[R] Calculations with aggregate data: mean +/- standard deviation
Rui Barradas
ruipbarradas at sapo.pt
Thu Mar 20 20:27:08 CET 2014
Hello,
Try
res[order(res[,1]), ]
Hope this helps,
Rui Barradas
Em 20-03-2014 17:48, Luigi Marongiu escreveu:
> Dear Rui,
> Thnak you very much: this works exactly as I requested, but the merged
> vetor (res) order the variables by alphabetical order rather than by the
> factors I indicated during the definition of the data frame; thus AVG,
> SD and res have different row order.
> When I tried to define the factors of AVG, SD and resthe original order
> is not kept:
> > AVG
> stimulation copy
> 1 Unstimulated 1470.080
> 2 ESAT6 2043.772
> 3 CFP10 6107.652
> 4 Rv3615c 1639.437
> 5 Rv2654 4025.472
> 6 Rv3879 2558.704
> 7 Rv3873 3538.781
> 8 PHA 213613.795
> AVG$stimulation<-factor(AVG$stimulation, levels = c("Unstimulated",
> "ESAT6", "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"))
> SD$stimulation<-factor(SD$stimulation, levels = c("Unstimulated",
> "ESAT6", "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"))
> res$stimulation<-factor(res$stimulation, levels = c("Unstimulated",
> "ESAT6", "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"))
> > res
> stimulation AVG SD lower upper
> 1 CFP10 6107.652 9597.686 -3490.0334 15705.338
> 2 ESAT6 2043.772 3674.133 -1630.3606 5717.905
> 3 PHA 213613.795 789614.399 -576000.6044 1003228.194
> 4 Rv2654 4025.472 5933.346 -1907.8739 9958.818
> 5 Rv3615c 1639.437 2546.439 -907.0025 4185.876
> 6 Rv3873 3538.781 6205.863 -2667.0813 9744.644
> 7 Rv3879 2558.704 5812.945 -3254.2414 8371.649
> 8 Unstimulated 1470.080 1698.197 -228.1178 3168.277
> May I ask whether there is a method to solve this discrepancy?
> best regards,
> Luigi
>
>
>
> On Wed, Mar 19, 2014 at 6:50 PM, Rui Barradas <ruipbarradas at sapo.pt
> <mailto:ruipbarradas at sapo.pt>> wrote:
>
> Hello,
>
> Maybe something like the following.
>
> res <- merge(AVG, SD, by = "stimulation")
> names(res)[2:3] <- c("AVG", "SD")
> res$lower <- res$AVG - res$SD
> res$upper <- res$AVG + res$SD
> res
>
>
> Hope this helps,
>
> Rui Barradas
>
> Em 19-03-2014 18:15, Luigi Marongiu escreveu:
>
> Dear all,
> I have obtained the averages (means) and standard deviations (SD) of
> different variable using the aggregate function, which I have
> found very
> useful for these kind of computation.
> However I would like to calculate the lower and upper ends of the
> data (that is mean - SD and mean + SD) varible-wise, but I don't
> know how
> to cope with this aggregate data. I cannot simply subtract the
> aggregated
> results (which I have called AVG and SD) and the aggregate
> function is a
> bit too complicated for me.
> Does anybody knows how to add and subtract the means and standard
> deviations obtained using the aggregate function?
>
> Best regards,
> Luigi
>
>
> my.data<-structure(list(
> column_1 = 1:120,
> column_2 = structure(c(
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8), .Label = c("Unstimulated", "ESAT6",
> "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
> column_3 = c(
> 192.0519108,183.6403531,53.46798757
> <tel:53.46798757>,83.__60638077,69.60749873,159.__4706861,256.8765622
> <tel:256.8765622>,499.__2899303,
> 2170.799076,1411.349719,2759.__472348,2098.973397
> <tel:2098.973397>,2164.739515
> <tel:2164.739515>,1288.676574,1611.__486543,6205.229575
> <tel:6205.229575>,
> 870.7424981
> <tel:870.7424981>,465.9967135,191.8962375,864.__0937485,2962.693675,1289.__259137,2418.651212,7345.__712517,
>
> 0,168.1198893,674.4342961,101.__1575401,47.81596237,0,0,1420.__793922,
> 142.6871331,5.466468742,291.__9564635,80.73914133
> <tel:80.73914133>,73.02239621,64.__47806871,144.3543635,3167.__959757,
> 3164.748333
> <tel:3164.748333>,1092.634557,28733.20269,1207.__87783,729.6090973,151.8706088,__241.2466141,9600.963594,
> 1411.718287,12569.96285,1143.__254476,6317.378481
> <tel:6317.378481>,16542.27718,79.__68025792,1958.495138,7224.__503437,
> 208.4382941
> <tel:208.4382941>,69.48609769,656.691151,0.__499017582,7114.910926,187.__6296174,41.73980805
> <tel:41.73980805>,8930.__784541,
> 4.276752185,0.432300363,60.89228665
> <tel:60.89228665>,1.__103924786,0.490686366,1.__812993239,7.264531581,1518.__610307,
> 2172.051528
> <tel:2172.051528>,595.8513744,17141.84336,589.__6565971,1340.287628,117.__350942,593.7034054,24043.__61463,
> 0,81.83292179
> <tel:81.83292179>,1539.864321,36.41722958,8.__385131047,161.7647376,65.__21615696,7265.573875,
> 97.84753179
> <tel:97.84753179>,154.051827,0.613835842,10.__06138851,45.04879285
> <tel:45.04879285>,176.8284258,18795.__75462,3067686.769
> <tel:3067686.769>,
> 5780.34957,944.2200834,2398.235596
> <tel:2398.235596>,1083.__393165,2541.714557,1251.__670895,1547.178549,1792.__679176,
> 3067.988416 <tel:3067.988416>,8117.210173,23676.02226
> <tel:23676.02226>,8251.937547,__17360.80494,18563.61561,16941.__865,31453.96708
> <tel:31453.96708>,
> 2767.493803 <tel:2767.493803>,4796.33016,12292.93705,3864.657567
> <tel:3864.657567>,9380.__673835,14886.44683,8457.88646,__26050.47191
> <tel:26050.47191>)),
> .Names = c("row", "stimulation", "copy"), row.names = c(NA, -120L),
> class = "data.frame")
> attach(my.data)
>
> AVG<-aggregate(copy ~ stimulation , my.data, mean, na.rm = T)
> SD<-aggregate(copy ~ stimulation , my.data, sd, na.rm = T)
>
> # ??? question: AVG-SD and AVG + SD ???
>
> [[alternative HTML version deleted]]
>
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