In GegznaV/BioStat: Routines for Basic (Bio)Statistics

knitr::opts_chunk$set(echo = TRUE)

library(Hmisc)
library(MASS)
library(tidyverse)
library(biostat)
library(ggridges)

hist(sort(rnorm(1e5)))

Sitka

Sitka89

SP500

Traffic %>% glimpse()

glimpse(UScereal)

psych::describe(UScereal)  %>% 
    pander::pander()

mad(UScereal$calories)

ggplot(anorexia, aes(x = Prewt, y = Postwt, color = Treat)) +
    geom_point() +
    geom_smooth(method = "lm", se = FALSE)

anorexia2 <-
    anorexia %>% 
    mutate(diff_wt = Postwt - Prewt)

ggplot(anorexia2, aes(x = Treat, y = diff_wt)) +
    geom_boxplot()

ggplot(anorexia2, aes(x = Treat, y = diff_wt, color = Treat)) +
    geom_violin() +
    geom_jitter(width = .1) +
    coord_flip()

ggplot(anorexia2, aes(x = diff_wt, fill = Treat)) +
    geom_density(alpha = 0.3, adjust = 1.6) +
    coord_flip()

ggplot(anorexia2, aes(x = diff_wt, y = Treat, fill = Treat)) +
    geom_density_ridges(alpha = 0.3, scale = 0.9, bandwidth = 5)

ggplot(anorexia2, aes(x = diff_wt, fill = Treat)) +
    geom_density(alpha = 0.3, adjust = 1.6) +
    coord_flip()

anorexia3 <- anorexia  %>% 
    mutate(id = row_number()) %>% 
    gather(key = "time", value = "weight", Prewt, Postwt)  %>% 
    separate(col = time, into = c("time", "del"), sep = -2)  %>% 
    select(-del)  %>% 
    mutate(time = fct_relevel(time, "Pre", "Post"))

ggplot(anorexia3, aes(x = time, y = weight, group = id)) +
    geom_line() +
    geom_point(color = "orange") +
    facet_grid(. ~ Treat)

qq_plot(diff_wt ~ Treat, data = anorexia2)
biostat::test_normality(diff_wt ~ Treat, data = anorexia2)
PMCMR::posthoc.kruskal.conover.test(diff_wt ~ Treat, data = anorexia2) %>% 
    make_cld()

Bin        Freq   Cum_freq   Percent   Cum_percent

---

4.3 -- 5.0 32 32 21.3 % 21.3 % 5.0 -- 5.7 41 73 27.3 % 48.7 % 5.7 -- 6.5 42 115 28.0 % 76.7 % 6.5 -- 7.2 24 139 16.0 % 92.7 % 7.2 -- 7.9 11 150 7.3 % 100.0 %

Table: Frequency table

| Bin | Freq | Cum_freq | Percent | Cum_percent | |:----------:|-----:|---------:|--------:|------------:| | 4.3 -- 5.0 | 32 | 32 | 21.3 % | 21.3 % | | 5.0 -- 5.7 | 41 | 73 | 27.3 % | 48.7 % | | 5.7 -- 6.5 | 42 | 115 | 28.0 % | 76.7 % | | 6.5 -- 7.2 | 24 | 139 | 16.0 % | 92.7 % | | 7.2 -- 7.9 | 11 | 150 | 7.3 % | 100.0 % |

Table: Frequency table

---

Bin        Freq   Cum_freq   Percent   Cum_percent

---

4.3 -- 5.0 32 32 21.3 % 21.3 %

5.0 -- 5.7 41 73 27.3 % 48.7 %

5.7 -- 6.5 42 115 28.0 % 76.7 %

6.5 -- 7.2 24 139 16.0 % 92.7 %

7.2 -- 7.9 11 150 7.3 % 100.0 %

Table: Frequency table

GegznaV/BioStat documentation built on Aug. 14, 2020, 9:30 p.m.