In databrew/saint: SAINT

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = NA, 
               echo = TRUE, 
               warning = FALSE, 
               message = FALSE, 
               error = TRUE, 
               cache = FALSE,
  fig.path = "figures/",
  out.width = "100%"
)

cat('Date-time: ', Sys.time())
## Load libraries
library(ggplot2)
library(lubridate)
library(dplyr)
library(readr)
library(gsheet)
library(anytime)
library(databrew)
options(scipen = '999')
ggplot2::theme_set(theme_bw())

# setwd("C:/Users/acasellas/Documents/2020/01_CC_COVID19_saint/SAINT")
# setwd('..')
cat(getwd())
library(readstata13)
library(ggplot2)
data<-data.frame(read.dta13("dta/ana/temp_symptom.dta"))
data_wide<-data.frame(read.dta13("dta/ana/temp_symptom_wide.dta"))
img_name <- paste("html/png/07_evolution_",names(data)[3],".png",sep="")
img_name_prev <- paste("html/png/07_prevalence_",names(data)[3],".png",sep="")
cols <- c("#ffffff","#327ad1")
if(names(data)[3]=="any_symptom") {
  symptom<-"Any symptom"
} else if (names(data)[3]=="fiebre") {
  symptom<-"Reported fever"
} else if (names(data)[3]=="tos_si_no") {
  symptom<-"Cough"
} else if (names(data)[3]=="malestar_si_no") {
  symptom<-"General malaise"
} else if (names(data)[3]=="dolor_cabeza") {
  symptom<-"Headache"
} else if (names(data)[3]=="anosmia") {
  symptom<-"Anosmia and/or hyposmia"
} else if (names(data)[3]=="mal_sabor") {
  symptom<-"Dysgeusia"
} else if (names(data)[3]=="fatiga_si_no") {
  symptom<-"Shortness of breath"
} else if (names(data)[3]=="congestion_si_no") {
  symptom<-"Nasal congestion"
} else if (names(data)[3]=="gi") {
  symptom<-"Gastrointestinal"
}


names(data)[3]<-"symptom"
data$studyno<-factor(data$studyno,levels=data_wide$studyno)
data<-data[which(data$day>=1),]

library(ggplot2)
library(gridExtra)

theme_black = function(base_size = 12, base_family = "") {

  theme_grey(base_size = base_size, base_family = base_family) %+replace%

    theme(
      # Specify axis options
      axis.line = element_blank(),  
      axis.text.x = element_text(size = base_size*0.8, color = "white", lineheight = 0.9),  
      axis.text.y = element_text(size = base_size*0.8, color = "white", lineheight = 0.9),  
      axis.ticks = element_line(color = "white", size  =  0.2),  
      axis.title.x = element_text(size = base_size, color = "white", margin = margin(0, 10, 0, 0)),  
      axis.title.y = element_text(size = base_size, color = "white", angle = 90, margin = margin(0, 10, 0, 0)),  
      axis.ticks.length = unit(0.3, "lines"),   
      # Specify legend options
      legend.background = element_rect(color = NA, fill = "black"),  
      legend.key = element_rect(color = "white",  fill = "black"),  
      legend.key.size = unit(1.2, "lines"),  
      legend.key.height = NULL,  
      legend.key.width = NULL,      
      legend.text = element_text(size = base_size*0.8, color = "white"),  
      legend.title = element_text(size = base_size*0.8, face = "bold", hjust = 0, color = "white"),  
      legend.position = "right",  
      legend.text.align = NULL,  
      legend.title.align = NULL,  
      legend.direction = "vertical",  
      legend.box = NULL, 
      # Specify panel options
      panel.background = element_rect(fill = "black", color  =  NA),  
      panel.border = element_rect(fill = NA, color = "white"),  
      panel.grid.major = element_line(color = "grey35"),  
      panel.grid.minor = element_line(color = "grey20"),  
      panel.margin = unit(0.5, "lines"),   
      # Specify facetting options
      strip.background = element_rect(fill = "grey30", color = "grey10"),  
      strip.text.x = element_text(size = base_size*0.8, color = "white"),  
      strip.text.y = element_text(size = base_size*0.8, color = "white",angle = -90),  
      # Specify plot options
      plot.background = element_rect(color = "black", fill = "black"),  
      plot.title = element_text(size = base_size*1.2, color = "white"),  
      plot.margin = unit(rep(1, 4), "lines")

    )

}

pd <- data %>%
  group_by(day, treat) %>%
  summarise(n = n(),
            yes = length(which(symptom == 'Yes')),
            no = length(which(symptom == 'No'))) %>%
  ungroup %>%
  mutate(p = yes / n * 100)

library(tidyverse)
base_size <- 11
cols <- rev(c('#5F7470','#66101F'))

ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 0.3) +
  geom_line(stat="smooth",
              size = 3.5,
              alpha = 0.5) +
  theme_void(
    base_size = 11,
    base_family = "",
    base_line_size = base_size/22,
    base_rect_size = base_size/22
  ) +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom')

cols <- c('darkorange','lightblue')

ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 0.3) +
  geom_line(stat="smooth",
              size = 3.5,
              alpha = 0.5) +
  theme_linedraw() +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom')

cols <- c('red','darkgrey')

ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 0.6) +
  geom_line(stat="smooth",
              size = 3.5,
              alpha = 0.8) +
  theme_black() +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom') +
  labs(x = 'Day',
       y = '% anosmia') +
  guides(fill=guide_legend(nrow=1,byrow=TRUE))

cols <- rev(c('#5F7470','#66101F'))
ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 1, size = 4) +
  geom_line(size = 3, alpha = 0.8) +
  # geom_line(stat="smooth",
  #             size = 3.5,
  #             alpha = 0.8) +
  theme_black() +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom') +
  labs(x = 'Day',
       y = '% anosmia') +
  guides(fill=guide_legend(nrow=1,byrow=TRUE))

cols <- rev(c('#5F7470','#66101F'))
ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 1, size = 1) +
  geom_line(size = 0.2, alpha = 0.8) +
  geom_line(stat="smooth",
              size = 1.4,
              alpha = 0.8) +
  theme_minimal() +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom') +
  labs(x = 'Day',
       y = '% anosmia') +
  guides(fill=guide_legend(nrow=1,byrow=TRUE))

cols <- rev(c('darkorange','lightblue'))
ggplot(data = pd,
       aes(x = day,
           y = p,
           color = treat,
           fill = treat)) +
  geom_point(alpha = 1, size = 1) +
  geom_line(size = 0.4, alpha = 0.8) +
  geom_line(stat="smooth",
              size = 1.8,
              alpha = 0.8) +
  theme_minimal() +
  scale_fill_manual(name = '',
                    values = cols) +
  scale_color_manual(name = '',
                    values = cols) +
  theme(legend.position = 'bottom') +
  labs(x = 'Day',
       y = '% anosmia') +
  guides(fill=guide_legend(nrow=1,byrow=TRUE))