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View regresion_diagnostics.R
# Model Diagnostics
**Reference only, remove from report before sending to the sponsor**
### Influential Observations
```{r influence_plot, out.extra = "figure", echo = F, warning = F, message = F, comment = NA, eval = F}
influencePlot(mods$iris_data, id.method = "identify", main = "Influence Plot", sub = "Circle size is proportial to Cook's Distance" )
```
View confidence_interval.R
dat %>%
mutate(conf.low = estimate - std.err * qnorm((1 + 0.95)/2),
conf.high = estimate + std.err * qnorm((1 + 0.95)/2))
@pgstevenson
pgstevenson / hist2.R
Created Oct 2, 2019
Create a histogram with a normal distribution overlay in ggplot2
View hist2.R
hist2 <- function(x) {
dat <- tibble(x = x) %>%
na.omit()
ggplot(dat, aes(x = x)) +
geom_histogram(aes(y =..density..),
bins = 30,
colour = "black",
fill = "white") +
stat_function(fun = dnorm, args = list(mean = mean(dat$x), sd = sd(dat$x)))
}
@pgstevenson
pgstevenson / excel_date_dmy.R
Created Sep 24, 2019
Convert the number of days since 1989-12-30 to a dd/mm/yyyy character string
View excel_date_dmy.R
#' Excel Date dmy
#'
#' Excel saves dates as the number of days since 1989-12-30. This needs to be
#' converted into a format that R can use. Unfortunatley, Excel doesn't always
#' store data in a column in the same way for all entries. This function looks
#' at the format of an input character string and if it can be converted to a
#' numeric format it converts the string to a dd/mm/yyyy format.
#'
#' @param x an integer (either numeric or character class) representing a date
#'
@pgstevenson
pgstevenson / VirtualBox_CentOS_7.md
Created Sep 7, 2019
Configuration instructions to get CentOS 7 (minimal) installed on a VirtualBox for Docker
View VirtualBox_CentOS_7.md

VirtualBox configuration (CentOS 7)

  • "Bridged Adapter", check "Cable Connected"

  • edit sudo vi /etc/sysconfig/network-scripts/ifcfg-enp0s3

    • Change to ONBOOT=yes
  • sudo service network start

  • sudo dhclient

  • sudo yum update

View navbar_toc.html
<!DOCTYPE HTML>
<html>
<head>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.1.0/css/bootstrap.min.css">
<title>Navbar from TOC example</title>
</head>
<body>
<span id="nav"></span>
@pgstevenson
pgstevenson / similar_strings.R
Last active Sep 5, 2019
Calculate string distance(s) & group into networks
View similar_strings.R
#### libraries ----
# install.packages("intergraph")
library(dplyr)
library(purrr)
library(furrr)
library(GGally)
library(igraph)
library(stringdist)
@pgstevenson
pgstevenson / paste_clip.R
Created Sep 4, 2019
Function to paste data from clipboard into R
View paste_clip.R
paste_clip <- function(header = TRUE, ...) {
read.table("clipboard", sep = "\t", header = header, ...)
}
@pgstevenson
pgstevenson / copy_clip.R
Created Sep 4, 2019
Function to copy data from R to the clipboard
View copy_clip.R
copy_clip <- function(x, row.names = FALSE, col.names = TRUE, ...) {
write.table(x, "clipboard", sep = "\t", row.names = row.names, col.names = col.names, ...)
}
@pgstevenson
pgstevenson / quick_text.R
Last active Sep 16, 2019
Create text summaries of model output for paragraph insertion, models in lists
View quick_text.R
#' quick_text
#'
#' improvements to biometrics::format_model
#'
#' @param mod_list a list of regression models
#' @param effects (default NULL) a broom::tidy option e.g. "fixed", "random"
#' @param conf.int (default TRUE) a broom::tidy option to generate confidence intervals, logical
#' @param exponentiate (default FALSE) a broom::tidy optoin, logical
#' @param conf.level (default 0.95) the reported confidence interval of model estimates
#' @param dp (default 2) the number of decimal points reported in returned strings
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