Myfanwy

# About time in R
# M. Johnston
# Thu Aug 10 13:06:35 2023 America/Los_Angeles ------------------------------

#---------------------------------------------------------# 
# Takeaway: For date-times in R (POSIXt objects), there are differences between what 
# your R session references, stores, and displays.  It's very important to be aware 
# of these differences to avoid date time gotchas.
#---------------------------------------------------------#

Myfanwy

install.packages(c('rmarkdown', 
                    'knitr', 
                    'lubridate', 
                    'ggplot2', 
                    'data.table', 
                    'readxl',
                    'RSQLite',
                    'dplyr'
                   )
                 )

Myfanwy

library(tidyverse)

# Previous version of SBM used 120 mm cutoff for rearing
# Exploring idea of using hypothetical continuous relationship between rearing probability and fork length

## Four-parameter logistic model gives nice control over the curve
# a = max value
# b = steepness of the curve
# c = inflection point
# d = min value

Myfanwy

#--------------------------------------------#
# ARTEMIS Demo
# Stantec presentation, 2020-03-03
# M. Johnston, Cramer Fish Sciences
# This script presents an introduction to data simulation in {artemis}.
#--------------------------------------------#

# Goal: Simlulate data and visualize relationships

#-------------------------------------------------------#

Myfanwy

# separates the vemco column formatting of freq-codespace-tagid, then returns the original dataframe with the codespace and tagids as separate columns

parse_tag_info <- function(df, tagcol = "TagID") {
  names(df)[names(df) == tagcol] <- "SepTagID" # rename the old combined tagid col
  out <- as.data.frame(do.call(rbind, strsplit(as.character(df$SepTagID),'-')), 
                       stringsAsFactors = FALSE)
  
  colnames(out) <- c("freq", "CodeSpace", "TagID")
  final <- cbind(df, out)
  drops <- c("freq", "SepTagID")

Myfanwy

If the original vrl files are unavailable, a drift-correction needs to be performed on the .csv file for each receiver in a deployment. You will need at least a .vdb with the receiver log of interest to be able to do this.

To do this, access the events tab in VUE for a receiver download. Export it to a csv.

Open it in Excel. Make sure the PC Time (very last cell in the Description column) is in an acceptable date/time format. Do this by copying and pasting it to the cell below it, and using the custom m/d/yyyy hh:mm:ss.00 format.

Events Tab:

In a new column, calculate the time between initialization and end time (days). Do this by subtracting A1 from the final cell in the A column. This is done in J2 in the example
Covert J2 to seconds (multiply by 84600). This is done in K2.

Myfanwy

hedgehog tweet

treerantula thread

that is a golden retriever

Myfanwy

#Goal: identify fieldwork periods by finding high tide on for each of the next 2 weeks.

# There are two high tides per day.  A high high tide and a lower high tide.  Adding ~25.3 hours to each one, respectively, gives you the # date/times of the next ones.

# So for the two high tides on 1/1/19:
tides <- structure(c(1546341300, 1546384500), class = c("POSIXct", "POSIXt"
), tzone = "Pacific/Pitcairn")

# adding 25.3 hours to this vector gives us the date/times of the next two high tides:
tides + as.difftime(25.3, units = "hours").

Myfanwy

# Depends on the `beepr` package by @rasmusab: https://cran.r-project.org/web/packages/beepr/README.html
# Code greatly improved by flodel on Stack Exchange Code Review (thanks flodel)
# Planned improvements/expansions: new end-of-timer sounds, add functionality for starting a separate R session so that it doesn't bogart the current one.

timer <- function(interval, units = c("secs", "mins", "hours", "days", "weeks")) {
   units <- match.arg(units)
   num_sec <- interval * switch(units, secs = 1, mins = 60, hours = 3600,
                                       days = 86400, weeks = 604800)
   Sys.sleep(num_sec)
   if (require(beepr)) beep(2) else message("TIMER DONE YO!")

Myfanwy

tt %>% 
  mutate(
    laststation = as.character(laststation),
    TagID = as.character(TagID)
  ) %>% 
  group_by(laststation) %>% 
  ggplot(aes(TagID, kmday)) +
  geom_segment(aes(xend=TagID, yend=0)) +
  geom_point(shape="—", size=5) +
  facet_wrap(~laststation, nrow=1, scales="free_x") +