low-decarie

How to report statistics in a class report or manuscript

This is a work in progress…feel free to suggest

Relevant to : ecology, evolution, behaviour

• Provide all the information required (with the exception of data, which should be linked to in a manuscript) to replicate the test in the "Methods". This may include:
  • Description of the model (response variable, explanatory variable, structure)
  • Reference for more exotic tests or for the application of standard tests in a specific context
• Any data manipulation (transformation, dropped data)

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DI
10.1099/ijs.0-011122-0
10.1099/ijs.0.009191-0
10.1099/ijs.0.009779-0
10.1099/ijs.0.011114-0
10.1099/ijs.0.002865-0
10.1099/ijs.0.007013-0
10.1099/ijs.0.006031-0
10.1099/ijs.0.008193-0
10.1099/ijs.0.002527-0

low-decarie

library("tm")
library("SnowballC")
library("wordcloud")
library("RColorBrewer")

#####
# Load ics data using code from
# https://stackoverflow.com/questions/43573982/how-to-import-ical-ics-file-in-r
###

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stat_smooth_func <- function(mapping = NULL, data = NULL,
                        geom = "smooth", position = "identity",
                        ...,
                        method = "auto",
                        formula = y ~ x,
                        se = TRUE,
                        n = 80,
                        span = 0.75,
                        fullrange = FALSE,
                        level = 0.95,

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#Creates a histogram of publications per year from text currently in the clipboard.  Must be edited for mac or windows.

require(stringr)
require(ggplot2)

#on windows
#text <- readLines("clipboard")


#for a mac

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######################################
## Function that organizes the data so that PGLMM can be fit
## Created by Matthew Helmus
##
## attempt at fixing the function for use with larger data sets
## diag is replaced with Matrix:::Diagonal
######################################

require(Matrix)

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######################################
## Function calls a PGLMM for logistic regression
## Created by Matthew Helmus
######################################

PGLMM.fit<-function(dat=NULL,Y=NULL,X=NULL,VV=NULL,sp.init=0.5,maxit=25,exitcountermax=50) # [B,B0,s,S95int,LL,flag]=PGLMM_nosparse_funct(Y,X,VV,s)
{
    if (!require(corpcor))
    {
      stop("The 'corpcor' package is required")

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gg.candisc.plot <- function(candisc.object){


# Plot with ellipses using ggplot2 ####
require(grid)
require(ggplot2)
require(devtools)
require(digest)
#For info : http://stackoverflow.com/questions/2397097/how-can-a-data-ellipse-be-superimposed-on-a-ggplot2-scatterplot
source_url("https://raw.github.com/low-decarie/FAAV/master/r/stat-ellipse.R") 

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dual_dendogram_tile_plot <- function(data.matrix, main="Title"){

#Dual dendrogram ############

x <- data.matrix
dd.col <- as.dendrogram(hclust(method="ward",dist(x)))
col.ord <- order.dendrogram(dd.col)

dd.row <- as.dendrogram(hclust(method="ward",dist(t(x))))
row.ord <- order.dendrogram(dd.row)

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tell application "Microsoft PowerPoint"
   activate
   
   set theView to view of document window 1
   
   repeat with slideNumber from 1 to count of slides of active presentation
       
       go to slide theView number slideNumber
       
       tell slide slideNumber of active presentation