This part of the study involved just one arm, animals treated in utero. This file was most recently updated on Thu Nov 13 16:56:04 2014.

## Loading required package: rJava
## Loading required package: xlsxjars

This data comes from the file ../data/Food Worksheet.xlsx using the worksheet Maternal-Summary.

Animals Treated with Particulate Matter Gestationally

ymax <- max(weekly.summary$se + weekly.summary$mean)
plot <- with(subset(weekly.summary, Treatment=="Control"), plot(Week, mean,
             pch=18, las=1, ylab="Calories per mouse per week", ylim=c(0,ymax)))

with(subset(weekly.summary, Treatment=="Particulate"), points(Week, mean, pch=18, col="red"))


superpose.eb <- function (x, y, ebl, ebu = ebl, length = 0.08, ...)
  arrows(x, y + ebu, x, y - ebl, angle = 90, code = 3,
  length = length, ...)

#lines
abline(lm(mean~Week, data=subset(weekly.summary, Treatment=="Control")), col="black")
abline(lm(mean~Week, data=subset(weekly.summary, Treatment=="Particulate")), col="red")

#error bars
superpose.eb(subset(weekly.summary, Treatment=="Control")$Week,
             subset(weekly.summary, Treatment=="Control")$mean,
             subset(weekly.summary, Treatment=="Control")$se)

superpose.eb(subset(weekly.summary, Treatment=="Particulate")$Week,
             subset(weekly.summary, Treatment=="Particulate")$mean,
             subset(weekly.summary, Treatment=="Particulate")$se, col="red")

legend("bottomleft", levels(raw.data$Treatment), col=c("black",'red'), pch=18, bty="n", lty=1)

plot of chunk weekly-food-intake

plot of chunk weekly-food-intake-cumulative

## Loading required package: Matrix
## Loading required package: Rcpp
## fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

We tested by Χ2-test whether there is a difference between mixed models considering the amount of food eaten and the treatment. The residuals of this model fit a normal distribution (p=0.1067 from a Shapiro-Wilk Test). The p-value for that test is Χ2 =1.58, p=0.4538 so there is no evidence of a difference between the treatments.

If we look at the cumulative food intake, the residuals are still normally distributed (p=0.9216 from Shapiro-Wilk Test). Comparing mixed linear models with an interaction term, and the slope forced to zero there was a significant difference between the two groups by Χ2 = 11.1952 and p=8.2007 × 10-4. Based on this, the control group ate 6.2864 kcal of food more per mouse per week, or a total of 75.4363, kcal throughout the diet. This corresponds to a decrease of 19.886% of caloric intake

Session Information

## R version 3.1.1 (2014-07-10)
## Platform: x86_64-apple-darwin13.1.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] lme4_1.1-7     Rcpp_0.11.2    Matrix_1.1-4   plyr_1.8.1    
## [5] xlsx_0.5.7     xlsxjars_0.6.1 rJava_0.9-6   
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.4     evaluate_0.5.5   formatR_1.0      grid_3.1.1      
##  [5] htmltools_0.2.6  knitr_1.6        lattice_0.20-29  MASS_7.3-33     
##  [9] minqa_1.2.3      nlme_3.1-117     nloptr_1.0.4     rmarkdown_0.3.10
## [13] splines_3.1.1    stringr_0.6.2    tools_3.1.1      yaml_2.1.13