restructured in move to git.soton

DESCRIPTION

@@ -10,4 +10,4 @@ Description: Code to support a paper on statistical power analysis.
 License: What license it uses
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(estimateMeanEffectSizes)
-export(estimateProportionEffectSizes)
+export(estimateProportionSampleSizes)
 import(data.table)
 import(pwr)
 import(reshape2)

code/makefile.R

+# run this to knit the .Rmd to an html file
+library(markdown)
+library(bookdown)
+library(dkUtils)
+
+library(weGotThePower)
+
+repoLoc <- dkUtils::findParentDirectory("weGotThePower")
+
+# this will fail if you do not have access to the UoO GREENGrid Data archive (via HCS)
+
+# it will also sometimes fail on the small sample section due to random processes. Just re-run it.
+
+rmdFile <- paste0(repoLoc, "/code/weGotThePower.Rmd")
+rmarkdown::render(input = rmdFile,
+                  output_format = "html_document2",
+                  output_file = paste0(repoLoc, "/output/weGotThePower.html")
+                  )
\ No newline at end of file

paper/weGotThePower.Rmd → code/weGotThePower.Rmd

@@ -468,12 +468,11 @@ linkedTestDT <- linkedTestDT[season == "Winter" & !is.na(nPeople)]
 
 # create small sample - be warned, this is a random process so you will get different results each time you run it
 
-smallTestDT <- sample_frac(linkedTestDT, 2, replace = TRUE)
+smallTestDT <- data.table::as.data.table(sample_frac(linkedTestDT, 2, replace = TRUE))
 
 t <- smallTestDT[, .("mean W" = mean(meanW),
                      "sd W" = sd(meanW),
-                     "n households" = .N),
-                 keyby = .(nPeople)]
+                     "n households" = .N), keyby = .(nPeople)]
 
 knitr::kable(t, caption = "Number of households and summary statistics per group (winter heat pump use)")
 ```
@@ -574,7 +573,7 @@ Now:
 ```{r creatLargeN}
 # fix.
 # we just randomly re-sample the GREEN Grid data
-largeTestDT <- sample_frac(linkedTestDT, 40, replace = TRUE)
+largeTestDT <- data.table::as.data.table(sample_frac(linkedTestDT, 40, replace = TRUE))
 
 t <- largeTestDT[, .("mean W" = mean(meanW),
                      "sd W" = sd(meanW),

docs/Readme.md

-# We Got The Power: Analysis for a short paper on statistical power & statistical significance
-
-And the various confusions that arise...
-
- * Latest draft: 
-   * [.Rmd](https://github.com/dataknut/weGotThePower/blob/master/paper/weGotThePower.Rmd) code (mostly stats & notes, little text)
-   * [.html](weGotThePower.html) output (as above)

docs/_config.yml

-theme: jekyll-theme-slate
\ No newline at end of file

man/estimateMeanEffectSizes.Rd

@@ -22,7 +22,7 @@ estimateMeanEffectSizes(mean, sd, samples, power)
 Returns a data.table of effect sizes for a given sample size. Calculates these for p = 0.01, 0.05, 0.1 & 0.2. Pick out the ones you want.
 }
 \seealso{
-Other Power functions: \code{\link{estimateProportionEffectSizes}}
+Other Power functions: \code{\link{estimateProportionSampleSizes}}
 }
 \author{
 Ben Anderson, \email{b.anderson@soton.ac.uk}

man/estimateProportionEffectSizes.Rd → man/estimateProportionSampleSizes.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/power.R
-\name{estimateProportionEffectSizes}
-\alias{estimateProportionEffectSizes}
+\name{estimateProportionSampleSizes}
+\alias{estimateProportionSampleSizes}
 \title{Estimate detectable proportion differences for given sample sizes using statistical power analysis}
 \usage{
-estimateProportionEffectSizes(samples, power)
+estimateProportionSampleSizes(p1, p2, samples, power)
 }
 \arguments{
+\item{p1}{the estimated proportion in sample 1}
+
 \item{samples}{a list of sample sizes to iterate over}
 
 \item{power}{power value to use}
 
-\item{mean}{the estimated mean value to use}
-
-\item{sd}{the estimated stadnard deviation to use}
+\item{sd}{the estimated proportion in sample 2}
 }
 \description{
 \code{estimateProportionEffectSizes} calculates required sample sizes for a given set of p values and samples.

paper/makePages.R

-# run this to knit the .Rmd to an html file in the docs/ directory for github pages
-library(markdown)
-library(bookdown)
-library(dkUtils)
-
-myParams$repoLoc <- dkUtils::findParentDirectory("weGotThePower")
-
-rmdFile <- paste0(myParams$repoLoc, "/paper/weGotThePower.Rmd")
-rmarkdown::render(input = rmdFile,
-                  output_format = "html_document2",
-                  output_file = paste0(myParams$repoLoc, "/docs/weGotThePower.html")
-
-)
\ No newline at end of file