Ok. I`m trying to run a Poisson glmm with an observation-level random
intercept. But I`m getting the following error for the 'Baci' variable:
'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in
pwrssUpdate'. I guess this message is because the baci variable is not a
an integer, and cannot be transformed into an integer as R has a threshold
of
2x10^9 even in 64 bit R.
It runs fine for the fungii variable.
If you guys want to run the data (attached), the full command is below.
Thanks.
---------------------------------------------
##Import data:
qPCR <- read.delim(file.choose(),
header = TRUE,
dec = ".")
##Load package
library(lme4)
##Other steps:
qPCR$obs <- 1:nrow(qPCR)
qPCR$fID<-as.factor(qPCR$ID)
qPCR$fDiet<-as.factor(qPCR$Diet)
##Run the model:
M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs),
family = poisson, data=qPCR)
Andre
On Tue, Apr 26, 2016 at 2:36 PM, jim holtman <jholtman at gmail.com>
wrote:
> Can you explain why you need them as 'integer', A floating point
> representation can hold a value upto ~4.5e15 as an "integer"
keeping the
> precision that you might need.
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Tue, Apr 26, 2016 at 1:11 PM, Andr? Luis Neves <andrluis at
ualberta.ca>
> wrote:
>
>> Dear all:
>>
>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
>> (using excel) and then imported the data (.txt) into R. Interestingly,
the
>> other three variables were loaded as INT, but the 'Baci' one
continued as
>> Num.
>>
>> I imported the data using the following command line:
>>
>> X <- read.delim(file.choose(),
>> header = TRUE,
>> dec = ".")
>>
>> Here is the structure of X:
>>
>> > str(X)
>> 'data.frame': 115 obs. of 5 variables:
>> $ ID : Factor w/ 61 levels
"107ZRED","112BLKW",..: 8 12 15 18 26 27
>> 29 31 32 36 ...
>> $ Baci : num 2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>> $ Meti : int 352645997 334146268 767208656 171567266 462747405
>> 414905627 237010514 387480048 214671355 328813226 ...
>> $ Fungii : int 43645 19009 15998 2189 8972 8240 3133 17922 6156
13746
>> ...
>> $ Protozoai: int 3220523 1851891 3252462 1665675 34123768 23175015
>> 203685
>> 4261780 43110492 69802572 ...
>>
>>
>> I need Baci as an integer, and tried to convert it using as.integer
>> function, but was not successful.
>>
>>
>> Could anyone please help me to solve this problem.
>>
>> Thanks,
>>
>>
>> ?
>> --
>> Andre
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>
>
--
Andre
-------------- next part --------------
ID Crossover Period Diet Pen Time Baci Fungii fNDF Starch
126BLK 1 1 Forage 1 End1 2.90E+12 43645 3.87056104 1.443771827
13ZBLK 1 1 Forage 1 End1 5.55E+11 19009 3.970286296 1.480970702
157BLK 1 1 Forage 1 End1 9.46E+11 15998 4.114130366 1.534626493
162ZRED 1 1 Forage 1 End1 8.13E+11 2189 3.600760128 1.343132423
17ZBLKY 1 1 Forage 1 End1 4.06E+11 8972 3.79087129 1.414046468
184ZBLK 1 1 Forage 1 End1 5.75E+11 8240 3.815881751 1.42337571
1ZBLKW 1 1 Forage 1 End1 34490836164 3133 3.295433507 1.229241447
2094ZBLK 1 1 Forage 1 End1 3.49E+11 17922 3.737865394 1.394274549
20LZBLK 1 1 Forage 1 End1 1.63E+11 6156 4.007824601 1.494972999
29ZBLK 1 1 Forage 1 End1 3.37E+11 13746 3.59031272 1.339235398
2ZBLKG 1 1 Forage 1 End1 3.13E+11 4003 3.964994752 1.478996884
60ZRED 1 1 Forage 1 End1 3.76E+11 12473 3.477652579 1.297211636
77BLK 1 1 Forage 1 End1 2.92E+11 13328 4.546906317 1.696057799
8ZBLK 1 1 Forage 1 End1 2.45E+11 2900 4.447927304 1.659137284
91ZRED 1 1 Forage 1 End1 5.62E+11 8584 4.118042491 1.536085769
112BLKW 2 1 Forage 2 End1 70249927920 192654 4.024558544 1.501214987
1226BLK 2 1 Forage 2 End1 18390770816 65524 3.933087193 1.467094931
12ZBLK 2 1 Forage 2 End1 64465242768 286966 3.678844325 1.372258889
134BLK 2 1 Forage 2 End1 9652868358 47474 3.902242465 1.455589429
160ZRED 2 1 Forage 2 End1 59600548800 155040 3.853736644 1.437496099
166ZRED 2 1 Forage 2 End1 81366127920 26056 4.037719564 1.506124226
17ZBLK G 2 1 Forage 2 End1 1.88E+11 74214 3.498366487 1.304938205
226ZBLK 2 1 Forage 2 End1 38794514336 291862 3.406420254 1.270641011
3ZBLK 2 1 Forage 2 End1 23837817696 46015 3.865246883 1.441789574
58BLK 2 1 Forage 2 End1 53734722624 50342 4.190382875 1.563069714
60ZBLK 2 1 Forage 2 End1 42301298024 146473 3.628258067 1.353389528
72ZRED 2 1 Forage 2 End1 95837208152 73205 4.123718464 1.538202984
7ZBLK 2 1 Forage 2 End1 47824296528 17068 4.028244534 1.502589911
95BLK 2 1 Forage 2 End1 41780037212 71368 4.099205498 1.529059315
9PZRED 2 1 Forage 2 End1 71202504840 178204 3.380912297 1.261126197
107ZRED 3 1 Grain 3 End1 1.18E+11 7074 2.146324344 3.007347766
129BLK 3 1 Grain 3 End1 10054798609 565 2.372894545 3.324809285
150ZRED 3 1 Grain 3 End1 1.48E+11 7869 2.152246315 3.015645405
168BLK 3 1 Grain 3 End1 94464253180 5281 2.500082872 3.503020716
174ZBLK 3 1 Grain 3 End1 62911040256 24635 2.273695448 3.185815296
185ZRED 3 1 Grain 3 End1 78074111590 1973 1.894214123 2.654100545
2ZBLKY 3 1 Grain 3 End1 4929843844 3183 2.483620769 3.479954645
4089ZBLK 3 1 Grain 3 End1 19370087262 1329 2.213050085 3.100841327
438XZRED 3 1 Grain 3 End1 7196105124 630 2.217241768 3.106714553
4ZBLK 3 1 Grain 3 End1 52954599928 1469 2.217302693 3.10679992
706ZBLK 3 1 Grain 3 End1 31205271204 2407 2.15080847 3.013630752
86BLK 3 1 Grain 3 End1 93866942272 417 2.753545642 3.858163077
86ZRED 3 1 Grain 3 End1 57127597772 7834 2.295665227 3.216598513
89BLK 3 1 Grain 3 End1 37992593088 6314 2.476126918 3.469454547
112XZBLKG 4 1 Grain 4 End1 9.56E+11 5205 1.890716993 2.649200499
1191ZBLK 4 1 Grain 4 End1 4.59E+11 35115 2.043372229 2.863095191
122ZRED 4 1 Grain 4 End1 2.93E+11 930 2.1174456 2.966883971
14ZBLK 4 1 Grain 4 End1 8.03E+11 5570 2.268248698 3.178183517
15ZBLK 4 1 Grain 4 End1 3.99E+11 1716 2.22233515 3.113851206
163BLK 4 1 Grain 4 End1 7.18E+11 20475 2.524745564 3.537577138
175ZRED 4 1 Grain 4 End1 2.08E+11 4421 2.113107696 2.960805865
1ZBLKY 4 1 Grain 4 End1 6.84E+11 43059 2.593311258 3.633648772
20SXZBLK 4 1 Grain 4 End1 3.16E+11 20297 1.878154129 2.631597894
22ZBLK 4 1 Grain 4 End1 7.70E+11 154975 2.263447759 3.171456625
63ZBLK 4 1 Grain 4 End1 2.10E+11 13317 2.444859889 3.425644379
6ZBLK 4 1 Grain 4 End1 1.31E+11 1395 2.630183444 3.685312672
82ZBLK 4 1 Grain 4 End1 1.10E+12 5368 2.102445712 2.945866701
92ZBLK 4 1 Grain 4 End1 4.32E+11 14981 2.137551055 2.995054968
94BLK 4 1 Grain 4 End1 1.54E+11 1680 2.533433557 3.549750423
126BLK 1 2 Forage 1 End2 2.22E+11 13000 4.760093885 1.775579657
13ZBLK 1 2 Forage 1 End2 6.75E+11 18291 4.585536093 1.71046723
157BLK 1 2 Forage 1 End2 2.88E+11 8904 5.286298418 1.971861094
162ZRED 1 2 Forage 1 End2 1.85E+11 3124 4.501846838 1.679250002
17ZBLKY 1 2 Forage 1 End2 1.02E+11 4288 4.722218572 1.761451651
184ZBLK 1 2 Forage 1 End2 4.28E+11 18173 4.787683496 1.785870957
1ZBLKW 1 2 Forage 1 End2 1.26E+11 3974 4.120447496 1.536982868
2094ZBLK 1 2 Forage 1 End2 2.80E+11 22940 5.320906238 1.98477028
20LZBLK 1 2 Forage 1 End2 3.00E+11 1865 4.910904822 1.831834185
29ZBLK 1 2 Forage 1 End2 2.75E+11 6551 4.64713525 1.733444553
2ZBLKG 1 2 Forage 1 End2 4.53E+11 12748 5.216415474 1.945793806
60ZRED 1 2 Forage 1 End2 2.45E+11 15630 4.320339869 1.611545438
77BLK 1 2 Forage 1 End2 1.44E+11 4192 4.946939294 1.845275532
8ZBLK 1 2 Forage 1 End2 66556874137 3308 5.369136284 2.002760742
91ZRED 1 2 Forage 1 End2 35178277612 861 5.194279355 1.937536734
112BLKW 2 2 Grain 2 End2 22345514304 35522 2.189470508 3.067802525
1226 BLK 2 2 Grain 2 End2 23881492608 48447 2.61032416 3.657486601
12ZBLK 2 2 Grain 2 End2 9521876928 21520 2.66964942 3.740610891
134BLK 2 2 Grain 2 End2 17265347752 62156 3.266154115 4.576410507
160ZRED 2 2 Grain 2 End2 1.06E+11 201494 2.801511562 3.925371093
166ZRED 2 2 Grain 2 End2 29245020768 9813 2.633190427 3.689525942
17ZBLKG 2 2 Grain 2 End2 28686200320 151168 2.684194907 3.760991472
226ZBLK 2 2 Grain 2 End2 35823496868 203516 2.656602944 3.722330667
3ZBLK 2 2 Grain 2 End2 19774776776 5962 3.01716587 4.22753768
58BLK 2 2 Grain 2 End2 6712885842 10103 2.776815993 3.890768604
60ZBLK 2 2 Grain 2 End2 41185544916 96469 2.757875102 3.86422935
7ZBLK 2 2 Grain 2 End2 7965902400 79680 2.876690768 4.030709327
95BLK 2 2 Grain 2 End2 29843174520 33088 3.319343593 4.650937575
9PZRED 2 2 Grain 2 End2 82361326080 274104 2.695285046 3.776530553
107ZRED 3 2 Forage 3 End2 1.59E+11 170772 4.574352981 1.706295778
129BLK 3 2 Forage 3 End2 7594466101 1081 5.509799583 2.055230063
150ZRED 3 2 Forage 3 End2 56872492896 33383 4.602932045 1.716956157
168BLK 3 2 Forage 3 End2 64542557920 5990 5.156588126 1.923477393
174ZBLK 3 2 Forage 3 End2 20398760236 601 4.777512847 1.782077167
185ZRED 3 2 Forage 3 End2 1.01E+11 12468 4.531116217 1.690167878
2ZBLKY 3 2 Forage 3 End2 1.74E+11 1757 5.336898548 1.990735629
4089ZBLK 3 2 Forage 3 End2 1.88E+11 2227 4.617405661 1.722355012
438XZRED 3 2 Forage 3 End2 3.83E+11 17545 4.698264622 1.752516503
4ZBLK 3 2 Forage 3 End2 3.96E+11 7375 4.899836763 1.827705648
706ZBLK 3 2 Forage 3 End2 3.35E+11 45618 4.437969639 1.655422939
86ZRED 3 2 Forage 3 End2 3.58E+11 3410 4.810601973 1.79441986
89BLK 3 2 Forage 3 End2 3.51E+11 22147 4.768193587 1.778600956
112XZBLKG 4 2 Grain 4 End2 2.68E+11 49973 2.531626089 3.547217868
1191ZBLK 4 2 Grain 4 End2 2.64E+11 6067 2.63885618 3.697464579
122ZRED 4 2 Grain 4 End2 8.69E+11 11653 2.389283575 3.347772968
14ZBLK 4 2 Grain 4 End2 9.29E+11 50505 2.780220526 3.895538906
15ZBLK 4 2 Grain 4 End2 9.35E+11 11492 2.662929278 3.731194885
163BLK 4 2 Grain 4 End2 5.01E+11 12751 2.616739418 3.666475416
175ZRED 4 2 Grain 4 End2 1.19E+12 14100 2.539769021 3.558627433
20SXZBLK 4 2 Grain 4 End2 5.57E+11 22956 2.310979313 3.238056024
22ZBLK 4 2 Grain 4 End2 2.60E+11 23005 2.772700065 3.885001523
63ZBLK 4 2 Grain 4 End2 2.98E+11 3578 2.921279989 4.093186042
6ZBLK 4 2 Grain 4 End2 4.77E+11 11550 2.511694326 3.519290242
82ZBLK 4 2 Grain 4 End2 2.55E+11 3153 2.781770351 3.897710461
92ZBLK 4 2 Grain 4 End2 1.95E+11 48511 2.666117852 3.735662593
94BLK 4 2 Grain 4 End2 1.02E+12 104139 2.966186797 4.156107749
Inline. -- Bert On Tue, Apr 26, 2016 at 2:25 PM, Andr? Luis Neves <andrluis at ualberta.ca> wrote:> Ok. I`m trying to run a Poisson glmm with an observation-level random > intercept. But I`m getting the following error for the 'Baci' variable: > > 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in > pwrssUpdate'. I guess this message is because the baci variable is not a > an integer,Why would you "guess" that? Given your magnitudes, I suspect it's a scaling issue. Try centering and scaling your Baci variable before fitting. Cheers, Bert and cannot be transformed into an integer as R has a threshold> of > 2x10^9 even in 64 bit R. > > It runs fine for the fungii variable. > > If you guys want to run the data (attached), the full command is below. > > Thanks. > > --------------------------------------------- > > ##Import data: > > qPCR <- read.delim(file.choose(), > header = TRUE, > dec = ".") > > ##Load package > > library(lme4) > > ##Other steps: > > qPCR$obs <- 1:nrow(qPCR) > qPCR$fID<-as.factor(qPCR$ID) > qPCR$fDiet<-as.factor(qPCR$Diet) > > ##Run the model: > > M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs), > family = poisson, data=qPCR) > > > > Andre > > > > On Tue, Apr 26, 2016 at 2:36 PM, jim holtman <jholtman at gmail.com> wrote: > >> Can you explain why you need them as 'integer', A floating point >> representation can hold a value upto ~4.5e15 as an "integer" keeping the >> precision that you might need. >> >> >> Jim Holtman >> Data Munger Guru >> >> What is the problem that you are trying to solve? >> Tell me what you want to do, not how you want to do it. >> >> On Tue, Apr 26, 2016 at 1:11 PM, Andr? Luis Neves <andrluis at ualberta.ca> >> wrote: >> >>> Dear all: >>> >>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers >>> (using excel) and then imported the data (.txt) into R. Interestingly, the >>> other three variables were loaded as INT, but the 'Baci' one continued as >>> Num. >>> >>> I imported the data using the following command line: >>> >>> X <- read.delim(file.choose(), >>> header = TRUE, >>> dec = ".") >>> >>> Here is the structure of X: >>> >>> > str(X) >>> 'data.frame': 115 obs. of 5 variables: >>> $ ID : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27 >>> 29 31 32 36 ... >>> $ Baci : num 2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ... >>> $ Meti : int 352645997 334146268 767208656 171567266 462747405 >>> 414905627 237010514 387480048 214671355 328813226 ... >>> $ Fungii : int 43645 19009 15998 2189 8972 8240 3133 17922 6156 13746 >>> ... >>> $ Protozoai: int 3220523 1851891 3252462 1665675 34123768 23175015 >>> 203685 >>> 4261780 43110492 69802572 ... >>> >>> >>> I need Baci as an integer, and tried to convert it using as.integer >>> function, but was not successful. >>> >>> >>> Could anyone please help me to solve this problem. >>> >>> Thanks, >>> >>> >>> >>> -- >>> Andre >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> 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. >>> >> >> > > > -- > Andre > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
Hi Bert: I thought in centering Baci variable, but I wouldn`t like to draw a conclusion based on the scaled response variable. On the other hand, if I had to center the explanatory variable, that would be great, but I cannot, as it is a factor. Thanks a lot for your time. I really appreciated your help. Best regards, Andre On Tue, Apr 26, 2016 at 4:11 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote:> Inline. > > -- Bert > > > On Tue, Apr 26, 2016 at 2:25 PM, Andr? Luis Neves <andrluis at ualberta.ca> > wrote: > > Ok. I`m trying to run a Poisson glmm with an observation-level random > > intercept. But I`m getting the following error for the 'Baci' variable: > > > > 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in > > pwrssUpdate'. I guess this message is because the baci variable is not a > > an integer, > > Why would you "guess" that? Given your magnitudes, I suspect it's a > scaling issue. Try centering and scaling your Baci variable before > fitting. > > Cheers, > Bert > > > > > > and cannot be transformed into an integer as R has a threshold > > of > > 2x10^9 even in 64 bit R. > > > > It runs fine for the fungii variable. > > > > If you guys want to run the data (attached), the full command is below. > > > > Thanks. > > > > --------------------------------------------- > > > > ##Import data: > > > > qPCR <- read.delim(file.choose(), > > header = TRUE, > > dec = ".") > > > > ##Load package > > > > library(lme4) > > > > ##Other steps: > > > > qPCR$obs <- 1:nrow(qPCR) > > qPCR$fID<-as.factor(qPCR$ID) > > qPCR$fDiet<-as.factor(qPCR$Diet) > > > > ##Run the model: > > > > M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs), > > family = poisson, data=qPCR) > > > > > > > > Andre > > > > > > > > On Tue, Apr 26, 2016 at 2:36 PM, jim holtman <jholtman at gmail.com> wrote: > > > >> Can you explain why you need them as 'integer', A floating point > >> representation can hold a value upto ~4.5e15 as an "integer" keeping the > >> precision that you might need. > >> > >> > >> Jim Holtman > >> Data Munger Guru > >> > >> What is the problem that you are trying to solve? > >> Tell me what you want to do, not how you want to do it. > >> > >> On Tue, Apr 26, 2016 at 1:11 PM, Andr? Luis Neves <andrluis at ualberta.ca > > > >> wrote: > >> > >>> Dear all: > >>> > >>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers > >>> (using excel) and then imported the data (.txt) into R. Interestingly, > the > >>> other three variables were loaded as INT, but the 'Baci' one continued > as > >>> Num. > >>> > >>> I imported the data using the following command line: > >>> > >>> X <- read.delim(file.choose(), > >>> header = TRUE, > >>> dec = ".") > >>> > >>> Here is the structure of X: > >>> > >>> > str(X) > >>> 'data.frame': 115 obs. of 5 variables: > >>> $ ID : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 > 26 27 > >>> 29 31 32 36 ... > >>> $ Baci : num 2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ... > >>> $ Meti : int 352645997 334146268 767208656 171567266 462747405 > >>> 414905627 237010514 387480048 214671355 328813226 ... > >>> $ Fungii : int 43645 19009 15998 2189 8972 8240 3133 17922 6156 > 13746 > >>> ... > >>> $ Protozoai: int 3220523 1851891 3252462 1665675 34123768 23175015 > >>> 203685 > >>> 4261780 43110492 69802572 ... > >>> > >>> > >>> I need Baci as an integer, and tried to convert it using as.integer > >>> function, but was not successful. > >>> > >>> > >>> Could anyone please help me to solve this problem. > >>> > >>> Thanks, > >>> > >>> > >>> > >>> -- > >>> Andre > >>> > >>> ______________________________________________ > >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>> 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. > >>> > >> > >> > > > > > > -- > > Andre > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. >-- Andre [[alternative HTML version deleted]]