nytimes-jama.R

library(tidyverse)
library(ggrepel)

dat <- structure(list(quarter = 1:48, 
                      year = c(2001L, 2001L, 2001L, 2001L, 2002L, 2002L, 2002L,
                               2002L, 2003L, 2003L, 2003L, 2003L, 2004L, 2004L,
                               2004L, 2004L, 2005L, 2005L, 2005L, 2005L, 2006L,
                               2006L, 2006L, 2006L, 2007L, 2007L, 2007L, 2007L,
                               2008L, 2008L, 2008L, 2008L, 2009L, 2009L, 2009L,
                               2009L, 2010L, 2010L, 2010L, 2010L, 2011L, 2011L,
                               2011L, 2011L, 2012L, 2012L, 2012L, 2012L), 
                      value = c(15.05244755, 16.52097902, 17.15034965, 
                                16.67832168, 14.79020979, 16.57342657, 
                                15.20979021, 14.10839161, 16.73076923, 
                                16.62587413, 18.46153846, 18.3041958, 
                                17.41258741, 18.09440559, 18.40909091, 
                                17.62237762, 17.77972028, 18.40909091, 
                                19.51048951, 20.76923077, 19.24825175, 
                                20.45454545, 19.66783217, 20.71678322,
                                19.56293706, 20.50699301, 21.34615385, 
                                19.24825175, 21.29370629, 23.07692308, 
                                24.02097902, 22.08041958, 23.4965035, 
                                24.54545455, 24.49300699, 24.80769231, 
                                24.54545455, 26.01398601, 26.11888112,
                                24.96503497, 26.53846154, 26.32867133, 
                                26.22377622, 25.85664336, 26.8006993, 
                                26.90559441, 27.27272727, 27.43006993), 
                      study = structure(c(1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 
                                          1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                          1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                          1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 
                                          1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                          1L, 1L, 1L), 
                                        .Label = c("", "Study 1", "Study 2"), 
                                        class = "factor"), 
                      series = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
                                 1L, 1L, 1L, 1L)), 
                 class = "data.frame", row.names = c(NA, -48L))

dat %>%
  ggplot(., aes(x = factor(quarter), y = value, 
                group = series)) +
    geom_line(color="grey50") +
    geom_point() +
    scale_y_continuous(breaks=c(0, 5, 10, 15, 20, 25, 30),
                       limits=c(0, 30),
                       minor_breaks = NULL) +
    scale_x_discrete(breaks = c(1, 5, 9, 13, 17, 21, 25, 29, 33, 37, 41, 45),
                     labels=c("2001", "2002", "2003", "2004", "2005", "2006",
                              "2007", "2008", "2009", "2010", "2011", "2012")) +
    geom_vline(xintercept=4, color = "grey", linetype = "dashed") + 
    geom_vline(xintercept=33, color = "grey", linetype = "dashed") + 
    # geom_label_repel(aes(label = study),
    #                 size = 3.5,
    #                 segment.color = "grey50",
    #                 nudge_y = 27 - dat$value) +
    annotate("text", x = 6, y = 29, label = "Study 1", color="grey50") +
    annotate("text", x = 35, y = 29, label = "Study 2", color="grey50") +
    theme_bw() +
    theme(plot.background = element_blank(),
          panel.grid.major.x = element_blank(),
          panel.grid.major.y = element_blank(),
          panel.grid.minor = element_blank(),
          panel.border = element_blank(),
          axis.line.x = element_line(color = 'black'),
          axis.title.x=element_blank(),
          axis.title.y=element_blank(),
          axis.ticks.y = element_blank()) +
    ggtitle("Percentage of I.C.U Admissions With Tight Glycemic Control")