SCH 1999 IRRI Biodiversity Software Series. V. RARE, SPPDISS, and SPPRANK: Programs for Detecting Between-Sample Differences in Community Structure Developed by K.G. Schoenly and WJ. Zhang INTERNATIONAL RICE RESEARCH INSTITUTE“The International Rice Rescarch Institute (IRR) was established in 1960 by the Ford and Rockefeller Foundations with the help and approval ofthe fovemment ofthe Philippines. Today IRRI is one of the 16 nonprofit in- temational research centers supported by the Consultative Group on Inte ‘national Agricultural Research (CGIAR). The CGIAR is sponsored by the FFood and Agriculture Organization of the United Nations, the International ‘Bank for Reconstruction and Development (World Bank). the United Na- tions Development Programme (UNDP), and the United Nations Environ- ‘ment Programme (UNEP). lis membership comprises. donor counties. jonal organization, and private foundations. ‘As listed in its most recent Corporate Report. IRRI receives support, through the CGIAR. from a number of donors including UNDP, World Bank, European Union, Asian Development Bank. Rockefeller Founda- tion, and the international aid agencies of the following governments: Australia, Belgium, Canada, People’s Republic of China, Denmark, France. Germany, India Indonesia, Islamic Republic of Iran Japan, Republic of Korea, The Netherlands, Norway. Peru, Philipines. Spun, Sweden, Swit- zerland, Thailand, United Kingdom. and United States. “The responsibility for this publication rests with the International Rice Research Institute IRRI Technical Bulletins ‘The IRRI Technical Bulletin is «rapid means of presenting results of re= ‘search on a specialized technical subject such as the development of ex- perimental methods, specialized software, or other solutions to complex research problems. Copyright International Rice Research Institute 1999 “Mailing Address: MCPO Box 3127, 1271 Makati Cit Phone: (63-2) 845-0563, 844-3351 to 53 Fax: (63-2) 891-1292, 845-0606 Enuil: IRRI@CGIAR.ORG ‘Telex: (ITT) 40890 Rice PM: (CWT) 14519 IRILB PS Cable: RICEFOUND MANILA URL: hupywww.cgiarorg isi Riceweb: hipa/www.riceweb.org Riceworld: hp:/lwwwriceworld.org Courier address: Suite 1099, Pacific Bank Building 6776 Ayala Avenue, Makati Metro Manila, Philippines ‘Tel. (63-2) 891-1236, 891-1174, 891-1258, 891-1303 Philippines Suggested citation: Schoenly KG. Zhang WJ. 1999. IRRI Biodiversity Software Series. V. RARE, SPPDISS. and SPPRANK: programs for detecting between-sam- ple diferences in comunity structure. IRRI Technical Bulletin No. 5. Ma nila (Philippines): Intemational Rice Research Institute. 17 p. Cover: All photos from IRRI archives except for photo of rat, which was taken by N.Q. Hung. ISBN 971-22.0033-7 ISSNechnical Bulletin 5 oo IRRI Biodiversity Software Series. V. RARE, SPPDISS, and SPPRANK: Programs for Detecting Between-Sample Differences in Community Structure Developed by K.G. Schoenly and W.). Zhang INTERNATIONAL RICE RESEARCH INSTITUTERARE, SPPDISS, and SPPRANK: Programs for Detecting Between-Sample Differences in Community Structure Developed by K.G. Schoenly and W.J. Zhang Biological, historical, and anthropogenic events influence the richness, abundance, and composi- tion of taxa in an ecological community, that is, its structure. If community structure changes over time or space, it may reflect shifts in ecologically important activities caused by environmental changes (Philippi et al 1998) or ‘human interventions. Ecostatistical methods for detecting and quantifying differences in commu- nity structure have included the use of rarefac- tion (e.g. Simberloff 1978, James and Rathbun 1981), diversity indices (e.g., Solow 1993), rank tests (Grossman et al 1982, 1985), taxonomic dissimilarity (Clarke 1993, Philippi et al 1998), and multivariate statistics (e.g., Gauch 1982, Digby and Kempton 1987). In an agrobiodiversity study, researchers may wish to compare a prevailing farmer practice or intervention with a new technology. If such a pair-wise test shows a treatment effect, as revealed by changes in community structure, this result suggests that one or more taxa in the community have been affected by the new technology. If the index of community structure weighs abundant taxa more than rare taxa, then abundant taxa may reflect the treatment effect more than rare taxa, Consequently, we advise users of these programs to consider the context of the weighting functions of the ecostatistical indices used in these programs. In rice ecosys- tems, pest populations are often the most abundant herbivores, while their most important arthropod biocontrol agents (Ooi and Shepard 1994) are among the most abundant natural enemies (K. Schoenly et al, unpublished data). ‘Thus, from integrated pest management (IPM) and arthropod biocontrol contexts, indices that ‘weigh abundant taxa more than rare taxa are scientifically justified. If multiple tests of community structure each reveal statistically significant differences for the same treatment effect, then the same treatment has affected different aspects of community structure simul- taneously and confidence is high that the treatment effect at the community level is real. Overview of three software programs This document describes three programs (RARE, SPPDISS, and SPPRANK) that stat cally analyze different aspects of community structure between different site, times, or treatments. RARE includes three spatial- distribution models (random, uniform, negative binomial) for users to choose from to produce a rarefaction curve (from rank-abundance data) to test the null hypothesis that two or more ‘sampled communities come from the same parent distribution and have the same species richness (Gottelli and Graves 1996). SPPDISS detects differences in taxonomic composition, using the algorithm of Clarke (1993), to test the ‘null hypothesis that the taxonomic dissimilarity between subsamples of two communities is not larger than the taxonomic dissimilarity within them. SPPRANK uses the nonparametric rank test of Spearman (1904), and its correction for excessive ties, to test the null hypothesis that species-abundance rankings of two communities are independent (Daniel 1978). For both SPPDISS and SPPRANK, bootstrap simulation is employed to test whether the observed test statistic (Clarke's R or Spearman's R.) is differ- ent from what would be expected by random chance. When used in combination, these threetests can distinguish whether the treatment of interest alters community structure in subtle ways, ie., one test shows significant differences, or in large ways, i., all tests show significant differences. (Throughout the text, taxa and. species are used synonomously.) Research questions 1. Do significant differences in herbivore and natural enemy assemblages occur between traditional and genetically altered varieties (eg., Brice), between rice and nonrice habitats, or between conventional and experimental practices of crop, nutrient, and pest management? 2. Do insecticides show equally toxic actions on herbivore and natural enemy assemblages, testable by rarefaction, when invertebrate abundances in sprayed and unsprayed treat- ‘ments are standardized to a common size, as pollution assessment studies have shown (Berger 1990, cited in Gotelli and Graves 1996)? 3. Do pesticide-treated ecological assemblages that have been sprayed once have similar community structure and recovery times as multiply sprayed assemblages? 4, Do different methods for sampling inverte- brates in the canopy (e.g.,. D-vac, FARMCOP, RiceVac, sweep-net) and in the floodwater (eg, area collector, FARMCOP, RiceVac, strainer-net) have similar catches at the population, guild, and community levels? Technical information ‘Two versions each of RARE, SPPDISS, and SPPRANK were written for use in MS-DOS (QBASIC™) and Windows (DELPHI-3™) environments to serve different operating systems in use at national agricultural research. stations. Both versions use the same algorithms but they vary in screen appearance and have different data/memory capacities. The QBASIC version of each program was developed using the Microsoft QBASIC language that runs under MS-DOS and Windows platforms and requires 6 kb of system memory for RARE, 7 kb for SPPDISS, and 7 kb for SPPRANK, for a total system memory of 20 kb. The Windows-based versions were created using development tools and Windows interfaces contained within the DELPHI-3 development kit. The source code in the DELPHI-3 version is Object PASCAL™, which is Borland’s object-oriented extension to the PASCAL language. The memory required to run the DELPHI-3 programs is 395 kb for RARE, 314 kb for SPPDISS, and 313 kb for SPPRANK. DELPHI-3 versions run under advanced Windows environments such as Windows 95 or later. Program RARE When two or more ecological communities are being compared, even if the same methods, persons, and sampling effort are followed, we expect that they will differ in their total sample abundance and species richness. This holds true for tropical rice communities for both the dry and wet seasons. Because species richness is positively correlated with abundance (Fig. 1), samples containing large numbers of individuals (e.g., 250) harbor more taxa than smaller samples (¢.g., 50). To statistically test for differences in species richness for different samples, the test is more valid if the samples are reduced (or rarefied) to a common abundance. In multiple-sample situations, all samples are ‘compared with the one harboring the lowest abundance. At this sample size, ecological ‘communities can then be ranked in terms of their species richness (James and Rathbun 1981). Sanders (1968) recognized this need and derived «a formula for rarefaction that assumed a random spatial distribution of individuals. Sanders* original formula was wrong, however, and was corrected independently by Hurlbert (1971) and Simberloff (1972). The corrected version is ES,) HV ‘here [isthe total number of organisms in the sample, $ is the species richness of the sample, 1m is the number of individuals of species i, and nis the number of individuals in the rarefied50 40 30 20 10 40 30 20 10 40 30 20 10 60 3 50 4 50 5 Number of invertebrate taxa per sample Teper rept © 50 100 150 200 250 300 350 71DT . 60 5 50 40 30 20 10 0 a a a 10 20 30 40 50 60 70 80 100 150 40 5 30 20 10 T T T T 1 50 150 200 250 100 98 DT 7 T T 1 100 150» -200 100 150 Total invertebrate abundance per sample Fig. 1. Relaionship between taxonomic richness and abundance of ee invertebrates in 80 suction samples at tree crep ‘stages during the dry (A) and wat (B) seasons. OT = days aftr transplantingsample. Summing S, overall taxa in the sample gives the expected taxonomic richness [E(S,)]. Rarefaction answers the question, Ifthe total sample has $ taxa and I individuals, what is the expected taxonomic richness (E,) for a smaller sample size of n individuals? Because the variance of the rarefaction metric can also be calculated, confidence intervals (e.g... 95%) around the rarefaction curve can be added, which allow users to ascertain, statistically, whether two or more communities have the same species richness. This formula is appli- cable if the spatial distribution of individuals is random (Gotelli and Graves 1996): Variance of E(S,) If, on the other hand, we know that the spatial distribution of individuals is uniform, the following rarefaction equation (Kobayashi 1982, 1983) applies: A+tl- ES, (mV) where A is the number of taxa whose relative abundance m/1 is larger than or equal to 1a. For cases where individuals are clumped in their spatial distribution, the negative binomial version of the rarefaction metric (Kobayashi 1982, 1983) may apply: ES,)= [1+ nm/(k)) 4] where k, is the k parameter of the negative bino- mial distribution for each taxon, i= 1,2, ..., 8 Figure 2 shows an application of rarefaction for randomly distributed invertebrate catches in ‘a transplanted rice field in the Philippines during the 1998 dry season. Invertebrates were suction- sampled from 10 hills at 4 different times on the same day (0730, 1030, 1330, and 1630 h) during the vegetative stage. After standardizing abun- dances to the smallest sample (304 individuals), plotted rarefaction curves at this crop stage show that samples taken in the early morning (0730 h) harbor significantly more taxa (58 + 4.3) than those taken later in the day (1030, 1330, and 1630 h). Thus, if researchers wish to maximize invertebrate richness at this crop stage, sampling should be conducted early in the moming. ‘The shape of a given rarefaction curve will reflect the underlying species-abundance distribution (Gotelli and Graves 1996). Curves drawn from actual data will fall between two extremes: one with a completely even distribu- tion of taxa (e.g., 10 taxa each represented by 100 individuals) and another with a completely uneven distribution (e.g., | taxon has 991 individuals, 9 taxa have | individual each). Users must be mindful of certain assump- tions and restrictions of the rarefaction model (Gotelli and Graves 1996): 1. Sampling is sufficient to guarantee adequate characterization of the parent distribution. This is difficult to ascertain in practice without additional information, Users wish- ing to apply collectors’ curves for this purpose, see program COLLECTI in this software series 2. The spatial distribution of individuals is random. In cases where users know the spatial distribution of the data, three choices are available in RARE (e.g., random, clumped, and uniform models). If users are tunaware of which spatial distribution fits their data, they should choose the random80 5 1330 98 + 4.3 taxa 1030 50 5 1030, E, = 49 +38 taxa 1990, E,' = 48 + 5.8 taxa 1630, S = 43 taxa 1630 30 4 10 “Same abundance 0 100 200 «300 ©6400» 500, 600700 Sample abundance Fig. 2. Rarefaction cures for sce invertebrates suction-sampled at four times of he day (0730, 1090, 1390, 1630) during the vegetaive stage, IRRI farm, dry season 1998.‘model. (Note: Variances for the uniform and aggregated models are not calculated in RARE.) 3. Samples to be compared are taxonomically alike (ie. drawn from the same ecosystem or community) and identical sampling methods are followed. 4, Rarefaction is applicable for interpolation Ge. estimating E,, for smaller sample sizes), but not for extrapolation. Users wishing to apply extrapolation methods to estimate total taxonomic richness from samples can consult programs EXTSPP! and EXTSPP2 in this, software series. Several guidelines have been suggested for using rarefaction curves: I. A rarefaction curve should be calculated along its full length, from its origin at 1,1 10 its maximum species richness and abundance (Tipper 1979, Gotelli and Graves 1996). In RARE, the user can choose either a selected ‘number of rarefaction points to estimate Es, or have the entire rarefaction curve produced on output. 2. In the unlikely event that two rarefaction curves should cross, Es, in these communities will depend on the abundance being com- pared (Simberloff 1978). 3. For a smooth, full, and accurate curve, Tipper (1979) recommends a minimum of $+ 1 points of n individuals. 4, To determine whether taxonomic richness differs between different samples at the nominal level of statistical significance (P = 0.05), the rarefaction curve should include its 95% confidence interval (Gotelli and Graves 1996). Program SPPDISS. ‘Two communities (or subsets of samples from two communities) will likely differ in their composition of taxa, that is, some taxa will be found in both communities (joint taxa) and some found in one community or the other (unique taxa), Moreover, the abundances of the joint taxa may also differ, perhaps substantially. Differences in taxonomic composition are commonly analyzed using similarity or distance measures (e.g., Ludwig and Reynolds 1989) that are computed for every pair-wise combination of samples. If changes in taxonomic composition occur as a result of a treatment, then pair-wise dissimilarities in taxa within control sites and ‘within treated sites will be smaller than pair- wise dissimilarities benween control and treated sites. Clarke’s (1993) R test compares between- community and within-community dissimilari- ties for all n(n ~ 1)/2 pair-wise dissimitarities between n sites and computes the average rank of the between-community (r,) and within- community (F,) pairs. The test statistic for Clarke's R is 4-1) If the smallest between-community differ- ence is larger than every within-community difference, then R = 1 and the two communities are taxonomically different. On the other hand, if between- and within-community differences are similar, R approaches 0 and the two commu- nities are taxonomically similar. In SPPDI users can choose either standard Euclide: distance (SED) or Manhattan distance (MD) as a measure of dissimilarity: SED =[1/S (X, -X,)"” ID = USE1X,-X,1 Clarke's R, by itself, is insufficient for determining whether between-community dissimilarities are large enough to be statistically significant, Conventional significance tests for this index are inappropriate because all possible pair-wise dissimilarities are not independent Philippi et al 1998). In such cases, a bootstrap test can be employed because this procedure is not restricted by this requirement. In each bootstrap simulation, the dissimilarities associated with each site or subsample are randomly reshuffled within and across treatments (without replacement) and R is recomputed (ie., a pseudo-R). Thus, the original dissimilarities for computing the observed R test statistic are reshuffled, but not recomputed, for each simula- tion, From these simulations, the P value is calculated as (x + IAs + 1), where x is the number of pseudo-R values from the s simula- tions that exceed the observed R. A P value of less than or equal to 0.05 indicates that the two communities are statistically different at this nominal level of signit Program SPPRANK A third statistical measure that can reveal ecological differences in community structure is to test whether the joint taxa in two communities have different ranks in their relative abundances. If the joint taxa show a different ordering of abundances between control and treated sites, for example, then the null hypothesis (H,: no association between ranks X and Y) is not rejected. Grossman (1982) used Kendall's W, a multiple-sample rank test, to determine the degree of concordance (agreement) in species ranks through time for an assemblage of inter tidal fish, In pair-wise tests of insecticide- sprayed and unsprayed plots, the most abundant herbivores in tropical rice fields tend to retain their ranks over pre-and postspray dates as opposed to natural enemies, whose ranks differ between pre- and postspray dates and between sprayed and unsprayed plots (Heong and Schoenly 1998). Program SPPRANK uses Spearman's R,, which varies along the interval -1 to +1, to determine whether the n pairs of species ranks [R(X), RCY))] between two ecological communi- ties differ: 6Ed? R, nin? 1) where ¥ d? = (R(X) — ROP If the rank of X is identical to the rank of Y for every pair of taxa, R_is equal to +1 and the result is a perfect direct relationship, Con- versely, if R, equals -I, the rank of one observa tion in each species pair (X,, Y,) is the reverse of the other, and the result is a perfect inverse relationship (Daniel 1978). R is affected little if few ties occur in the species ranks. Unfortunately, samples taken from ecological communities frequently have large numbers of singleton and doubleton taxa that can yield many ties. Therefore, program SPPRANK uses the following correction for ties where t, and f, are the number of X and Y taxa that are'tied ata specific rank. When the tie correction above is used, the final form of the test statistic for R, becomes Dx+dy da? PRs Users must remember certain assumptions of Spearman’s R, test (Daniel 1978): 1. The data come from a bivariate population, designated as the n pairs of observations (X,, YJ (Xp Ye oor Ky Yi) 2. If ties occur among the X's or Y's, each tied value is assigned the average of the rank positions for which itis tied, 3. Each X or Y is ranked relative to all other X or ¥ values, from smallest to largest. A look-up table of critical values for R, is available in practically every statistics book to determine whether an observed value is statis! cally significant. In addition, SPPRANK per-forms a bootstrap test that reshuffles species abundances (without replacement) in one of the two communities. For each bootstrap simulation, R is recomputed (i.e., a pseudo-R ). Two P values are computed from this simulation and tell users whether there is a direct (positive) association between the two samples (P1) or whether there is an inverse (negative) associa- tion (P2). PI from this test is calculated as x/s, where x is the number of pseudo-R,’s from the s simulations that exceed the observed R,, whereas P2 is calculated as x/s, where x is the number of pseudo-R,’s that are less than the observed R,. A PI value of £ 0.05 indicates a direct association between these two communi- ties at the nominal level of significance when R, is positive, whereas a P2 value of < 0.08 indi cates an inverse association between these communities when R, is negative. Input file format For these programs, two file formats are re- ‘quired, Data for SPPDISS must be in the form of a matrix in which taxa (immatures or adults) correspond to rows and samples correspond to columns. Cells of the matrix contain integers corresponding to sampled abundances separated by one or more spaces for clarity, For RARE and SPPRANK, data must be in the form of a three- column matrix in which the first column is the taxon’s integer label (sorted in ascending order), followed by its ID number from the master list, and its sampled abundance. Although not required by RARE and SPPRANK, taxa may first be arranged in descending order of abun- dance. These file formats must be space-delim- ited text files. DELPHI-3 versions, unlike QBASIC versions, require that all input files be given the extension “.txt” because this is a default extension for input files (in the input file dialog boxes) of RARE. SPPRANK, and SPPDISS. The space-delimited text format ‘The space-delimited format has been incorpo- rated to make it easier to export data from spreadsheet files, such as Microsoft Excel or Core! Quattro Pro. Two different file formats are required for RARE, SPPRANK, and SPPDISS. For SPPDISS, two input files that represent different sites or samples require that the first row of each space-delimited text file have a numerical label for each sample, separated by spaces. Subsequent rows contain the taxon ID number, taken from the master list, followed by the sampled abundance for that taxon in each sample, all separated by spaces (Figs. 3 and 4). The two data files for comparison must have the same number of rows and species sequence but ‘may differ in their number of columns (samples). A second file format, required for RARE and SPPRANK, is a space-celimited text file that contains two numerical labels for each taxon, followed by its abundance (Fig. 5). m4 -270 3000 378 378 914 094 “58 Fig. 3. Sample data matrix (1st of 2 required) containing the ‘space: delimited fie format for program SPPDISS, m7 0 9 o ° 2 eons ° ° ye 3 3 620 0 9 ° 0 coor H 1 3 Oo 0 6 ° ° eG ° ° ees 3 3 4 a ° ° Fig, 4. Sample data matnx (2nd of 2 required) containing the space-dolnted fe format Tor program SPPDISS,Fig. 5. Three-column matrix containing the space-delinited fe format for programs RARE and SPPRANK, Using Excel to create space-delimited text files The following procedure describes how to create a space-delimited .txt file using Microsoft Excel 97 1. Using the mouse, highlight the matrix you wish to create as a text file 2. Choose the Edit/Copy command to copy the contents of the matrix in the clipboard. 3. Choose the File/New command to create a new file, then click Edit/Paste to transfer the contents of the clipboard to the new file. 4. Ifthe file to be saved has 50-100 data columns, use the Format/Column/Width ‘option to change the width of the first column (taxon ID number) to 7 spaces. Highlight the remaining columns with the pointer and click Format/Column/Width again and enter 4 spaces for these columns. This step will ensure that the width of this data matrix does not exceed 240 spaces, the maximum width allowed by Excel. 5. Choose the File/Save As/Formatted Text ited) (*.prn) command and click 6, In the file name box, type in a file name. Change the “.pm” extension (entered by default by MS Excel) to "txt" 7. A warning box appears informing you that the “selected file type will save only the active sheet.” Click Save. If your spreadsheet software is other than Excel, consult your user manual on how to create space-delimited text files. Program installation QBASIC versions of RARE, SPPDISS, and SPPRANK (*.bas) require the executable file {gbasie.exe to run. You should copy all of these files into the same MS-DOS or Windows directory on the hard drive. DELPHI-3 versions are stand-alone executable files that do not require ll (dynamic link library) files for installation. As ordinary executable files, RARE, SPPDISS, and SPPRANK can be copied into MS-DOS, Windows, and other environ- ments that have a screen resolution of 800 x 600 pixels or more Starting RARE, SPPDISS, and SPPRANK For the QBASIC version, double-click ‘qbasic.exe, then click File/Open to see and select the program of interest. After opening the program, click Run and follow the data input instructions. For DELPHI-3 versions, double- click the program icon in Windows Explorer or in the Program Manager or enter the program name on the MS-DOS command line. After a few seconds, a window appears containing different buttons and options for data input. Algorithm details become available by clicking Help along the bottom panel. Running the programs Because of space limitations, our tutorial below will show only the DELPHI-3 (Windows) versions of RARE, SPPDISS, and SPPRANK. QBASIC versions lack the familiar Windows format but retain inputting instructions and numerical algorithms like those of the DELPHI- 3 versions. Program windows in RARE, SPPDISS, and SPPRANK The program windows in RARE, SPPDISS, and SPPRANK look similar and query users for similar information. After you start program SPPDISS, for example, and wait several sec- nds, its first program window appears (Fig. 6).In the right panel, choose between Buclidean and Manhattan distance for computing Clarke’s R statistic. In the second program window, the middle-right panel requires you to enter the number of Group | and Group 2 samples and the ‘number of Monte Carlo simulations desired (e.g., 100), and then click Enter (Fig. 7). In the third and fourth program windows, the middle- right panel requires you to specify the path and file name of the Group | and Group 2 data files (Fig. 8) After inputting the final data details, click Rum (o run the program. Hint statements, activated when the mouse pointer approaches an input box, specify the nature of the input param- eters needed for each step of input. The task bar at the bottom is an action panel that includes options to Run the program (after data inputting is complete), Stop it (during program execu- tion), Restart it, and seek Help. In the top-right comer of the window, two buttons familiar to Windows users let you Minimize the window but keep the program running (_) and Close the ‘window so you can exit the program (x). While running, each program will display approximate running time and remaining time in the progress window. Running time refers to the approximate real time (elapsed time) RARE, SPPDISS, and SPPRANK have taken to run the program from execution, whereas remaining time refers to approximate time left to comple- tion in minutes and seconds (Fig. 9). After execution, you can scan the results in the display window by scrolling up or down on the scroll bar. Figs. 6 and 7. 6 oR 10Figs. 8 and 8 8 cape | — — ee fee distance (depending on the selection), for 9 Output files After program execution, you can save the ‘output as a space-delimited text file (Fig. 9) or print it, or specify the path and file name of the ‘graph. For each option, you can save or cancel by using the appropriate button. For RARE, the output lists abundance (n) and expected taxonomic richness (E(s)] values, in ascending order of n, of the full rarefaction curve (Fig. 10). The last two columns are 95% confidence intervals for each point that can be joined together to form confidence interval arcs. For SPPDISS, the output includes the matrix of dissimilarity values, Euclidean or Manhattan within-group and between-group comparisons (Fig. 11). The next section includes the observed value of Clarke’s R and its interpretation. The final section of the output gives the results of the randomization test and an interpretation. For SPPRANK, the first section of the output identifies the taxa that were found in both samples, their abundances and ranks, and their differences in rank (Fig. 12). The latter statistic can be used to determine which jointly occurring taxa differ most in rank abundance. The next section lists the observed value of the Spearman rank uncorrected and corrected for ties. The last section of the output gives the results of the randomization test and an interpretation. "Filenane: threlr.out has 28 taxa and 982 individuals a Bis var ‘sD BtS)-260 B18)-280 ast 2.85 1.69 e.13 14.89 70 15.16 2189 1:70 11.75 18.56 05 ava 2165 163 13.96 20.47 40 36.58 26 1s? 15.4 ail72 175 ass 2.1 152 16.51 22.60 210 20.31 2120 148 3734 23.27 2465 20.91 2116 aay 17.97 23.85 280 aes 216 a7 28109 24137 315 21.88 2116 aay 36.96 24.62 350 22.29 29 248 29.04 25.25 385 22.68 2120 148 in 25.66 420 23.04 aia 249 20.06 26.02 455 23.38 2120 148 20.41 26.35 a0 23.72 219 148 20.76 26. 525 24.08 215 147 21.33 26 560 24.37 2110 14s. 2147 27 595 24.68 2103 aaa 21164 2 630 25.00 isa 139 22.21 2 565 25.31 183 13s 22.60 20 700 28.61 1:70 230 23.00 2a 335 25.92 136 225 23.2 28 0 26.22 1139 Feet) 23.86 28. 805 26.52 121 aio 24.32 28 240 26.82 ton 2.00 24.61 28 875 rect on19 o-89 25.33 28 910 27.40 0155 0.74 25.92 28 3s 2169 0.30 0154 26.60 28. 980 27.98 0.02 on16 29.66 28 Fig. 10. Sample output of raretaction results Case study: comparison of than the other methods. After running RARE to floodwater sampling methods standardize (rarefy) invertebrate abundances to a ‘common size, results showed thatthe strainer- ‘A comparison of invertebrate catches from the net caught more taxa than both the FARMCOP_ floodwater zone of an irrigated rice field was and RiceVac during the reproductive stage conducted at the IRRI farm in the 1998 dry (Table 1), in part because of a deeper scooping season. Catches from three sampling methods— motion that tended to dislodge more mud and its namely, the FARMCOP (Carino et al 1979), associated fauna (Schoenly and Domingo 1999). RiceVac (Domingo and Schoenly 1998), and Rank abundance tests (using program strainer-net (Schoenly et al 1998)—were judged SPPRANK) revealed that catches from the against catches from an area collector (Schoenly _strainer-net came closest to the area collector for and Domingo 1999, modified after Takahashi et rank abundances of its joint taxa, followed by al 1982), the RiceVac and FARMCOP. Similarity of taxa, as judged by Clarke's R (program SPPDISS), Raw comparisons between the different ‘was closest between FARMCOP and the area ‘methods showed that, as expected, the area collector, followed by the RiceVac and the collector caught more organisms and more taxa__strainer-net. Taking the three indices into 12Clarke test for comparing between-group and among-aroup dissimilarities in taxonomic composition: observed results Analysis of datatiles:C: \DELPKI\TOPRE.TXT and C+\DELPHI\TERE-Tar Dissimilarity matrix of combined groups: A = Cols. 1 to 10 and B = Cols. 11 to 20 (dissimilarities calculared as Euclidean distance 0.0000 3.9232 7.2186 10.0423 6.8826 7.4804 3.8786 15.9823 2.8704 21.9158 11,9873 11.4446 11.9401 11.1023 10.8728 9.0782 10.7975 12.5004 8.2515 9.1580 3.9232 0.0000 6.2467 12.4806 6.0988 8.6351 4.4721 18.5097 3.9215 24.0624 11,7566 10.8638 11.4872 10.6791 11.5326 10.0033 10.9871 12.5923 8.8293. 9.1247 7.2186 6.2467 0.0000 9.7334 13.9338 5.0258 22.3884 7.4308 25.1668, 6.5089 5.8792. 7.0325 9.0870 7.8988 6.6004 8.0014 7.7277 5.7729, 10.0423 12.4904 16.4806 11,7510 8.0528 13.1389 10.2395 11.5194 22.0627 21,0739. 20.7018 20.0926 18,7634 17.0217 19.5926 21.3445 16.1951 18.0392 6.8826 6.0988 9.7336 0.0000 9.6965 8.6338 18.4220 6.8747 26.1612, 15,1937 14.4989 15.3701 13.7200 14.6518 13.2599 14.1882 15.9898 12.8393 12.9707 7.4804 8.6351 13.9338 8.0528 9.6965 0.0000 9.4570 12.5248 7.3025 21.5916 16,7686 18.0042 18.2352 17.5140 26.2625 14.4966 17.6444 18,9255 13.3156 15.3764 3.8786 .4721 5.8254 13.1389 6.6339 9.4570 6.0000 17.4792 3.1312 20.7985 9.5531 8.7141 9.0746 8.3092 7.9126 6.5756 8.8600 9.7042 5.2446 6.3246 15.9823 18.5097 22.3868 10.2395 18.4220 12.524 17.4792 0.0000 16.1475 15.9354 25.2518 24.9055 24.4789 23.7404 20.6050 19.6872 23.8624 24.7492 18.6198 21,5729 2.704 3.9315 7.4308 11.5194 6.8747 7.3025 3.1312 16.3475 0.0000 21.4623, 12.8496 11.1433 11.6666 10.5840 20.1564 8.7327 10.9087 12.1467 7.8111 8.7836 21.9158 24.0624 25.1668 22.0627 26.1612 21.5316 20.7385 15.3354 21.4623 0.0000 24.5941 24.3645 23.0529 23.0915 18.5156 19.4495 24.2222 22.9565 18.2423 21.3694 11.9873 11,7566 6.5869 21.0739 15.1937 18.7686 9.5531 25.2518 11.8496 24.5941 0.0000 2.4539 3.2437 3.5447 6.0271 7.3765 3.2604 3.2571 7.8822, 4.3838 in.eaes 10.8636 "5.0792 30.7028 14.4969 ia.coa2 @.7141 24.9055 11.1433 24,645 2.4539 0.0000 2.6986 2.8920 6.4757 7.6755 4.9078 3.1726 7.2816 4.1310 in.9401 12.4972 "7.0325 30.8926 15.3701 9.2352 9.0746 24.4789 11.6606 23.0529 3.2437 2.6586 0.0000 2.8742 5.6260 6.8223 5.2181 2.4389 6.1961 3.4704 in.2023 0.6791 “6.4791 20.1111 13.7200 17.5140 8.3092 23.7408 10.5840 23,0915 3.5647 2.8930 2.8742 0.0000 5.0130 6.7486 5.1012, 2.4326 6.2145 3.2706 10.0729 12.5326 9.0470 18.7634 i¢.6510 16.2615 7.9126 20.6050 10.1564 18.5156 6.8271 6.4757 5.6260 5.0130 0.0000 5.4752 7.4382 5.2956 4.2631 4.4085. 9.0782 10.0033 7.8988 17.0217 13.2599 14.4966 "6.5756 19.6872 8.7327 19.4495, 7.3765. 7.6755 6.9223 6.7486 5.4752 0.0000 6.3623. 7.7361 4.4502 4.9373 10.7975 0.9871 "6.6004 19.5926 14.1862 i7.c¢4e 8.8600 23.8624 10.9087 24.2222 3.2604 4.9078 5.3101 5.1012 7.4362 6.3623 0.0000 5.5266 7.7693 4.6742, 12,5004 12.5923 8.0014 21.2445 15.9898 18.9253 9.7043 24.7492 12.1467 22.9565 3.2571 3.1726 3.4389 3.4326 5.2956 7.7361 5.5266 0.0000 7.3277 4.7598 8.2515 8.8293 7.7277 16.1951 12.8393 13.3156 5.3446 18.6198 7.8311 18.2423 7.8823. 7.2826 6.1961 6.2345 4.2631 4.4502. 7.7893 7.3377 0.0000 3.9342 9.1580 9.1247 5.7729 18,0392 12.9707 15.3764 6.3246 21.5719 8.7836 21.3696 4.3638 4.1310 3.4708 3.2708 4.4085 4.5373 4.6742 4.7594 3.9342 0.0000 Ava. rank of between-group pairs = 121.2400 Avg. rank of within-group pairs = 66.9000 Obeerved R = 0.5720 (R= 1 Lf the gmallest between-group dissimilarity is > every dissinilarity within groups; R= 0 if between-group dissimilarity is identical to within-group diseinilarity) Results of the randomization test: Expected R= 0.0026 and ite standard deviation - 0.0886 Based on 999 simulations, the P value = 0.0010 Between-group dissinilarities are statistically different at 99% confidence level Fig. 11, Sample ouput of Clarke's R results 13Nonparametric Spearman rank test for reasuring association between ranked (w/ties) ‘abundances of Ewo groups: observed vesuite Datafilea: C:\DELPIT\TOPREL.TXT and C:\DELPHT\TBRE1.TXT, number of jointly occurring taxa = 26, Group X = 32 taxa, Group Y= 28 taxa, number of unique taxa = 34 sp1p abun x abun ¥ Rank % Rank ¥ —DLEE(K-¥I 2097 300.000 26.0 25.0 Lo 525.000 25.0 26.0 oto 131.000 24.0 22.0 200 121,000 230 15.0 8.0 94.000 22.0 21.0 Lo 3.000 210 2410 -20 60.000 20.0 85 ans 55.000 19.0 12.8 65 46.000 18.0 10 ao 35.000 ato 2300 -6.0 25.000 16.0 10.0 6.0 20.000 15.0 16.0 -L0 14,000 1s 10 2315 14,000 13.5 a5 10.0 12,000 12.0 es 35 10,000 10 as 75 9.000 10.0 12's. “25 7000 910 18.0 <910 -1083 5.000 8.0 20.0 azo 2099 31000 65 as 300 ass 31000 6s as 300 -20675, 2/000 as 35 Lo 2087 2/000 as zo -2s 9 1000 200 as ous 2082 1000 2.0 19.0 ano 20705 lo00 2.0 1.0 3.0 observed Re (uncorrected for ties) = 0.6058 Observed Re (corrected for ties) = 0.6028 Results of the randomization test Lower-tail Pl value = 0.0020 Upper-tail P2 value = 0.9980 It $9 concluded that there 1s 2 direct agsociation between x and ¥ ranks. Fig. 12. Sample output of Spearman Frank resus. ‘Table 1. Summary catch statistics for floodwater ‘sampling methods, judged against the area collector, taken at IRRI farm during the reproductive stage, dry ‘season 1998, Numbers in parentheses are ranks for ‘each index or statistic (1 = best, = worst). Floodwater method Index or stastic FARMCOP —AleaVac_Strainer-net Rarelacton 2392.93) 24722912) 2811) (@o.taxat 25D) Spearman, 03523) 0.603(2) 9.05.) larke 05351) 087312) 0583(3)account and after giving them equal weight, Table 1 shows that (after the area collector) the strainer-net is the single best method for sam- pling the floodwater fauna at this crop stage as judged by the sum of its ranks (5), followed by the RiceVac (6) and the FARMCOP (7, Table 1). Execution errors in RARE, SPPDISS, and SPPRANK If a problem develops during execution of these programs, an error will be displayed on the Jower-right panel. The list below includes some ‘common errors and their explanation, which may help in troubleshooting: Evor Explanation Divided by zero [An integer value divided by zero ‘nth integer! Divided by 20.0 Aloating point value civiced wth floating point by 2270 Range check eror! —_Inleger value exceeds defined range Floating point Atoating point value exceeds overtiow upper Emit Floating point Atioaing pont value falls below undertow! lower imt Fle cannot be Fig not open, or read-only, oc ‘accesses! Too many samples File has too many taxa or taxa! or too many samples Invalid floating point Square root of negative value, et. ‘operation! Math or ther error! Not enough memory on hard ik, te Other features of RARE, SPPDISS, and SPPRANK Using the Stop button You can stop a program at any time during execution (after data entry) by clicking the Stop button near the bottom of the program window. It Stop is clicked, the program will return to its first program window. Saving output ‘The program window(s) for saving results will appear automatically following program execu- tion. As each file save option appears, you can save any or all ofthe files by simply entering the path and a unique file name in the file-naming box. Likewise, if you wish to ignore certain files, simply click the Caneel button. Printing results Afier you save a file(s), the program box for printing appears. If you wish to print all results, then click the All Results and Print buttons. If you wish to print a partial set of results, then Click the Selected Results and Print buttons. If 1no printing is desired, simply click the Cancel button. Using the Restart and Help buttons To return a program to the starting window, you only need to click the Restart button. RARE, SPPDISS, and SPPRANK also come with a Help button, located near the bottom of each program window. Information in help includes the mathematical steps of each algorithm description, which can be scrolled up and down using the vertical scroll bar in the Windows interface. The QBASIC versions (e.g., RARE.BAS) include help text. Disclaimer This software was tested on IBM-compatible PCs in 1998-99 using field data collected at IRRL in 1998. In this version, we made every effort to test RARE, SPPDISS, and SPPRANK thoroughly and have corrected known program- ming errors. Nevertheless, a computer program subjected to repeated use by different users on different machines will invariably reveal addi- tional errors. Should you uncover what you believe is a new programming bug, please advise us, preferably by e-mail (b.hardy @cgiar.org), and send us the following: (1) a description of the problem, (2) your computer model and processor, and (3) a copy of the data set you were using. We also welcome suggestions on how these programs can be improved 15Acknowledgments This project was supported by the Asian Devel- ‘opment Bank through RETA 5711, “Exploiting Biodiversity for Sustainable Rice Pest Manage- ment.” We thank the participants of the three lighthouse sites from the Philippines (L. Flor, A. Velilla), China (J. Tang), and Vietnam (L.P. Lan) for beta-testing these programs and for giving us helpful suggestions during the April 1999 training workshop at IRI. For the data in the field study that we cited and analyzed in this manual, we thank L. Datoon for processing the invertebrate samples; 1. Domingo for supervis- ing the field work; E. Rico, R. Abuyo, J. Reyes, and B, Aquino for collecting the field samples; and AT. Barrion for his taxonomic assistance, We also thank V. Salazar for producing the cover page for this software series, and the staff of IRRI’s Communication and Publications Ser- vices, particularly B. Hardy, G. Reyes, and B. Lazaro. 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