[R] median of grouped data

From: Bricklemyer, Ross S <rsb_at_wsu.edu>
Date: Fri, 27 Jun 2008 16:19:51 -0700


I am having difficulty calculating the median of grouped data. I have 8 to 10 repeated measures per sample and I have successfully used the following code to calculate the average for each sample.

libs.norm.preds.median[,7:9]<-apply(libs.norm.preds.median[,7:9],MARGIN=2, FUN=ave,libs.norm.preds.median[,1])

I then use the unique function to collapse the data into one line per sample.

I would also like to calculate the median, standard error, and coefficient of variation as well. I have not been able to get median to work properly. I have tried this and variants:

libs.norm.preds.median[,7:9]<-apply(libs.norm.preds.median[,7:9],MARGIN=2, FUN=median,libs.norm.preds.median[,1])

I receive the following error:

	Warning messages:
       1: In if (na.rm) x <- x[!is.na(x)] else if (any(is.na(x))) 	return(x[FALSE][NA]) :the condition has length > 1 and only the first 	element will be used

Here is a subset of my data (tab delimited):

samp.id	core	field	TC	IC	SOC	TC.15 comps	IC.16 comps	SOC.17 comps	TC.15 comps	IC.16 comps	SOC.17 comps
HOR006_3	HOR006	HOR	7.157	0	7.157	8.008273281	0.786161341	6.402343153	8.008273281	0.786161341	6.402343153
HOR006_3	HOR006	HOR	7.157	0	7.157	6.258510623	-1.117567268	6.987405984	6.258510623	0	6.987405984
HOR006_3	HOR006	HOR	7.157	0	7.157	14.21306811	7.968072165	6.818917226	14.21306811	7.968072165	6.818917226
HOR006_3	HOR006	HOR	7.157	0	7.157	17.73301788	9.017994045	9.035508792	17.73301788	9.017994045	9.035508792
HOR006_3	HOR006	HOR	7.157	0	7.157	12.54204929	6.285521186	6.052762372	12.54204929	6.285521186	6.052762372
HOR006_3	HOR006	HOR	7.157	0	7.157	10.07603128	3.485872902	6.937777459	10.07603128	3.485872902	6.937777459
HOR006_3	HOR006	HOR	7.157	0	7.157	11.02330763	4.963708049	7.03753441	11.02330763	4.963708049	7.03753441
HOR006_3	HOR006	HOR	7.157	0	7.157	11.02330763	4.963708049	7.03753441	11.02330763	4.963708049	7.03753441
HOR006_3	HOR006	HOR	7.157	0	7.157	9.249550001	1.92641169	7.675586354	9.249550001	1.92641169	7.675586354
HOR006_3	HOR006	HOR	7.157	0	7.157	7.414208739	-0.020533568	7.057048733	7.414208739	0	7.057048733
HOR006_4	HOR006	HOR	11.73	0	11.73	14.42894814	8.998403641	5.752994239	14.42894814	8.998403641	5.752994239
HOR006_4	HOR006	HOR	11.73	0	11.73	13.65284466	6.757373476	6.388413921	13.65284466	6.757373476	6.388413921
HOR006_4	HOR006	HOR	11.73	0	11.73	10.72185703	5.053095924	6.016783029	10.72185703	5.053095924	6.016783029
HOR006_4	HOR006	HOR	11.73	0	11.73	14.68382689	7.557801473	6.667911142	14.68382689	7.557801473	6.667911142
HOR006_4	HOR006	HOR	11.73	0	11.73	2.287381003	-3.074174656	6.654986023	2.287381003	0	6.654986023
HOR006_4	HOR006	HOR	11.73	0	11.73	14.57145428	8.812845515	6.625453309	14.57145428	8.812845515	6.625453309
HOR006_4	HOR006	HOR	11.73	0	11.73	21.12964238	13.27394496	6.568626499	21.12964238	13.27394496	6.568626499
HOR006_4	HOR006	HOR	11.73	0	11.73	19.46136803	8.03100103	6.910126723	19.46136803	8.03100103	6.910126723
HOR006_4	HOR006	HOR	11.73	0	11.73	13.16591198	4.738398449	6.051036242	13.16591198	4.738398449	6.051036242
HOR006_5	HOR006	HOR	20.339	14.383	5.956	24.17001811	15.44634892	8.095868636	24.17001811	15.44634892	8.095868636
HOR006_5	HOR006	HOR	20.339	14.383	5.956	19.17125764	12.28559645	7.468646662	19.17125764	12.28559645	7.468646662
HOR006_5	HOR006	HOR	20.339	14.383	5.956	20.18713584	13.12584843	6.985808635	20.18713584	13.12584843	6.985808635
HOR006_5	HOR006	HOR	20.339	14.383	5.956	25.58402927	18.23958469	6.960777883	25.58402927	18.23958469	6.960777883
HOR006_5	HOR006	HOR	20.339	14.383	5.956	24.04109959	16.32371239	7.12821025	24.04109959	16.32371239	7.12821025
HOR006_5	HOR006	HOR	20.339	14.383	5.956	19.809507	12.28987767	7.290354063	19.809507	12.28987767	7.290354063
HOR006_5	HOR006	HOR	20.339	14.383	5.956	22.37852335	13.66636406	7.814588276	22.37852335	13.66636406	7.814588276
HOR006_5	HOR006	HOR	20.339	14.383	5.956	20.67374067	12.99877903	6.997267952	20.67374067	12.99877903	6.997267952
HOR006_5	HOR006	HOR	20.339	14.383	5.956	24.69721989	16.10787468	8.381673118	24.69721989	16.10787468	8.381673118


*******************************************************************
Ross Bricklemyer
Dept. of Crop and Soil Sciences
Washington State University
251 Johnson Hall
PO Box 646420
Pullman, WA 99164-6420
Work: 509.335.3661
Cell/Home: 406.570.8576
Fax: 509.335.8674
Email: rsb_at_wsu.edu

 



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Fri 27 Jun 2008 - 23:23:51 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 30 Jun 2008 - 09:30:51 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive