this next command is necessary to make the graph save, I don't know why.  It makes the graph disappear from the screen though
+# I also have trouble viewing the file with external editor unless I close out of R.  Obviously doing something wrong.
+# dev.off()
+