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Introductory Applied Statistics for the Life Sciences

by: Mrs. Triston Collier

Introductory Applied Statistics for the Life Sciences STAT 371

Marketplace > University of Wisconsin - Madison > Statistics > STAT 371 > Introductory Applied Statistics for the Life Sciences
Mrs. Triston Collier
GPA 3.57


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This 4 page Class Notes was uploaded by Mrs. Triston Collier on Thursday September 17, 2015. The Class Notes belongs to STAT 371 at University of Wisconsin - Madison taught by Staff in Fall. Since its upload, it has received 17 views. For similar materials see /class/205079/stat-371-university-of-wisconsin-madison in Statistics at University of Wisconsin - Madison.


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Date Created: 09/17/15
STAT 371 Discussion 11 Diagnostics of ANOVA Model and Multiple Comparison Review of lecture examples and R function learning 1 Steps of Working on ANOVA Model 11 Load data into R 1 Create your dataset using notepadsave as txt or excelsave as csv 2 Set the working directory using setwd 3 Import data using readtable for txt file and readcsv for csv file 12 Fit an ANOVA model use aovyx data function 1 y is the response For example you want to compare the mean weight of several groups of rats then the weight is y 2 x is the variable indicating groups 13 Checking the model assumptions 1 Underlying populations normally distributed QQ plot of residuals 2 Underlying populations have equal variance residual vs fitted 3 Observations are independent residuals against index of observation or time order of taking observations and so on 14 Transformation 1 Log transformation When the plot of residuals vs fitted values show a right open mouth horn shape Use log in R 2 Square transformation When data are counts Use is sqrt in R 15 Multiple comparisons 1 Unplanned comparisons and planned comparisons 2 Adjustment of significance level for multiple comparisons 7 Bonferroni adjustment and Tukey adjustment 2 Example for model assumptlon checklng 21 Load data 1nt0 R i110 lt7 readcsvquothltpwwwbinstalwiscedukbrnmanteachingslmj71i110xsvquot The tlrst 15 observatlons of dataset 1110 straln ILlU 22 Flt an ANOVA model use aovyx data tunctlon l Flt model aovi110 lt aovIL10 Strain datau10 2 Use anovaO to get the ANOVA table anovaaov1110 Response ILlU Df sum s Mean sq F value PrgtF straln 3757424 1687871 17001 004154 Reslduals l25 124099169 23 Checklng the model assumpuons lUnderly1ng populatlons normally dlstrlbuted QQ plot pam colc22 specify the layout of plate 07 Four plots use the Normal QeQ39 plot SCa eiLocalmn Resvdua S vs Fltled 34 s g 13 3 g 5 E 3 SUD IEUD g Fmed values Fmed va ues Normal Q Q Residuals vs Leverage c so ya 72 012 standardren msmuuls 2 2 o Theoreucm Guanmes Leverage z Underlylng populatluns have equal Varlance resldual plats vse plat Reslduals vs Fltted glven n 1 Observatluns are ndependent vntlun nd between groups 3 a Reslduals agalnst ndex of observatlun plnuanvdll sxesldh anv ll10resld 1000 ndex The reslduals are evenly dlstrlhuted nat correlated tbus ndependent 4 Transformatlun algbteapenenautb barn sbape lug transformatlun 5 Ref the ANOVA model uslng luglILID nstead of ILJD for respanse anv1nqlll lte anvungublnl s straln dataeulnl 5 check made assumptluns for model auvluglD 3 Example for Hultlple Comparlsuns Unplanned 31 Use dataset In last Frlday s lettare better use excel ta create a alataset rep lte c175677 75657l676776EE 575asn59szsnsn5759sl 5E61565E5756616 5753 5a595sal575s5a575759 aas55s3sasza5s5az67l ttt lte faclnx1xeptct c l llsbllsllreplln5ll suqax lte dalafxamz1xsp ttn 32 F ANovA model anvnnt lte anvlrsp ttt dalasuqax annvannt lte annualanvnntl 32 Unplanned pair wise comparisons compare mean response of each pair of groups 1 Bonferroni adjustment sourcequothttpwww biostatwiscedukbr0m anteachingstat371func29Rquot sugarbonf lt cibonfsugarrsp sugarttt sugarbonf est lower upper C F 11 9 909056 1470944 C G 10 8 799056 1360944 C GF 12 1 929056 1490944 C S 60 319056 880944 F G 11 390944 170944 F GF 02 260944 300944 F S 59 870944 309056 G GF 13 150944 410944 G S 48 760944 199056 GF S 61 890944 329056 No significant difference if confidence interval covers 0 2 Tukey adjustment sugartuk lt TukeyHSDaovout sugartukttt diff 1wr upr p adj FC 119 14868072 8931928 3370637e13 GC 108 13768072 7831928 2079004e12 GFC 121 15068072 9131928 3010925e13 SC 60 8968072 3031928 7223105eO6 GF 11 1868072 4068072 8291029e01 GFF O2 3168072 2768072 9996878e01 SF 59 2931928 8868072 9983469eO6 GFG 13 4268072 1668072 7256157e01 SG 48 1831928 7768072 3242398eO4 SGF 61 3131928 9068072 5222269eO6


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