initial import of material for public archive into git

We're creating a fresh archive because the history for our old chapter includes
API keys, data files, and other material we can't share.

code/prediction/01-build_control_variables.R

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+source("code/prediction/utils.R")
+
+# use this to store things for use in the paper
+pred.descrip <- NULL
+
+abstracts <- read.delim("processed_data/abstracts.tsv", header=TRUE,
+                stringsAsFactors=FALSE, sep="\t")
+
+abstracts <- subset(abstracts, select = -abstract)
+
+abstracts <- abstracts[abstracts$aggregation_type != "Trade Journal" &
+                     is.na(abstracts$aggregation_type) == FALSE, ]
+
+names(abstracts)[names(abstracts) == 'num_citations'] <- 'works_cited'
+abstracts$works_cited[is.na(abstracts$works_cited) == TRUE] <- 0
+
+# affiliations
+affiliations <- read.delim("processed_data/paper_aff_table.tsv",
+                           header=TRUE, stringsAsFactors=FALSE,
+                           sep="\t")
+
+# eliminate missing values
+affiliations <- affiliations[!is.na(affiliations$affiliation_id) &
+                             affiliations$organization != "", ]
+
+
+remap.affiliations <- function(aff.id,
+                               aff.df = affiliations){
+    org.modal <- names(tail(sort(table(affiliations$organization[
+        affiliations$affiliation_id == aff.id])),1))
+    return(org.modal)
+}
+
+affiliations$organization <- sapply(affiliations$affiliation_id, remap.affiliations)
+
+affiliations <- subset(affiliations, select = c(paper_eid,
+                           organization))
+names(affiliations) <- c("eid", "affiliation")
+
+# need to remove repeat affiliations
+affiliations <- affiliations[duplicated(affiliations$eid) == FALSE,]
+
+
+######################################
+d <- abstracts[, c("eid", "language", "modal_country",
+                   "source_title", "works_cited")]
+
+# dichotomous dependent variable
+d$cited <- abstracts$cited_by_count > 0
+
+
+# store this here for use in the paper before we run any restrictions: 
+pred.descrip$cited <- d$cited
+pred.descrip$cites <- abstracts$cited_by_count
+
+
+# We want these to be categorical variables
+d$modal_country <- factor(d$modal_country)
+d$language <- factor(d$language)
+d$subject <- factor(abstracts$first_ASJC_subject_area)
+d$source_title <- factor(d$source_title)
+d$month <- factor(strftime(abstracts$date, format= "%m"))
+# except for pub year - keep that continuous
+d$year <- as.numeric(strftime(abstracts$date, format="%Y"))
+
+# bring in org affiliations
+d <- merge(d, affiliations, by="eid") # note that this drops papers
+                                      # w/out org info
+
+d$affiliation <- factor(d$affiliation)
+
+##### Restrictions:
+
+### do this explicitly so that changes are easy:
+d <- restrict(d, d$affiliation, 1)
+d <- restrict(d, d$subject, 1)
+d <- restrict(d, d$source_title, 1)
+d <- restrict(d, d$language, 1)
+d <- restrict(d, d$modal_country, 1)
+
+# n.authors
+# per author prior citations
+
+pred.descrip$covars <- d
+save(pred.descrip, file = "paper/data/prediction_descriptives.RData")
+
+
+rm(d, abstracts, affiliations)
+