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RnwMaker.py
164 lines (116 loc) · 4.8 KB
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RnwMaker.py
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import os
from statistician import Statistician
import mongoTools
import statistician
class RnwMaker:
def __init__(self, db, table, title="Data Party", author = "Christian Battista", human = ""):
if human:
self.human = human
else:
self.human = Statistician(db)
self.title = title
self.author = author
self.name = title
self.fname = self.name.replace(' ', '_')
path = os.path.join("output", self.fname)
f = open("%s.Rnw" % path, "w")
self.f = f
self.lvl = 1
self.WriteTitle()
def WriteTitle(self):
output = "\documentclass{article}\n\usepackage[utf8x]{inputenc}\n"
output += "\\title{%s}\n\\author{%s}\n" % (self.title, self.author)
output += "\\begin{document}\n\maketitle\n\\tableofcontents\n\\newpage\n"
self.f.write(output)
def AddText(self, text):
self.f.write(str(text))
def AddTextFile(self, textfile):
f = open(textfile, r)
lines = textfile.read()
f.close()
self.f.write(lines)
def ChangeLevel(self, lvl):
self.lvl = lvl
def AddSection(self, factors, prefix = "Effect of"):
lvl = self.lvl
if lvl == 1:
tag = "\section"
else:
self.lvl = lvl
tag = "\%ssection" % ("sub" * (lvl-1))
label = "%s %s" % (prefix, self.human.translate(factors))
self.f.write("%s{%s}\n" % (tag, label))
def addFigure(self, figure, caption=""):
output = """\\begin{figure}\n\\begin{center}\n<<echo=false,fig=true>>==\n%s\n@\n\end{center}\n\caption{%s}\n\end{figure}\n""" % (figure, caption)
return output
def compareMeans(self, factors, measure, datFile, caption="", interpret = False):
output, dfName, fName, tag = self.AddAnalysis(factors, measure, datFile)
model = "%s~%s+Error(s_id/%s)" % (measure, fName, fName)
#model = "%s~%s" % (measure, fName)
output += "%s{%s}\n" % (tag, self.human.translate(measure).title())
if interpret:
output += self.human.interpret(factors, measure, model, datFile)
#contin, paired = self.human.describeFactor(factors)
caption += ". %s" % self.human.hypothesize(fName, measure)
output += """<<>>==\n%sModel = aov(%s, data=%s)\nsummary(%sModel)\n""" % (measure, model, dfName, measure)
output += """tapply(%s$%s, %s$%s, mean)\n""" % (dfName, measure, dfName, factors)
output += """tapply(%s$%s, %s$%s, sd)\n""" % (dfName, measure, dfName, factors)
output += "print(model.tables(%sModel,\"means\"),digits=4)\n" % (measure)
output += "print(var(%s$%s),digits=4)\n" % (dfName, measure)
output += """@\n"""
#if measure == "count" or type(factors) == list:
figure = """boxplot(%s~%s,data=%s, ylab="%s", main="%s")""" % (measure, fName, dfName, self.human.translate(measure),self.human.translate(fName))
#elif contin:
# figure = """plot(tapply(%s$%s, %s$%s, mean), xlab="%s", ylab="%s", main="%s")\nlines(tapply(%s$%s, %s$%s, mean)) """ % (dfName, measure, dfName, factors, self.human.translate(factors), self.human.translate(measure),self.human.translate(fName), dfName, measure, dfName, factors)
#else:
# figure = """barplot(tapply(%s$%s, %s$%s, mean), ylab="%s", main="%s")""" % (dfName, measure, dfName, factors, self.human.translate(measure),self.human.translate(fName))
output += self.addFigure(figure, caption)
self.f.write(output)
def correlate(self, factors, measure, datFile, caption=""):
output, dfName, factors, tag = self.AddAnalysis(factors, measure, datFile)
sig, r, p = self.human.correlate(measure[0], measure[1], datFile)
output += "\nr=%2.2f, p<%0.2f\n\n" % (r, p)
if not factors:
figure = "plot(%s$%s, %s$%s, xlab = \"%s\", ylab = \"%s\")" % (dfName, measure[0], dfName, measure[1], self.human.translate(measure[0]), self.human.translate(measure[1]))
output += self.addFigure(figure, caption)
else:
for f in factors:
output += self.addFigure("scatterplot(%s ~ %s | %s, data=%s)" % (measure[0], measure[1], f, dfName), caption)
self.f.write(output)
def AddAnalysis(self, factors, measure, datFile):
if type(factors) == str:
factors = [factors]
lvl = self.lvl
dfName = ""
fName = ""
output = ""
if lvl == 1:
tag = "\section"
else:
tag = "\%ssection" % ("sub" * (lvl-1))
output += "<<echo=false>>=\n"
output += "library(car)\n"
#output += "library(gplots)\n"
for f in factors:
dfName = dfName + "_" + f
fName = fName + "*" + f
dfName = dfName.lstrip("_")
fName = fName.lstrip("*")
if type(measure) == list:
m = ""
for meas in measure:
m+= "_%s" % meas
dfName += m
else:
dfName+= "_%s" % measure
dfName = dfName.lstrip("_")
output += "%s = read.table(\"%s\", header=TRUE, sep=\",\")\n@\n" % (dfName, datFile)
return output, dfName, fName, tag
def Close(self, execute=False):
self.f.write("\end{document}\n")
self.f.close()
if execute:
os.chdir(os.path.join(os.getcwd(), "output"))
os.system("R CMD Sweave %s.Rnw" % self.fname)
os.system("R CMD pdflatex %s.tex" % self.fname)
del self.f