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library(nlme) data(Phenobarb) na.include <- function(x)x phe1 <- nlme(conc~phenoModel(Subject, time, dose, lCl, lV), data = Phenobarb, fixed = lCl+lV~1, random= pdDiag(lCl+lV~1), start = c(-5,0), na.action = na.include, naPattern = ~!is.na(conc)) phe.ranef <- ranef(phe1,augFrame=T...

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Hi all! I am desperately trying to figure out the solution to this error, but nothing as of yet is working. As noted in an earlier post I am using GenABEL. In an attempt to read in the phenotype file, in the format .dat, R keeps giving me the error "more columns than column names" I have tried to read in the data without the headers; I have also tried to trim the data to remove any trailing tabs or spaces but it doesn't solve the problem. All missing values have been...

I have a full data set like this: aa bas aas bms ams bcu acu omega y 1 ALA 0 127.71 0 69.99 0 -0.2498560 79.91470 outward 2 PRO 0 68.55 0 55.44 0 -0.0949008 76.60380 outward 3 ALA 0 52.72 0 47.82 0 -0.0396550 52.19970 outward 4 PHE 0 22.62 0 31.21 0 0.1270330 169.52500 inward 5 SER 0 71.32 0 52.84 0 -0.1312380 7.47528 outward 6 VAL 0 12.92 0 22.40 0 0.1728390 149.09400 inward ...................................................................................... aa have 19 levels, and there are dif...

...Reports per week") # add the 2017 weekly counts points(rep_tab[,5],type="b",col="red") legend(1,4,c("5 yr average","2017"),pch=1,lty=1,col=c("black","red")) Jim On Wed, May 9, 2018 at 4:37 PM, Shakeel Suleman <Shakeel.Suleman at phe.gov.uk> wrote: > Hi, > > I am fairly new to 'R' and would like advice on the following. I want to calculate a weekly average number of reports (e.g. of flu, norovirus) based on the same weeks for the last five years. I will then use this to plot a chart with 52 points for the av...

I have a question in R. In directory H:/Delta_angle I have 19 files like this: ALA.delta ASN.delta ASP.delta CYS.delta GLN.delta GLU.delta HIS.delta ILE.delta LEU.delta LYS.delta MET.delta PHE.delta PRO.delta SER.delta THR.delta TRP.delta TYR.delta VAL.delta I want to read these files to 19 data sets in R. All these data sets have "P","AA",index","delta" columns I want to do histogram for variable "delta" in each data set, and label the histo...

...value pertains i.e. # SQG Chemical #1 0.07918 Cd #2 -0.15490 Cd #3 -0.15490 Cd #4 0.95904 Cd #5....etc. etc. #assign correct plotting order for each chemical level OrderedLevels<-factor(Chemical,levels=c("Cd", "Cu", "Zn", "Phen", "Ant", "Flu", "Pyr", "Tot")) #set axis label and tick mark label font sizes to be readable when pasted into final document par(cex.lab=1.2,cex.axis=1.3) #produce plot with plotting symbols of round black dots with cex multiplier of 1.5 plot.default(SQ...

...error: "more columns than column names". I have tried to read in the .dat file (and alternately the .csv file) without the header, that does not work. I have checked my data-set and there aren't any discernible columns that are missing. Here's my code: mix <- load.gwaa.data (phe = "Z:/.../CCF Pheno.csv", gen = "pedmap-0.raw", force = T) Any help will be appreciated. Thanks! Euphie [[alternative HTML version deleted]]

...show_flag(buffer, hardware->cpu.flags.hypervisor, "hypervisor ", false); - show_flag(buffer, hardware->cpu.flags.ace2, "ace2 ", false); - show_flag(buffer, hardware->cpu.flags.ace2_en, "ace2_en ", false); - show_flag(buffer, hardware->cpu.flags.phe, "phe ", false); - show_flag(buffer, hardware->cpu.flags.phe_en, "phe_en ", false); - show_flag(buffer, hardware->cpu.flags.pmm, "pmm ", false); - show_flag(buffer, hardware->cpu.flags.pmm_en, "pmm_en ", false); - show_flag(buffer, hardwa...

These patches fix a few compiler warnings. Tested on top of commit aee0dc5565711ef5be7c30fb5fc1c5f3f98db09f Jonathan Boeing (6): Use z width specifier when printing size_t variable pxe: fix truncation warning gpllib: fix sizeof(char *) misuse hdt: fix sizeof(char *) misuse hdt: fix sizeof(char *) misuse hdt: fix sizeof(char *) misuse com32/gpllib/dmi/dmi.c | 24 +++---

...m2.2 = c(2,1,2,1,2,2,2,1,1,1)) x1 <- as.ped(x) y <- data.frame(pid = c(1,1,1,2,2,2,2,3,3,3), id = c(1,2,3,1,2,3,4,1,2,3), age = c(55,50,22,38,37,15,11,42,41,17), weight = c(185,170,130,165,170,90,60,170,160,120)) y1 <- as.phe(y) 1. I first consider a model with the disease as a phenotype, and two SNPs as predictors (on covariates) as bellow: pbat.m(AffectionStatus ~ NONE, y1, x1, fbat="gee", distribution='categorical', offset='none') But some error messages were returned: Error in writeComm...

...fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat clflush acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc rep_good nopl pni monitor vmx est tm2 ssse3 cx16 xtpr sse4_1 popcnt rng rng_en ace ace_en ace2 phe phe_en pmm pmm_en lahf_lm ida bogomips : 2801.77 clflush size : 64 cache_alignment : 128 address sizes : 36 bits physical, 48 bits virtual power management: -Sam

...fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat clflush acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc rep_good nopl pni monitor vmx est tm2 ssse3 cx16 xtpr sse4_1 popcnt rng rng_en ace ace_en ace2 phe phe_en pmm pmm_en lahf_lm ida bogomips : 2801.77 clflush size : 64 cache_alignment : 128 address sizes : 36 bits physical, 48 bits virtual power management: -Sam

...coreduo Genuine Intel(R) CPU T2600 @ 2.16GHz x86 kvm32 Common 32-bit KVM processor x86 kvm64 Common KVM processor x86 n270 Intel(R) Atom(TM) CPU N270 @ 1.60GHz x86 pentium x86 pentium2 x86 pentium3 x86 phenom AMD Phenom(tm) 9550 Quad-Core Processor x86 qemu32 QEMU Virtual CPU version 2.5+ x86 qemu64 QEMU Virtual CPU version 2.5+ x86 host KVM processor with all supported host features (only available in KVM mode) Recognized CPUID flags: fpu vme de pse tsc ms...

Motivated by the discovery of 'loglet analysis' (http://phe.rockefeller.edu/LogletLab/) that allows one to decompose growth curves into a series of logistic equations, I attempted to do the same thing in R. SIMULATED DATA Time <- 1:200 pop.size <- SSlogis(Time,10,20,5) + SSlogis(Time,20,100,20) + rnorm(length(Time)) MY ANALYSIS results <- nls(siz...

Dear list, Apologies, I have sent this message before but received no replies so I'm trying again just in case... Motivated by the discovery of 'loglet analysis' (http://phe.rockefeller.edu/LogletLab/) that allows decomposition of growth curves into a series of logistic equations, I attempted to do the same thing in R. #SIMULATED DATA Time <- 1:200 pop.size <- SSlogis(Time,10,20,5) + SSlogis(Time,20,100,20) + rnorm(length(Time)) ts.plot(pop.size) #MY ANALYSIS r...

...in p1982, p has 1982 levels, in dataset pr, p should have 1 levels. But I do str(pr), it shows that p still has 1982 levels. also for these > pr$aa [1] ARG THR ASP CYS TYR ASN VAL ASN ARG ILE ASP THR THR ALA SER CYS LYS THR ALA LYS Levels: ALA ARG ASN ASP CYS GLN GLU HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL it seems pr$aa don't have level GLU, but it list this level. I don't understand this, Is there some reason for these? thanks, > str(p1982) 'data.frame': 465979 obs. of 6 variables: $ p : Factor w/ 1982 levels "154l_aa","1A0P_aa...

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Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some