{"title":"Survivorship.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0218","DOIUrl":"https://doi.org/10.1079/9781789245349.0218","url":null,"abstract":"Abstract\u0000 This chapter describes the use of statistical models to determine the factors affecting the survival of killdeer (Charadrius vociferus) nests at gravelled oil pads and on native grass cover in western Oklahoma, USA.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125729856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Statistics: choosing the right test.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0095","DOIUrl":"https://doi.org/10.1079/9781789245349.0095","url":null,"abstract":"Abstract\u0000 Whilst this is not a book on statistics per se, one of the things R is most used for is doing statistical analyses. There are many sorts of statistical analyses and choosing the most appropriate ones can be very confusing for students. This chapter outlines the basic sorts of tests and analyses.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134122600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Installing and running R.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0002","DOIUrl":"https://doi.org/10.1079/9781789245349.0002","url":null,"abstract":"Abstract\u0000 This chapter focuses on downloading and installing R in a computer. Installing packages are also discussed.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"126 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116089141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Population modelling including spatially explicit models.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0303","DOIUrl":"https://doi.org/10.1079/9781789245349.0303","url":null,"abstract":"Abstract\u0000 R is an open-source statistical environment modelled after the previously widely used commercial programs S and S-Plus, but in addition to powerful statistical analysis tools, it also provides powerful graphics outputs. R can be used for some quite fast modelling jobs but its speed is nowhere near that of a compiled programming language such as C++. This chapter shows how user-defined functions can be used to perform highly repetitive jobs efficiently, and demonstrates various mathematical functions. The first example shows how a vector can be incremented and the calculated points plotted on a graph as the simulation proceeds. The second example runs a loop, and each time passes values to a user-defined function, and receives back multiple values from that function, which it then stores for plotting later. The third example is necessarily more complex and shows how R code can be used to carry out spatially explicit analyses. Finally, a simple example shows how R can be used to teach how evolution takes place, even in the absence of natural selection due to genetic drift and population bottle-necking.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127470372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mapping and parsing text input for data.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0021","DOIUrl":"https://doi.org/10.1079/9781789245349.0021","url":null,"abstract":"Abstract\u0000 Increasingly, data are becoming available about the distributions of organisms around the world and are being collated as freely available online resources in various formats. This chapter introduces the maptools library and plot distributions of taxa at country level on maps.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128897290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How to use this book.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0001","DOIUrl":"https://doi.org/10.1079/9781789245349.0001","url":null,"abstract":"Abstract\u0000 This book takes a simple step-by-step approach to give a good grounding in the use of R for undergraduate/beginning postgraduate biology students. R is a freely available, open-source statistical programming environment which provides powerful statistical analysis tools and graphics outputs. This chapter provides some steps on how to use the book, from setting up the computer to running the code as you go along. The chapter structure is also introduced.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127244619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Count data as response variable.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0147","DOIUrl":"https://doi.org/10.1079/9781789245349.0147","url":null,"abstract":"Abstract\u0000 This chapter is devoted specifically to count data for three reasons: (i) they are common in ecological studies (e.g. clutch sizes, numbers of fledglings from a nest, numbers of seeds per pod...); (ii) they are simple to collect and are therefore often the data collected by students (e.g. numbers of beetles in a pitfall trap, number of pollinator visits to flowers...); and (iii) they pose numerous issues that linear models with their normal error structure cannot deal with. Two studies will be examined with the response variable being counts, starting with one that nearly fits the ideals of a Poisson distribution well, the other less so. Example 1 deals with fledgling numbers in relation to clutch initiation date. The data are on the northern cardinal bird, Cardinalis cardinalis, and were collected to test the hypothesis that birds that start their clutches later may suffer higher pre-fledging offspring mortality. Example 2 focuses on pollinator flower visits in Passiflora speciosa in relation to flower size.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123779938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sets and Venn diagrams.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0085","DOIUrl":"https://doi.org/10.1079/9781789245349.0085","url":null,"abstract":"Abstract\u0000 This chapter focuses on sets and Venn diagrams. Venn diagrams, also known as set diagrams, are commonly used to represent the overlap between sets. However, there is no in-built Venn diagram function in R so packages are used.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125899425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Standard distributions in R.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0030","DOIUrl":"https://doi.org/10.1079/9781789245349.0030","url":null,"abstract":"Abstract\u0000 There are a number of in-built probability distributions, including uniform, binomial, negative binomial, normal, log-normal, logistic, exponential, Chisquared, Poisson, gamma, Fisher's F, Student's t, Weibull and others. These are used to generate p-values from test statistics, to generate random values from a distribution or to generate expected distributions. This chapter deals with standard distributions in R (a programming language that has a huge range of inbuilt statistical and graphical functions), focusing on the normal, Student's t, lognormal, logistic, Poisson, gamma, and the Chi-squared.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126937683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"More on apply family of functions - avoid loops to get more speed.","authors":"D. Quicke, B. A. Butcher, R. K. Welton","doi":"10.1079/9781789245349.0322","DOIUrl":"https://doi.org/10.1079/9781789245349.0322","url":null,"abstract":"Abstract\u0000 This chapter focuses on the 'apply' set of functions. These functions are for those who need to process very large datasets, or who need to perform loop-type operations on largish datasets but perhaps in a nested fashion.","PeriodicalId":167700,"journal":{"name":"Practical R for biologists: an introduction","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125451266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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