## ----include = FALSE---------------------------------------------------------- library(knitr) knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) options(rmarkdown.html_vignette.check_title = FALSE) # to supress R-CMD check ## to fold/hook the code hook_output <- knit_hooks$get("output") knit_hooks$set(output = function(x, options) { lines <- options$output.lines if (is.null(lines)) { return(hook_output(x, options)) # pass to default hook } x <- unlist(strsplit(x, "\n")) more <- "..." if (length(lines) == 1) { if (length(x) > lines) { # truncate the output, but add .... x <- c(head(x, lines), more) } } else { x <- c(if (abs(lines[1]) > 1) more else NULL, x[lines], if (length(x) > lines[abs(length(lines))]) more else NULL ) } # paste these lines together x <- paste(c(x, ""), collapse = "\n") hook_output(x, options) }) modern_r <- getRversion() >= "4.1.0" ## ----setup, message = F------------------------------------------------------- library(injurytools) library(ggplot2) library(dplyr) library(gridExtra) library(grid) library(knitr) ## ----fig.width = 13.7, fig.height = 7----------------------------------------- gg_photo(injd, title = "Overview of injuries:\nLiverpool FC 1st male team during 2017-2018 and 2018-2019 seasons", by_date = "2 month", fix = TRUE) + ## plus some lines of ggplot2 code.. xlab("Follow-up date") + ylab("Players") + labs(caption = "source: transfermarkt.com") + theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 22), axis.text.x.bottom = element_text(size = 13, angle = 20, hjust = 1), axis.text.y.left = element_text(size = 12), axis.title.x = element_text(size = 20, face = "bold", vjust = -1), axis.title.y = element_text(size = 20, face = "bold", vjust = 1.8), legend.text = element_text(size = 20), plot.caption = element_text(face = "italic", size = 12, colour = "gray10")) ## ----warning = FALSE---------------------------------------------------------- # warnings set to FALSE df_summary <- calc_summary(injd) df_summary_perinj <- calc_summary(injd, by = "injury_type") # injds ## ----eval = F----------------------------------------------------------------- # df_summary |> # mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), # burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> # dplyr::select(2, 7, 1, incidence_new, burden_new) |> # kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), # caption = "Injury incidence and injury burden are reported as 100 player-matches", # align = "c") # # df_summary_perinj |> # mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), # burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> # dplyr::select(1:2, 9, 4, incidence_new, burden_new) |> # kable(col.names = c("Type of injury", "N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), # caption = "Injury incidence and injury burden are reported as 100 player-matches", # align = "c") ## ----echo = F, eval = modern_r------------------------------------------------ df_summary |> mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> dplyr::select(2, 7, 1, incidence_new, burden_new) |> kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), caption = "Injury incidence and injury burden are reported as 100 player-matches", align = "c") ## ----echo = F, eval = modern_r------------------------------------------------ df_summary_perinj |> mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> dplyr::select(1:2, 9, 4, incidence_new, burden_new) |> kable(col.names = c("Type of injury", "N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), caption = "Injury incidence and injury burden are reported as 100 player-matches", align = "c") ## ----eval = F----------------------------------------------------------------- # # warnings set to FALSE # gg_riskmatrix(injd, # by = "injury_type", # title = "Risk matrix") ## ----eval = F----------------------------------------------------------------- # # warnings set to FALSE # palette <- c("#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", # Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ # theme3 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), # axis.text.x.bottom = element_text(size = 20), # axis.text.y.left = element_text(size = 20), # axis.title.x = element_text(size = 15), # axis.title.y = element_text(size = 15), # legend.title = element_text(size = 15), # legend.text = element_text(size = 15)) # # gg_riskmatrix(injd, # by = "injury_type", # title = "Risk matrix") + # scale_fill_manual(name = "Type of injury", # values = palette) + # guides(fill = guide_legend(override.aes = list(size = 5))) + # theme3 ## ----echo = F, fig.width = 9, fig.height = 5.8, warning = F------------------- palette <- c("#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ theme3 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), axis.text.x.bottom = element_text(size = 18), axis.text.y.left = element_text(size = 18), axis.title.x = element_text(size = 18), axis.title.y = element_text(size = 18), legend.title = element_text(size = 15), legend.text = element_text(size = 15)) gg_riskmatrix(injd, by = "injury_type", title = "Risk matrix") + scale_fill_manual(name = "Type of injury", values = palette) + guides(fill = guide_legend(override.aes = list(size = 5))) + theme3 ## ----warning = F-------------------------------------------------------------- # warnings set to FALSE injd1 <- cut_injd(injd, datef = 2017) injd2 <- cut_injd(injd, date0 = 2018) ## ----eval = F----------------------------------------------------------------- # ## Plot just for checking whether cut_injd() worked well # p1 <- gg_photo(injd1, fix = TRUE, by_date = "3 months") # p2 <- gg_photo(injd2, fix = TRUE, by_date = "3 months") # grid.arrange(p1, p2, ncol = 2) ## ----echo = F, fig.width = 18, fig.height = 4--------------------------------- p1 <- gg_photo(injd1, fix = TRUE, by_date = "3 months") p1$layers[[3]]$aes_params$size <- 2 p2 <- gg_photo(injd2, fix = TRUE, by_date = "3 months") p2$layers[[3]]$aes_params$size <- 2 grid.arrange(p1, p2, ncol = 2) ## ----warning = FALSE---------------------------------------------------------- # warnings set to FALSE df_summary1 <- calc_summary(injd1, quiet = T) df_summary2 <- calc_summary(injd2, quiet = T) ## ----eval = F----------------------------------------------------------------- # ## **Season 2017/2018** # df_summary1 |> # mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), # burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> # dplyr::select(2, 7, 1, incidence_new, burden_new) |> # kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), # caption = "Injury incidence and injury burden are reported as 100 player-matches", # align = "c") # # ## **Season 2018/2019** # df_summary2 |> # mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), # burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> # dplyr::select(2, 7, 1, incidence_new, burden_new) |> # kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), # caption = "Injury incidence and injury burden are reported as 100 player-matches", # align = "c") ## ----echo = F, eval = modern_r------------------------------------------------ df_summary1 |> mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> dplyr::select(2, 7, 1, incidence_new, burden_new) |> kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), caption = "Injury incidence and injury burden are reported as 100 player-matches", align = "c") ## ----echo = F, eval = modern_r------------------------------------------------ df_summary2 |> mutate(incidence_new = paste0(round(incidence, 2), " (", round(incidence_lower, 2), ",", round(incidence_upper, 2), ")"), burden_new = paste0(round(burden, 2), " (", round(burden_lower, 2), ",", round(burden_upper, 2), ")")) |> dplyr::select(2, 7, 1, incidence_new, burden_new) |> kable(col.names = c("N injuries", "N days lost", "Total expo", "Incidence (95% CI)", "Burden (95% CI)"), caption = "Injury incidence and injury burden are reported as 100 player-matches", align = "c") ## ----------------------------------------------------------------------------- p11 <- gg_rank(injd1, line_overall = TRUE) p12 <- gg_rank(injd1, summary_stat = "burden", line_overall = TRUE) p21 <- gg_rank(injd2, line_overall = TRUE) p22 <- gg_rank(injd2, summary_stat = "burden", line_overall = TRUE) # grid.arrange(p11, p21, p12, p22, nrow = 2) ## ----eval = F----------------------------------------------------------------- # theme2 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 26), # axis.text.x.bottom = element_text(size = 18), # axis.text.y.left = element_text(size = 13), # axis.title.x = element_text(size = 11, vjust = 1), # axis.title.y = element_text(size = 22, face = "bold", vjust = 1)) # # p11 <- p11 + # xlab("Injury incidence") + # ylab("Player-wise incidence (injuries per 100 player-match)") + # ggtitle("2017/2018 season") + # scale_y_continuous(limits = c(0, 80)) + ## same x axis # theme2 + # theme(plot.margin = margin(0.2, 0.2, 0.2, 0.5, "cm")) # p12 <- p12 + # xlab("Injury burden") + # ylab("Player-wise burden (days lost per 100 player-match)") + # scale_y_continuous(limits = c(0, 6110)) + # theme2 + # theme(plot.margin = margin(0.2, 0.2, 0.2, 0.65, "cm")) # # p21 <- p21 + # ylab("Player-wise incidence (injuries per 100 player-match)") + # ggtitle("2018/2019 season") + # scale_y_continuous(limits = c(0, 80)) + # theme2 # p22 <- p22 + # ylab("Player-wise burden (days lost per 100 player-match)") + # scale_y_continuous(limits = c(0, 6110)) + # theme2 # # grid.arrange(p11, p21, p12, p22, nrow = 2) ## ----echo = F, fig.width = 14, fig.height = 11.8------------------------------ theme2 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 26), axis.text.x.bottom = element_text(size = 18), axis.text.y.left = element_text(size = 13), axis.title.x = element_text(size = 11, vjust = 1), axis.title.y = element_text(size = 22, face = "bold", vjust = 1)) p11 <- p11 + xlab("Injury incidence") + ylab("Player-wise incidence (injuries per 100 player-match)") + ggtitle("2017/2018 season") + scale_y_continuous(limits = c(0, 80)) + ## same x axis theme2 + theme(plot.margin = margin(0.2, 0.2, 0.2, 0.5, "cm")) p12 <- p12 + xlab("Injury burden") + ylab("Player-wise burden (days lost per 100 player-match)") + scale_y_continuous(limits = c(0, 6110)) + theme2 + theme(plot.margin = margin(0.2, 0.2, 0.2, 0.65, "cm")) p21 <- p21 + ylab("Player-wise incidence (injuries per 100 player-match)") + ggtitle("2018/2019 season") + scale_y_continuous(limits = c(0, 80)) + theme2 p22 <- p22 + ylab("Player-wise burden (days lost per 100 player-match)") + scale_y_continuous(limits = c(0, 6110)) + theme2 grid.arrange(p11, p21, p12, p22, nrow = 2) ## ----warning = F-------------------------------------------------------------- # warnings set to FALSE p1 <- gg_riskmatrix(injd1, by = "injury_type", title = "Season 2017/2018", add_contour = FALSE) p2 <- gg_riskmatrix(injd2, by = "injury_type", title = "Season 2018/2019", add_contour = FALSE) # Print both plots side by side # grid.arrange(p1, p2, nrow = 1) ## ----eval = F----------------------------------------------------------------- # palette <- c("#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", # Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ # theme3 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), # axis.text.x.bottom = element_text(size = 18), # axis.text.y.left = element_text(size = 18), # axis.title.x = element_text(size = 18), # axis.title.y = element_text(size = 18), # legend.title = element_text(size = 15), # legend.text = element_text(size = 15)) # # ## Plot # p1 <- gg_riskmatrix(injd1, by = "injury_type", # title = "Season 2017/2018", add_contour = T, # cont_max_x = 5.2, cont_max_y = 125, ## after checking the data # bins = 10) # p2 <- gg_riskmatrix(injd2, by = "injury_type", # title = "Season 2018/2019", add_contour = T, # cont_max_x = 5.2, cont_max_y = 125, # bins = 10) # # p1 <- p1 + # scale_x_continuous(limits = c(-0.05, 5.2)) + # scale_y_continuous(limits = c(-0.05, 125)) + # scale_fill_manual(name = "Type of injury", # values = palette) + # guides(fill = guide_legend(override.aes = list(size = 5))) + # theme3 # p2 <- p2 + # scale_x_continuous(limits = c(-0.5, 5.2)) + # scale_y_continuous(limits = c(-0.5, 125)) + # scale_fill_manual(name = "Type of injury", # values = palette) + # keep the same color coding # guides(fill = guide_legend(override.aes = list(size = 5))) + # theme3 # # grid.arrange(p1, p2, ncol = 2, # top = textGrob("Risk matrices", gp = gpar(fontsize = 26, font = 2))) ## for the main title ## ----echo = F, fig.width = 13, fig.height = 5.8, warning = FALSE, message = FALSE---- palette <- c("#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ theme3 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), axis.text.x.bottom = element_text(size = 18), axis.text.y.left = element_text(size = 18), axis.title.x = element_text(size = 18), axis.title.y = element_text(size = 18), legend.title = element_text(size = 15), legend.text = element_text(size = 15)) ## Plot p1 <- gg_riskmatrix(injd1, by = "injury_type", title = "Season 2017/2018", add_contour = T, cont_max_x = 5.2, cont_max_y = 125, ## after checking the data bins = 10) p2 <- gg_riskmatrix(injd2, by = "injury_type", title = "Season 2018/2019", add_contour = T, cont_max_x = 5.2, cont_max_y = 125, bins = 10) p1 <- p1 + scale_x_continuous(limits = c(-0.05, 5.2)) + scale_y_continuous(limits = c(-0.05, 125)) + scale_fill_manual(name = "Type of injury", values = palette) + # get rid off the green (pos: 4) guides(fill = guide_legend(override.aes = list(size = 5))) + theme3 p2 <- p2 + scale_x_continuous(limits = c(-0.5, 5.2)) + scale_y_continuous(limits = c(-0.5, 125)) + scale_fill_manual(name = "Type of injury", values = palette) + # keep the same color coding guides(fill = guide_legend(override.aes = list(size = 5))) + theme3 grid.arrange(p1, p2, ncol = 2, top = textGrob("Risk matrices", gp = gpar(fontsize = 26, font = 2))) ## for the main title ## ----eval = F----------------------------------------------------------------- # gg_prevalence(injd, time_period = "monthly", # line_mean = TRUE) ## ----eval = F----------------------------------------------------------------- # theme4 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), # axis.text.x = element_text(size = 13.5), # axis.text.y = element_text(size = 18), # legend.title = element_text(size = 20), # legend.text = element_text(size = 20), # strip.text = element_text(size = 20)) # # # gg_prevalence(injd, time_period = "monthly", # line_mean = TRUE, # title = "Monthly prevalence of sports injuries") + # theme4 ## ----echo = F, fig.width = 12.8, fig.height = 5.2----------------------------- theme4 <- theme(plot.title = element_text(face = "bold", hjust = 0.5, size = 20), axis.text.x = element_text(size = 13.5), axis.text.y = element_text(size = 18), legend.title = element_text(size = 20), legend.text = element_text(size = 20), strip.text = element_text(size = 20)) gg_prevalence(injd, time_period = "monthly", line_mean = TRUE, title = "Monthly prevalence of sports injuries") + theme4 ## ----eval = F----------------------------------------------------------------- # gg_prevalence(injd, time_period = "monthly", # by = "injury_type", line_mean = TRUE) ## ----eval = F----------------------------------------------------------------- # palette2 <- c("seagreen3", "#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", # Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ # # # gg_prevalence(injd, time_period = "monthly", # by = "injury_type", line_mean = TRUE, # title = "Monthly prevalence of each type of sports injuries") + # scale_fill_manual(name = "Type of injury", # values = palette2) + # theme4 ## ----echo = F, fig.width = 12.8, fig.height = 5.2----------------------------- palette2 <- c("seagreen3", "#000000", Ligament = "#E69F00", Muscle = "#56B4E9", "#009E73", Unknown = "#F0E442", "#0072B2", Bone = "#D55E00", Concussion = "#CC79A7") # source of the palette: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ gg_prevalence(injd, time_period = "monthly", by = "injury_type", line_mean = TRUE, title = "Monthly prevalence of each type of sports injuries") + scale_fill_manual(name = "Type of injury", values = palette2) + theme4