knitr
Optionsknitr::opts_chunk$set(fig.align = "center")
knitr::opts_chunk$set(results = "hold")
R
Packageslibrary(readr, warn.conflicts = FALSE)
library(tidyr, warn.conflicts = FALSE)
library(ggplot2, warn.conflicts = FALSE)
library(dplyr, warn.conflicts = FALSE)
table_1 <- read_csv("GoodwinTable1.csv", col_types = "cdddddddddddddd")
table_2 <- read_csv("GoodwinTable2.csv", col_types = "cdddddddddddddd")
table_3 <- read_csv("GoodwinTable3.csv", col_types = "cdddddddddddddd")
colors <- c("#999999", "#56B4E9", "#E69F00", "#0072B2", "#000000")
shapes <- c(21:25)
table_1 %>%
gather("Year", "Prevalence", 2:15) %>%
ggplot(aes(Year, Prevalence, color = `Smoking status`)) +
geom_point(aes(shape = `Smoking status`)) +
geom_line(aes(group = `Smoking status`, linetype = `Smoking status`)) +
guides(color = guide_legend(ncol = 1)) +
scale_color_manual(values = colors) +
scale_shape_manual(values = shapes) +
theme_minimal() +
theme(legend.position = "bottom", legend.title = element_blank()) +
ggtitle("Prevalence of smoking status from 2002 to 2015",
subtitle = "(The National Survey on Drug Use and Health, aged 12+)")
table_2 %>%
gather("Year", "Prevalence", 2:15) %>%
mutate(CPD = factor(CPD, levels = unique(CPD))) %>%
ggplot(aes(Year, Prevalence, color = CPD)) +
geom_point(aes(shape = CPD)) +
geom_line(aes(group = CPD, linetype = CPD)) +
scale_color_manual(values = colors) +
scale_shape_manual(values = shapes) +
theme_minimal() +
theme(legend.position = "bottom", legend.title = element_blank()) +
ggtitle("Prevalence of CPD among current smokers from 2002 to 2015",
subtitle = "(The National Survey on Drug Use and Health, aged 12+)")
subtitle <- "(The National Survey on Drug Use and Health, 2002–15, aged 12+)"
table_3 %>%
gather("Year", "Prevalence", 2:15) %>%
filter(`Current smokers` == "TTFC (%)" |
`Current smokers` == "No TTFC (%)") %>%
mutate(`Current smokers` = factor(`Current smokers`,
levels = unique(`Current smokers`))) %>%
ggplot(aes(Year, Prevalence, color = `Current smokers`)) +
geom_point(aes(shape = `Current smokers`)) +
geom_line(aes(group = `Current smokers`, linetype = `Current smokers`)) +
scale_color_manual(values = colors) +
scale_shape_manual(values = shapes) +
theme_minimal() +
theme(legend.position = "bottom", legend.title = element_blank()) +
ggtitle("Prevalence of TTFC nicotine dependence among current smokers",
subtitle = subtitle)
table_3 %>%
gather("Year", "Prevalence", 2:15) %>%
filter(`Current smokers` != "TTFC (%)" &
`Current smokers` != "No TTFC (%)") %>%
mutate(`Current smokers` = factor(`Current smokers`,
levels = unique(`Current smokers`))) %>%
ggplot(aes(Year, Prevalence, color = `Current smokers`)) +
geom_point(aes(shape = `Current smokers`)) +
geom_line(aes(group = `Current smokers`, linetype = `Current smokers`)) +
scale_color_manual(values = colors) +
scale_shape_manual(values = shapes) +
theme_minimal() +
theme(legend.position = "bottom", legend.title = element_blank()) +
ggtitle("Prevalence of TTFC nicotine dependence stratified by number of CPD",
subtitle = subtitle)
sessionInfo()
## R version 3.4.2 (2017-09-28)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
##
## 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] bindrcpp_0.2 dplyr_0.7.4 ggplot2_2.2.1 tidyr_0.7.2 readr_1.1.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.13 bindr_0.1 knitr_1.17
## [4] magrittr_1.5 hms_0.3 tidyselect_0.2.2
## [7] munsell_0.4.3 colorspace_1.3-2 R6_2.2.2
## [10] rlang_0.1.2 plyr_1.8.4 stringr_1.2.0
## [13] tools_3.4.2 grid_3.4.2 gtable_0.2.0
## [16] htmltools_0.3.6 assertthat_0.2.0 lazyeval_0.2.1
## [19] yaml_2.1.14 rprojroot_1.2 digest_0.6.12
## [22] tibble_1.3.4 purrr_0.2.4 glue_1.2.0
## [25] evaluate_0.10.1 rmarkdown_1.5.9000 labeling_0.3
## [28] stringi_1.1.5 compiler_3.4.2 scales_0.5.0
## [31] backports_1.1.1 pkgconfig_2.0.1