Merge branch 'master' of code.communitydata.science:cdsc_examples_repository

R_examples/automation/OnYourMachine/lib-00-utils.R

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+library(data.table)
+library(parallel)
+
+## how remember works:
+## pass it a variable you want to keep
+## it will store it in a list 
+## then at the bottom of your R document
+## add the following:
+##
+##
+##
+# if (!nosave) {
+## setup for the next thing to save
+#r <- list()
+
+## save the output and clean up
+#remember(core.reg.table, "core.reg.table.tex")
+#remember(model.sums, silent=TRUE)
+
+## also save a copy of editsweeks that we used to fit these models
+#remember(d, "editweeks")
+#save(r, file="paper/knitr_rdata/02-models_for_presentation.RData")
+#rm(r)
+#}
+##
+##
+##
+
+
+remember <- function (v, k, silent=FALSE) {
+  if (missing(k)) {
+    k <- deparse(substitute(v))
+  }
+  
+  ## save to the global r variable/list
+  r[[k]] <<- v
+  
+  if (!silent) {
+    print(r[[k]])
+    flush.console()
+  }
+  
+  invisible(r[[k]])
+  ## return(r[[k]])
+}
+
+## function help with building reduced summaries
+reduced.summary <- function (m) {
+  magic.pattern <- "(wikia.com|jedipedia.de)"
+  
+  if (class(m)[1] == "coeftest") {
+    x <- do.call(cbind, lapply(1:4, function (i) {m[,i]}))
+    rownames(x) <- names(m[,1])
+    colnames(x) <- c("Estimate","Std. Error","z value","Pr(>|z|)")
+  } else {
+    x <- coef(summary(m))
+  }
+  
+  if (!class(x) == "list") {  
+    x <- list(x)
+  }
+  
+  out <- lapply(x, function (y) { y[!grepl(magic.pattern, rownames(y)),] })
+  
+  ## it's possible that this will only include one line/parameter (blocked)
+  if (class(out[[1]]) == "numeric") {
+    out <- lapply(out, function (y) {
+      y <- as.data.frame(rbind(y))
+      rownames(y) <- "blocked"
+      return(y)
+    })
+  }
+  
+  Lower.95 <- round(out[[1]][,1] - (1.96*out[[1]][,2]),2)
+  Upper.95 <- round(out[[1]][,1] + (1.96*out[[1]][,2]),2)
+  cbind(out[[1]], Lower.95, Upper.95)
+}
+
+## make sure that appendix and nosave are always defined
+if (!exists("appendix")) { appendix <- FALSE }
+if (!exists("nosave")) { nosave <- FALSE }

R_examples/automation/OnYourMachine/local.R

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+
+## replace the below paths with your actual path to dropbox 
+## e.g., '/home/kaylea/Dropbox/Apps/Overleaf/WhateverICalledMyProject/figures/'
+figPath = '../InOverleaf/figures/'
+## e.g., '/home/kaylea/Dropbox/Apps/Overleaf/WhateverICalledMyProject/knitr_rdata/'
+knitrPath = '../InOverleaf/knitr_rdata/'
+source('lib-00-utils.R') # enables the remember command
+set.seed(424242) # always!
+
+library('texreg')
+library('ggplot2')
+
+magicNumberOne <- rnorm(1, 0, 1)
+magicNumberOne
+magicNumberTwo <- rnorm(1, 0, 1)
+magicNumberTwo
+
+Importance <- data.frame(value=rbeta(100,3,6)+0.1, source='Importance')
+Quality <- data.frame(value=cumsum(rbeta(10,1,4)/10), source='Quality')
+sampleDF <- rbind(Importance, Quality)
+head(sampleDF)
+head(Quality)
+head(Importance)
+
+
+g <- ggplot(sampleDF, aes(value, color=source)) +
+  geom_density(data=Importance, alpha=0.25, size=1) +
+  stat_ecdf(data=Quality, aes(x=value), geom='step') +
+  theme_classic() +
+  xlab("Time") +
+  ylab("Standard Deviation Units") +
+  theme(axis.ticks.x=element_blank(), axis.text.x=element_blank(),
+        axis.ticks.y=element_blank(), axis.text.y=element_blank(),
+        axis.title.x=element_text(size=8),
+        axis.title.y=element_text(size=8),
+        legend.position="bottom", legend.title=element_blank(),
+        legend.key.size= unit(.1, 'cm'), legend.key.height = unit(.1, 'cm'),
+  legend.margin=margin(0,0,0,0),
+        legend.key.width = unit(.1, 'cm'), legend.text = element_text(size=8)) +
+  annotate("text", size=3, label="Risk", x=.32, y =1.4) +
+geom_segment(aes(x=.275, y=1.3, xend=.4, yend=1.3), color='black', size=0.13) +
+geom_segment(aes(x=.275, y=1.33, xend=.275, yend=1.27), color='black', size=0.14) +
+geom_segment(aes(x=.4, y=1.33, xend=.4, yend=1.27), color='black', size=0.14)
+
+g
+
+png(paste0(figPath, "simCurve.png"), units = "in", res = 300, width = 3, height = 3)
+g
+dev.off()
+
+m1 <- lm(Importance ~ Quality, data=sampleDF)
+
+summary(m1)
+
+m2 <- lm(Importance ~ poly(Quality, degree=2, raw=2), data=sampleDF)
+
+summary(m2)
+
+con <- textConnection("model.texreg", "w") #remembered
+sink(con, split=TRUE, type="output")
+texreg(list(m1,m2), omit.coef = 'factor', stars=NULL, digits=2,
+       custom.model.names=c('M1 Description', 'M2 Description'), 
+       #custom.coef.names=c('(Intercept)', 'Quality', 'Quality Squared'), # run without specifying first, just to be sure these are right!
+       use.packages=FALSE, table=FALSE, ci.force = TRUE)
+sink()
+close(con);rm(con)
+
+m1.coefs <- summary(m1)$coefficients ## for easy reference within the latex document
+m2.coefs <- summary(m1)$coefficients ## for easy reference within the latex document
+
+
+
+
+if (!nosave) {
+  r <- list()
+  remember(magicNumberOne) #put everything you want to have access to inside latex here
+  remember(magicNumberTwo) #put everything you want to have access to inside latex here
+  remember(model.texreg)
+  remember(m1.coefs)
+  remember(m2.coefs)
+  save(r, file=paste0(knitrPath, "main.RData"), version=2) ## this creates the file, and we need to specify the version
+  print("Remembrances complete")
+}
+