padpadpadpad

# try weighted bootstrapping of many curves
# combines approach from weighted bootstrapping and bootstrapping many curves
# https://padpadpadpad.github.io/rTPC/articles/bootstrapping_many_curves.html
# https://padpadpadpad.github.io/rTPC/articles/weighted_bootstrapping.html

# load in packages
librarian::shelf(tidyverse, rTPC, nls.multstart, broom, minpack.lm, car)

# load in data
data("chlorella_tpc")

padpadpadpad

# example of using cowplot and patchwork to make a plot with legends in the bottom right of a four panel plot

# load in packages
librarian::shelf(tidyverse, patchwork, cowplot)

# make a random plot with colour
p1 <- ggplot(mpg, aes(hwy, cty, col = class)) +
  geom_point()

# make other plot with colour on

padpadpadpad

# random modelling example for Stephen

# load in packages
librarian::shelf(rTPC,tidyverse, nls.multstart)

# create data
d <- chlorella_tpc %>%
  filter(curve_id < 4) %>%
  nest(data = c(everything(), -curve_id))

padpadpadpad

# compare Gompertz model to Logistical growth model

# load packages
library(tidyverse) #install.packages(tidyverse)
library(zoo) #install.packages(zoo)
library(broom) #install.packages(broom)
library(growthcurver) # install.packages(growthcurver)
library(nls.multstart) # install.packages(nls.multstart)
# remotes::install_github('padpadpadpad/MicrobioUoE)

padpadpadpad

# muhisse example
# from https://speciationextinction.info/articles/MuHiSSE-vignette.html

# load packages
library(hisse)
library(diversitree)

# simulate simple four state model
pars <- c(.1,  .15,  .2, .1, # lambda 1, 2, 3, 4
          .03, .045, .06, 0.03, # mu 1, 2, 3, 4

padpadpadpad

# example of map2

# load packages
library(nls.multstart)
library(rTPC)
library(tidyverse)

# load data and keep only 2 curves
data("chlorella_tpc")
d <- chlorella_tpc %>%

padpadpadpad

# quick and dirty example of not italicising the whole label.

# Italicise certain words only in facet labels in ggplot2
library(tidyverse)

# create random data frame
species <- c('Chlorella sp.', 'Buteo buteo')

d <- tibble(species = species) %>%
  group_by(species) %>%

padpadpadpad

# try and recreate famous Ed Hawkins climate change spiral graphic in R and ggplot2

# load packages
library(tidyverse)
library(MetBrewer)
library(gganimate)

# load in dataset from NASA
d <- read.csv('https://data.giss.nasa.gov/gistemp/tabledata_v4/GLB.Ts+dSST.csv', skip = 1)
head(d)

padpadpadpad

# nls.multstart example calculating rsquared and RMSE

# load packages
library(nls.multstart)
library(soilphysics)
library(modelr)

# load in data

data("Chlorella_TRC")

padpadpadpad

# load in packages
library(growthcurver) 
library(tidyverse)

# load in example data
d <- growthdata                          # load some sample, simulated data
gc_fit <- SummarizeGrowthByPlate(d)  # do the analysis
plot(gc_fit)                             # plot your data and the best fit
gc_fit$model %>% broom::augment()