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BIO773P Analysis Assignment

创建日期：2024-05-14 17:53:12

所属分类：生物biology

标签： BIO773P

Analysis Assignment

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BIO773P Analysis Assignment

Introduction
You have been allocated a unique dataset to analyse. To find yours, look at the table
at the end of this document. Your datasets are supplied as .csv files in a zip archive
called “Data.zip. Having read the description of the way the data were collected, you
need to import each dataset into R. Remember to check the datasets when you import
them for things like proper allocation of each variable as a factor or a numeric
variable, and to carry out proper exploratory data analysis. Once you're happy that
you've got the data into a condition where it can be analysed, fit a model and use that
to try to answer the questions given below. Your writeup should consist of two
documents: a properly annotated R script that will allow me to exactly replicate your
analysis, and the results section of a paper describing your findings. The latter should
be no more than 1000 words (and can be a lot less...) and should not contain any
unnecessary figures or tables: I would recommend no more than two figures. If in
doubt have a look at some papers in (for example) Proceedings B or Journal of
Animal Ecology to see how it's done. Please don’t paste output from R directly into
your report, by which I mean don’t just paste a summary table or an ANOVA table in,
not that you shouldn’t use graphics from R.
The deadline for this work is 5PM on Friday 4th November, submission via QM+
please.
Endophytic fungi and plant growth
Many plants harbour endophytic fungi, and these often seem to exist in mutualistic
relationships with their hosts: plants harbouring endophytes have increased growth
and vigour and the fungus benefits from a ready supply of sugar and a protected place
to live. Some recent work, however, has suggested that this mutualism only holds
under some environmental conditions and that when nutrients are limiting it can break
down. Here, you have the data from two experiments investigating the nature of this
mutualism in red fescue grass, Festuca rubra. In the experiment, seeds of the grass
from a cultivar that is known to house endophytic fungi were grown in three nutrient
treatments: a high nutrient condition with 10ml of 3g.L-1 20-20-20 NPK fertiliser
applied biweekly, a medium nutrient condition with 3ml of fertiliser and a low
nutrient condition which received tap water.
After 11 weeks all plants were harvested by cutting at soil level. A sample was taken
of the leaf sheath, mounted on a microscope slide, stained with aniline blue and
examined at x400 on a compound microscope. The number of hyphae present in three
800 um diameter fields of view were counted as an indication of the degree of
infection of each plant. Leaf area was measured by arranging the plant on a clean flat
surface, photographing the plant next to a scale and then using the image analysis
programme ImageJ to measure the area.

Report
For the report, please use an appropriate analysis to produce a results section which
addresses the following questions:
1) How is leaf area related to the degree of infection in F. rubra?
2) Is this relationship dependent on nutrient supply, and if so how?

General feedback from previous years
Overall, I was impressed with the standard of most of these reports. Most of you
managed to get the analyses more or less right, and most of you produced good-
quality scripts. None of them had too much annotation - remember that when you’re
annotating a script you’re really writing a guide to yourself describing what it does.
Think about the information that might be useful if you come back to the analysis a
year or two in the future.
Regarding the “results section” of the reports, these were a lot more variable. Many of
you put too much analysis into these, and in particular included material that would
not normally go in a journal results section. Preliminary and exploratory analysis,
diagnostic plots and the like are not generally included in journal results sections.
Many of you had redundant graphs – you shouldn’t show the reader the same set of
data twice. A common problem was too much focus on the statistics and not enough
on what the statistical results mean in terms of the biology of the system, or in terms
of effect sizes: don’t just tell me that there’s an effect, tell me how big the effect is,
and put it in meaningful biological terms.
Figure captions are something that most of you need to work on. When you’re writing
a figure caption, it’s a good idea to try to write it so that a casual reader who is
skimming through the paper can look at the figure, have a look at the caption and
have at least a rough idea about what the figure is showing. That doesn’t mean that
each figure should have the whole methods section reproduced, but you can include a
sentence or two that gives the casual reader a basic idea of what’s going on.
Other common problems included:
• Including p-values without test statistics or degrees of freedom
• Including multiple tests of the same thing (e.g. using a post-hoc test on a fitted
model, collapsing two factor levels and then comparing models with a partial
F-test)
• Carrying out tests for normality on data prior to analysis (I explained in one of
the lectures why this is a bad idea)
• Mixing p-values and AIC as criteria for model selection - the philosophy
behind these is very different and you should use one or the other but not both.
• Giving significance levels for main effects when they are also included in
higher-order interaction terms

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COMP532 MAS275 COMP5318 COMP4002 FIT5086 MAST20004 FIT3152 FIT5129 CIS2380 CS521 COMP 1005 EECMS CITS5501 ECE 462 ECON 6002 ENG 4051 CSC 648 CMT654 MECHENG 713 PHYS1002 AMME 2000 FP0060 DDES3200 MECHENG 743 BINF90002 FIT2081 ISYS90081 ELECTENG 722 BUS 360 ECOS3010 BUS2810 ETF2100 ENG2048 STAT5002 COMP2017 CEME 2003 MATS3004 COMP9319 PHYS1001 COMP5349 AMME2261 COMP-381 FIT3173 COSC2757 ENG4025 QBUS2820 COMP9414 MATH2021 EOSC118 MFIN6690 PMATH 321 CSE-141L MATH575A COMPSCI5002 COMP1511 management comp2123 FINS3616 COMP 3331 COMS30034 DTSC 71 AcF 702 AcF702 DTSC71 MAT021 ELE8083 ACFI213 EG-127J 127J FIT5163 FIT2001 ELE00113M CMT310 CS 245 ENGL 1101 MTH6115 EE497 CS 325 Math 124A MTH5130 MBA502 MGT 5380 ARCH 1261 F033800 20LLP109 ELE4009 FINANCIAL COMP3331 Computer ECE4179 20T3 COMP9311 COMP9311 UNSW MFIN6210 ACCT 5930 EE590 ENG2029 ECO100 SIT315 ACCT3610 COMP3600 STK2100 FIT2004 COMP30020 ACTL1101 Stat 101B BANA 200 COSC2473 ENGG1400 AI COMP90043 MMF 1914H PHYS 127 CS584 CIVL2010 ECMT2150 CS 333 CP1406 KIT308 Economics 701 ECON3740 ECE 5759 BFC3340 FINC2012 COMP4500 MATH3871 FIT3080 18-819C Economic ECO202Y5Y PHY100 FINC-780 Econ 100B EC602 IE582 EE450 COMP9517 WRDS 150B ECON 570 LECTURE 2 ECA5101 ECE 4420 ADAD9311 FIT3031 CS 544 MF 703 CS 6140 KIT501 ENGSCI 344 CSC171 IE 332 FINM8007 21S2 COSC 1114 FE545 E471 SIT102 CSC108 MAT301 IAE 101 COP3503 STAT2004 EC 303 CS1026 STAT1203 MATH3171 ISOM5160 IFN657 FIT2014 ACCT2102 DSCI550 STATS 330 ELEC421 COMP3670 QBUS6840 MEES:698B MAST30027 MIET1077 Economics IFT 6758 FIT5122 BUSN5101 CptS 111 HRMT5502 Math2018 PP 312 INFS3200 CZ3005 CSSE1001 SENG 2011 MKTG 553Q BUFN 640 COMP507 ETF5952 DATA 311 ECE4043 BANK3011 finance M3H623544 HW1 INFS 7410 AI6103 STAT3888 INFS3208 ACCT7103 ECOS3013 PSYCH 20B F79MA STAT3006 ENGG952 2X MGSC 7000 ECE4132 MSF 526 MATH 3033 CDS 511 EEEE4120 EEET2465 ECA5103 MATH2070 ELEC3104 BU51019 EEE8147 ENGR20003 COSC 1107 ETF3200 FNCE 435 MSFI 435 ISyE6420 GENG4405 HW ETC5523 IE 7315 MOEC0021 STA 106 ENGG 1300A ENGG 1300 OLET1139 STAT 3503 STAT 206 FEM11149 ELEN 4720 COMP20003 SOLA1070 CS574 C11CS LINB29H3 MAST90083 ECON7200 STAT 610 LINB29 DSM-5 COMP3161 EEEN40010 MATH 4431 K353 STA 3386 IERG4300 COMS W4167 ENG5298 AMME 2302 CS3910 COMPSCI 320 STATS 369 GR5242 COSC 328 CSCI435 MGTS1301 INFS2200 COMP3900 CIS 375 Module AE03 COMP3121 CS260 HAM503 MGMT5050 INT3075 COSC 285 GEOL0029 GEGE2X01 STAT1201 MATH1061 MMF1941H STAT 5060 CS 520 COMP 4320 MSIN0104 000T FINS3648 ECMT2160 ECON4003 Phys 129L CSE 142 CS 3130 MGEB01 EECS 340 Finance (20443/20444) ECMM149 COMP5310 EEEN60180 CSC 111 AT2 CSCI 4430 STAB57 MA/CSC 427 MATH322 D100 CSCI544 CITS3004 CI6227 CSE 565 APCO 1P01 852L1 ELEC S411F COMP3207 STATS330 ECON7530 FIT5149 CSI4104 CMPT 371 COMP201 SEHS4696 FI4003 MATH6182 CG1 WS MATH401 MGT 205 QTM 110 COMP 0137 MACE12201 FIT5210 ECE 544 BISM7206 HUDM 6055 ECON3203 STATS 210 MSCI 570 MATH6173 COMPSCI4039 Accounting COM3503 AOE2024 ECON213 PSYC10004 Control Data 100/200A PHIL2617 PHYS3116 MIE250 BCPM0008 ECN 620 QBUS6830 ECSE-415 ECON5102 MGMT20005 MAT 653 ECO 480 COMP 5/600 CSSE 5600 ME 571 7CCMMS61 CS 550 COMP2865 MATH3075 STATS 506 QTM 220 ISYS2120 FIT5106 STAT 153 MKTG3112 ECON2102 ELE2018 COMP3031 MSIN0010 SCC461 MATH237 CS246 CSC3065 CSE 101 ICTWEB411 COMP9313 ECOS 2025 FN620 MATH11111 MATH 3018 KE1068 FINA 6112 C++ MISM 6202 MSIN0105 CSC8631 MECO6935 COMP4121 ACCT2011 DPBS1150 EEL 3701C F19PL OPM 661 CSE 310 CS918 BIOL30001 ACCT3563 BANK3600 MET CS622 MATH367 ACCT5907 Continuing COMP5048 COMP61021 CS3334 GSOE9210 CSCI-570 COMP 5322 HW 2 ALY-6020 IEOR 4706 DATA 200 EBUS504 CGE12412 COMP4108 7SSMM800 ECMM171P MATE50002 CS225 RS 6003 BH2274 ELEC3111 MAT6669 ECON-UA 227 PHIL 1012 7SSMM603 TB028A P6 ECS708 CSC 427 CS6476 CSE 250A A1A2 ITS61504 EECS 376 model HW6 UV0010 ECON 6074 MG4F7 CMP-7030Y INFO3008 BFIP013 ECON 5068 MATH6002 CS3483 PSTAT 131 C31FM CSOR W4246 AAEC 5307 DATA ELEC362 COMSM0047 ECN6006 MA20224 BST351 MATH 323 MATH323 AA2021 COMP3811 COMP2013 IB9X60 INVP001 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ATMS 201 COMP3425 MATH7861 SOLA2060 MA 325 7CCEMCTH ECON 432 INFT2051 SOLA 2060 ECOS2002 Stats141XP BIOA02H3 S2022 MA4601 K5 COMP5329 EG 284 IB3A70 WECO1020 COMP3027 Energy ACS61011 MAST20026 STAT 533 MATA31 ENVS257 BEM2031 EC 486 COMP0172 CS3214 EECE5644 IB2B20 COSC2536 COSC1147 COMP6214 5CCM242A COMP0130 AMME2000 MTMG50: EG238 ACF6006 QBUS2810 COSC2391 ECON7560 MATH377 STA305 CS 486 COMP1117B EL648 ELEC3909 ECON 241 COMP 4901W BUSI4428 ENEN20002 ENGN4524 ELEC3115 CSC 413 PSYC 100B ECON1002 MATH256 ANSC20005 MTHS2008 MATH40082 COSC 2406 FIT3174 STA 238 CMT202 Differential Equations MTHM017 GARCH 101 MATH2069 CSC336S ACSC12 ETF2121 CEME 2001 DB B474F ARHT1001 EECS 3311 3220 STATS 786 CS 484 COMP20008 MATH4091 ECE 455 CSCI 204 BUS B200F BA 875 BU5562 COSC 1147 X11 GEOG 101 IMM250F CSE 584A MATH38172 LAB 4 ELEC5882M FINS5523 EE 430 COMP 465 6CCS3PRE 7CCSMNSE FINANCE ACMB02H3 ENGG2112 ELEC5616 SCM B371 CHEM3120 CS22 ECMT2130 MAST30011 ADSPBF706 CENG0013 ACCOUNTING BUSS1040 CHEM 181 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