r - General linear mixed-effect (glmer) heteroscedasticity modelling -


my variables measured on randomized block subsampling design treatments 23 accesion. have 3 complete blocks , 6 samples per block. example dataframe has 4 response variables (lh, ren, ftt, dfr), accesion (treatment), bloque (block number) , plot (that variable accounting subsampling). head of data is:

  plot accesion bloque   lh  ren ftt dfr 1  221       22      1 20.6 1127  23  88 2  221       22      1 20.5 1638  20  88 3  221       22      1 24.5 1319  16  88 4  221       22      1 21.4  960  17  88 5  221       22      1 25.7 1469  18  88 6  221       22      1 25.8 1658  21  88

so, data non-normal , heteroscedastic of 100 response variables after types of transformations (log, boxcox, power, etc). of variables show chi-squared or poisson-like distribution different variance each accesion.

histogram ftt

so far i've beeng working on running generalized linear model-effect poisson using glmer() on ftt response variable. using code:

fttglme = glmer(ftt ~ accesion + bloque + (1|plot), data = lyc,    family=poisson(link="identity"))

the residuals non-normal according shapiro.test(). that, assume, because of heteroscedasticity observed in residuals. boxplot of residuals accesion, shows difference of variances:

boxplot of residuals accesion

the heteroscedasticity expected between plant populations, know can modelled inside glme. code should add, have investigated already, is:

vf <- varident(form=~accesion)  fttglme = glmer(ftt ~ accesion + bloque + (1|plot), data = lyc,    family=poisson(link="identity"), weights = vf)

i want different variances account each accesion category. keep getting error:

error in model.frame.default(data = lyc, weights = varident(form = ~accesion),  :    variable lengths differ (found '(weights)')

does know how account differences of variance between accesions inside glmer()?

any other suggestions analyze data welcome.

i've solved issue. in glmer() weights argument correspond vector of same length original. model heteroscedaticity generated variance dataframe:

var<-aggregate(lyc[,6],by=list(lyc$accesion), var) colnames(var)<-c("accesion", "var")

that yields dataframe treatment/variance, head of is:

 accesion       var 1       22  4.369281 2       23 16.251634 3       24 13.911765 4       25 15.404412 5       26 15.895833 6       27 44.838095

then create new dataframe merging both dataframes 

lyc2<-merge(var, lyc, by="accesion")

and saw doing wrong 1 time, needed use inverse variance, in order correct variance.

lyc2$var<-(1/lyc2$var)

after data steps, run code:

fttglme = glmer(ftt ~ accesion + bloque + (1|plot), data = lyc2,     family=poisson(link="log"), weights = lyc2$var)

that fixes variance issue:

corrected variance residuals boxplot


Comments

Post a Comment

Popular posts from this blog

python - Operations inside variables -

this question has answer here: evaluating mathematical expression in string 12 answers i want make python script finds maximum possible output using 2 operations. problem says there syntax error @ 2nd last line, in b in there. how can fix it? x = 0 = int(input("1st number:")) c = int(input("2nd number:" )) e = int(input("3rd number:" )) in range(4): if == 0: b = "+" elif == 1: b = "-" elif == 2: b = "/" else: b = "*" j in range(4): if j == 0: d = "+" elif j == 1: d = "-" elif j == 2: d = "/" else: d = "*" k = b c d e print(k) if you're after variables e on single line, couldn...
Read more

Generic Map Parameter java -

i having lot of methods of type: public static list<eduusers> getdetails(class c, map<string, integer> params) { list<eduusers> details = null; session session = hibernateutil.getsessionfactory().opensession(); transaction tx = null; try { tx = session.begintransaction(); criteria cr = session.createcriteria(c); (map.entry<string, integer> entry : params.entryset()) { cr.add(restrictions.eq(entry.getkey(), entry.getvalue())); } details = cr.list(); tx.commit(); } catch (exception asd) { log.debug(asd.getmessage()); if (tx != null) { tx.commit(); } } { session.close(); } return details; } i trying have generic method them , have written far: public static <t> list<t> getdetails(class<t> c, class<t> b) { l...
Read more

arrays - What causes a java.lang.ArrayIndexOutOfBoundsException and how do I prevent it? -

what arrayindexoutofboundsexception mean , how rid of it? here code sample triggers exception: string[] name = {"tom", "dick", "harry"}; for(int = 0; i<=name.length; i++) { system.out.print(name[i] +'\n'); } your first port of call should documentation explains reasonably clearly: thrown indicate array has been accessed illegal index. index either negative or greater or equal size of array. so example: int[] array = new int[5]; int boom = array[10]; // throws exception as how avoid it... um, don't that. careful array indexes. one problem people run thinking arrays 1-indexed, e.g. int[] array = new int[5]; // ... populate array here ... (int index = 1; index <= array.length; index++) { system.out.println(array[index]); } that miss out first element (index 0) , throw exception when index 5. valid indexes here 0-4 inclusive. correct, idiomatic for statement here be: for (int index = 0; index <...
Read more