SNR_R_GroupRepository for SNR's R User Group
https://chrischizinski.github.io/SNR_R_Group/
Applied Multivarite: Differences between groups
Next up we were utilizing multivariate methods to assess the statistical difference among groups.
Here are the class notebooks covering this material:
R notebook-Discriminant function analysis
Fri, 01 Dec 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-12-01-GroupDifferences
https://chrischizinski.github.io/SNR_R_Group//2017-12-01-GroupDifferencesApplied Multivarite: Latent variable analysis
We spent some time covering the latent variable analysis this semester. Here are the class notebooks covering this material
R notebook-Factor Analysis part 1
R notebook-Factor Analysis part 2
R notebook-Latent Class Analysis
Fri, 13 Oct 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-10-13-LatentVariables
https://chrischizinski.github.io/SNR_R_Group//2017-10-13-LatentVariablesApplied Multivarite: Identifying groups in multivariate data. Part 2
We continue to cover identifying groups in multivariate data. This class will focus on cluster analysis. This is a broad topic and could probably cover most of a semester, if you want more in depth start by looking at: Notebook files R notebook-Cluster part 2 R notebook Rmarkdown file-Cluster part...
Fri, 06 Oct 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-10-06-Cluster2
https://chrischizinski.github.io/SNR_R_Group//2017-10-06-Cluster2Applied Multivarite: Dissimilarity and Distance measures
This class covers an introduction to dissimilarity and distance measures. Detailed notes from previous semesters can be found here: 2016-08-12-SimilarityDistance.
R notebook
R notebook Rmarkdown file
Weekly challenge
Take home challenges
No challenge this week
Fri, 29 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-29-Dissimilarites
https://chrischizinski.github.io/SNR_R_Group//2017-09-29-DissimilaritesApplied Multivarite: Identifying groups in multivariate data. Part 1
This topic will span a couple classes and include topics such as cluster analysis, factor analysis, and latent class analysis
R notebook-Cluster part 1
R notebook Rmarkdown file-Cluster part 1
Fri, 29 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-29-Cluster1
https://chrischizinski.github.io/SNR_R_Group//2017-09-29-Cluster1Applied Multivarite: Data Standardizations (continued)
This class continues to cover an introduction to multivariate statistics and data transformations and standardizations. Detailed notes from previous semesters can be found here: 2016-08-10-Data-Transformations.
R notebook
R notebook Rmarkdown file
Weekly challenge
Take home challenges
No challenge this week
Fri, 22 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-22-Datastandardizations
https://chrischizinski.github.io/SNR_R_Group//2017-09-22-DatastandardizationsApplied Multivarite: Intro to multivariate stats
This class covers an introduction to multivariate statistics and data transformations and standardizations. Detailed notes from previous semesters can be found here: 2016-08-10-Data-Transformations. Introduction presentation Introduction presentation Rmarkdown file R notebook R notebook Rmarkdown file Weekly challenge Take home challenges Input the file from "https://ndownloader.figshare.com/files/2292169" Use data from Rodents only...
Fri, 15 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-15-Introtomultivariate
https://chrischizinski.github.io/SNR_R_Group//2017-09-15-IntrotomultivariateApplied Multivarite: Intro to data visualization with ggplot2
This class covers an introduction to graphing using the functions from ggplot2. Similar to the introduction with tidyverse This is only meant to serve as a brief introduction and we will keep developing these skills throughout the semester. I have similar lessons graphing from a previous semester 2016-10-03-BasicPlots and information...
Fri, 08 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-08-Introtoggplot2
https://chrischizinski.github.io/SNR_R_Group//2017-09-08-Introtoggplot2Applied Multivarite: Intro to Data Wrangling
This class covers an introduction to wrangling and summarizing data using the functions from tidyr and dplyr. This is only meant to serve as a brief introduction, as we will keep developing these skills throughout the semester. I have a similar lesson on data wrangling from a previous semester 2016-09-23-Wrangling...
Fri, 01 Sep 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-09-01-IntrotoDataWrangling
https://chrischizinski.github.io/SNR_R_Group//2017-09-01-IntrotoDataWranglingApplied Multivarite: Intro to R
Welcome back to another semester of our UseR. R script from class Powerpoint from class Weekly challenge The data Work with the ecology data set from datacarpentry. An explanation of the dataset can be found here library(tidyverse)mydata <- read_csv("https://ndownloader.figshare.com/files/2292169")glimpse(mydata) ## Observations: 34,786## Variables: 13## $ record_id <int> 1, 72, 224,...
Fri, 25 Aug 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-08-25-IntrotoR
https://chrischizinski.github.io/SNR_R_Group//2017-08-25-IntrotoRThe Confrontation: Sum of squares
library(tidyverse)library(broom) Sources of the notes for this lecture are from Ecological Detective (Chapter 5). Simplest technique for the confrontation between models and data is sum of squares It is simple and makes few assumptions Long and successful history in science Computers can do remarkable calcualations associated with sum of squares...
Fri, 14 Apr 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-04-14-SumofSquares
https://chrischizinski.github.io/SNR_R_Group//2017-04-14-SumofSquaresIncidental catch in fisheries: seabirds in the New Zealand squid trawl fisheries
library(tidyverse)library(broom) Sources of the notes for this lecture are from Ecological Detective (Chapter 4). Motivation Non-target species are often caught during fishing operations Observer programs are used to monitor this incidental catch Understanding of the coverage of the program and how to interpret the data is needed hauls = c(807,...
Thu, 30 Mar 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-03-30-IncidentalCatch
https://chrischizinski.github.io/SNR_R_Group//2017-03-30-IncidentalCatchEcological Detective - Probability and probability models. Part 2
library(tidyverse)library(broom) Sources of the notes for this lecture are a combination of Aho(2013) (Chapters 2 and 3) and Ecological Detective (Chapters 3 and 4). Common distributions Discrete Negative binomial distribution Negative binomial gives the probability that x independent Bernoulli failures will occur prior to obtaining the rth success - two...
Fri, 17 Mar 2017 00:00:00 -0500
https://chrischizinski.github.io/SNR_R_Group//2017-03-17-EcologicalDetective6
https://chrischizinski.github.io/SNR_R_Group//2017-03-17-EcologicalDetective6Ecological Detective - Probability and probability models. Part 1
library(tidyverse) Classical Probability Sources of the notes for this lecture are a combination of Aho(2013) (Chapters 2 and 3) and Ecological Detective (Chapters 3 and 4). As we become familiar with the behavior of random variables, we may become aware of probabilistic patterns Disjoint If two events can not occur...
Fri, 10 Mar 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-03-10-EcologicalDetective5
https://chrischizinski.github.io/SNR_R_Group//2017-03-10-EcologicalDetective5Six-sided die
What about for a six sided die? Letâ€™s take the coin-flipping example from last week and run a similar test on a six sided dice. Lets run a simulation from 1 to 5000 dice rolls and calculated the proportion of each number. For example, a 1 will be a single...
Fri, 03 Mar 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-03-03-SixSidedDieRolls
https://chrischizinski.github.io/SNR_R_Group//2017-03-03-SixSidedDieRollsEcological Detective - Relationships and probability
Exploring the relationship between two variables First lets bring in the data from the previous lesson library(tidyverse)library(broom) fish_data <- read_csv("https://raw.githubusercontent.com/chrischizinski/MWFWC_FishR/master/CourseMaterial/data/wrkshp_data.csv") ## Parsed with column specification:## cols(## .default = col_character(),## WaterbodyCode = col_integer(),## Area = col_integer(),## MethodCode = col_integer(),## surveydate = col_datetime(format = ""),## Station = col_integer(),## Effort = col_integer(),## SpeciesCode...
Thu, 23 Feb 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-02-23-EcologicalDetective3
https://chrischizinski.github.io/SNR_R_Group//2017-02-23-EcologicalDetective3Ecological Detective - Know your data
Recreating Figure 2.1 in Ecological Detective There are many different hypotheses that can explain the basic relationship between two variables. Figure 2.1 in the Ecologial Detective suggest 4 possible models. The models have no parameter values. Try to iteratively find the parameter values to get your figure to look like...
Fri, 10 Feb 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-02-10-EcologicalDetective2
https://chrischizinski.github.io/SNR_R_Group//2017-02-10-EcologicalDetective2Ecological Detective - Introduction
Ecological Detective Preface: Beyond the Null hypothesis Tools of an Ecological Detective Classic Hypothesis Testing M~1~: Boom and bust (complete extinction between colonizations) hypothesis M~2~: Constant prevalance of population but only is detected when certain conditions arise H~0~: Model M1 is true H~A~: Some other model is true Outcome: M~2~...
Fri, 03 Feb 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-02-03-EcologicalDetective1
https://chrischizinski.github.io/SNR_R_Group//2017-02-03-EcologicalDetective1RMarkdown tutorial
This is just a gentle introduction to what you can do with Rmarkdown. There are lots of tutorials out there to help you further (Software carpentry, Data carpentry). There is also a lot more you can do with it than I have shown here. For example, you can alter the...
Fri, 20 Jan 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-01-20-Rmarkdowntutorial
https://chrischizinski.github.io/SNR_R_Group//2017-01-20-RmarkdowntutorialGetting to know R again (with some new stuff thrown in)
Getting to know R again (with some new stuff thrown in) Using data from Google sheets (kind of) Google Forms is a quick and cheap way to put together an online survey. I asked you all to do the survey through Google Forms so that we can run some of...
Fri, 13 Jan 2017 00:00:00 -0600
https://chrischizinski.github.io/SNR_R_Group//2017-01-13-GettingtoKnowRAgain
https://chrischizinski.github.io/SNR_R_Group//2017-01-13-GettingtoKnowRAgain