I have a data.frame mydf, that contains data from 27 subjects. There are two predictors, congruent (2 levels) and offset (5 levels), so overall there are 10 conditions. Each of the 27 subjects was tested 20 times under each condition, resulting in a total of 10*27*20 = 5400 observations. RT is the response variable. The structure looks like this:
> str(mydf)
'data.frame': 5400 obs. of 4 variables:
$ subject : Factor w/ 27 levels "1","2","3","5",..: 1 1 1 1 1 1 1 1 1 1 ...
$ congruent: logi TRUE FALSE FALSE TRUE FALSE TRUE ...
$ offset : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 5 5 1 2 5 5 2 2 3 5 ...
$ RT : int 330 343 457 436 302 311 595 330 338 374 ...
I've used daply() to calculate the mean RT of each subject in each of the 10 conditions:
myarray <- daply(mydf, .(subject, congruent, offset), summarize, mean = mean(RT))
The result looks just the way I wanted, i.e. a 3d-array; so to speak 5 tables (one for each offset condition) that show the mean of each subject in the congruent=FALSE vs. the congruent=TRUE condition.
However if I check the structure of myarray, I get a confusing output:
List of 270
$ : num 417
$ : num 393
$ : num 364
$ : num 399
$ : num 374
...
# and so on
...
[list output truncated]
- attr(*, "dim")= int [1:3] 27 2 5
- attr(*, "dimnames")=List of 3
..$ subject : chr [1:27] "1" "2" "3" "5" ...
..$ congruent: chr [1:2] "FALSE" "TRUE"
..$ offset : chr [1:5] "1" "2" "3" "4" ...
This looks totally different from the structure of the prototypical ozone array from the plyr package, even though it's a very similar format (3 dimensions, only numerical values).
I want to compute some further summarizing information on this array, by means of aaply. Precisely, I want to calculate the difference between the congruent and the incongruent means for each subject and offset.
However, already the most basic application of aaply() like aaply(myarray,2,mean) returns non-sense output:
FALSE TRUE
NA NA
Warning messages:
1: In mean.default(piece, ...) :
argument is not numeric or logical: returning NA
2: In mean.default(piece, ...) :
argument is not numeric or logical: returning NA
I have no idea, why the daply() function returns such weirdly structured output and thereby prevents any further use of aaply. Any kind of help is kindly appreciated, I frankly admit that I have hardly any experience with the plyr package.
Since you haven't included your data it's hard to know for sure, but I tried to make a dummy set off your str(). You can do what you want (I'm guessing) with two uses of ddply. First the means, then the difference of the means.
#Make dummy data
mydf <- data.frame(subject = rep(1:5, each = 150),
congruent = rep(c(TRUE, FALSE), each = 75),
offset = rep(1:5, each = 15), RT = sample(300:500, 750, replace = T))
#Make means
mydf.mean <- ddply(mydf, .(subject, congruent, offset), summarise, mean.RT = mean(RT))
#Calculate difference between congruent and incongruent
mydf.diff <- ddply(mydf.mean, .(subject, offset), summarise, diff.mean = diff(mean.RT))
head(mydf.diff)
# subject offset diff.mean
# 1 1 1 39.133333
# 2 1 2 9.200000
# 3 1 3 20.933333
# 4 1 4 -1.533333
# 5 1 5 -34.266667
# 6 2 1 -2.800000
Related
I'm trying to apply the lme function to my data, but the model gives follow message:
mod.1 = lme(lon ~ sex + month2 + bat + sex*month2, random=~1|id, method="ML", data = AA_patch_GLM, na.action=na.exclude)
Error in MEEM(object, conLin, control$niterEM) :
Singularity in backsolve at level 0, block 1
dput for data, copy from https://pastebin.com/tv3NvChR (too large to include here)
str(AA_patch_GLM)
'data.frame': 2005 obs. of 12 variables:
$ lon : num -25.3 -25.4 -25.4 -25.4 -25.4 ...
$ lat : num -51.9 -51.9 -52 -52 -52 ...
$ id : Factor w/ 12 levels "24641.05","24642.03",..: 1 1 1 1 1 1 1 1 1 1 ...
$ sex : Factor w/ 2 levels "F","M": 1 1 1 1 1 1 1 1 1 1 ...
$ bat : int -3442 -3364 -3462 -3216 -3216 -2643 -2812 -2307 -2131 -2131 ...
$ year : chr "2005" "2005" "2005" "2005" ...
$ month : chr "12" "12" "12" "12" ...
$ patch_id: Factor w/ 45 levels "111870.17_1",..: 34 34 34 34 34 34 34 34 34 34 ...
$ YMD : Date, format: "2005-12-30" "2005-12-31" "2005-12-31" ...
$ month2 : Ord.factor w/ 7 levels "January"<"February"<..: 7 7 7 7 7 1 1 1 1 1 ...
$ lonsc : num [1:2005, 1] -0.209 -0.213 -0.215 -0.219 -0.222 ...
$ batsc : num [1:2005, 1] 0.131 0.179 0.118 0.271 0.271 ...
What's the problem?
I saw a solution applying the lme4::lmer function, but there is another option to continue to use lme function?
The problem is that you have collinear combinations of predictors. In particular, here are some diagnostics:
## construct the fixed-effect model matrix for your problem
X <- model.matrix(~ sex + month2 + bat + sex*month2, data = AA_patch_GLM)
lc <- caret::findLinearCombos(X)
colnames(X)[lc$linearCombos[[1]]]
## [1] "sexM:month2^6" "(Intercept)" "sexM" "month2.L"
## [5] "month2.C" "month2^4" "month2^5" "month2^6"
## [9] "sexM:month2.L" "sexM:month2.C" "sexM:month2^4" "sexM:month2^5"
This is in a weird order, but it suggests that the sex × month interaction is causing problems. Indeed:
with(AA_patch_GLM, table(sex, month2))
## sex January February March April May June December
## F 367 276 317 204 43 0 6
## M 131 93 90 120 124 75 159
shows that you're missing data for one sex/month combination (i.e., no females were sampled in June).
You can:
construct the sex/month interaction yourself (data$SM <- with(data, interaction(sex, month2, drop = TRUE))) and use ~ SM + bat — but then you'll have to sort out main effects and interactions yourself (ugh)
construct the model matrix by hand (as above), drop the redundant column(s), then include all the resulting columns in the model:
d2 <- with(AA_patch_GLM,
data.frame(lon,
as.data.frame(X),
id))
## drop linearly dependent column
## note data.frame() has "sanitized" variable names (:, ^ both converted to .)
d2 <- d2[names(d2) != "sexM.month2.6"]
lme(reformulate(colnames(d2)[2:15], response = "lon"),
random=~1|id, method="ML", data = d2)
Again, the results will be uglier than the simpler version of the model.
use a patched version of nlme (I submitted a patch here but it hasn't been considered)
remotes::install_github("bbolker/nlme")
*I have a large data set including 2000 variables, including factors and continuous variables.
For example:
library(finalfit)
library(dplyr)
data(colon_s)
explanatory = c("age", "age.factor", "sex.factor", "obstruct.factor")
dependent = "perfor.factor"
I use the following function to compare the mean of each continuous variable among the level of the categorical dependent variable (ANOVA) or the percentage of each categorical variable among the level of the categorical dependent variable (CHI-SQUARE)
summary_factorlist(colon_s, dependent ="perfor.factor", explanatory =explanatory , add_dependent_label=T, p=T,p_cat="fisher", p_cont_para = "aov", fit_id
= T)
But as soon as running the above code, I got the following error:
Error in dplyr::summarise():
! Problem while computing ..1 = ...$p.value.
Caused by error in fisher.test():
! 'x' and 'y' must have at least 2 levels
*In the data set, there are some variables which do not include at least two levels or just one of their levels has a non-zero frequency. I was wondering if there is any loop function to remove the variable if one of these conditions satisfies.
If the variable includes just one level
If the variable includes more than one level but the frequency of just one level is no-zero.
if all values of the variable are missing*
Update (partial answer):
With this code we can remove factors with only one level and keep other non factor variables:
x <- colon_s[, (sapply(colon_s, nlevels)>1) | (sapply(colon_s, is.factor)==FALSE)]
The OP's code does work with the data provided
library(dplyr)
library(finalfit)
summary_factorlist(colon_s, dependent ="perfor.factor",
explanatory =explanatory ,
add_dependent_label=TRUE, p=TRUE,p_cat="fisher", p_cont_para = "aov", fit_id = TRUE)
Dependent: Perforation No Yes p fit_id index
Age (years) Mean (SD) 59.8 (11.9) 58.4 (13.3) 0.542 age 1
Age <40 years 68 (7.5) 2 (7.4) 1.000 age.factor<40 years 2
40-59 years 334 (37.0) 10 (37.0) age.factor40-59 years 3
60+ years 500 (55.4) 15 (55.6) age.factor60+ years 4
Sex Female 432 (47.9) 13 (48.1) 1.000 sex.factorFemale 5
Male 470 (52.1) 14 (51.9) sex.factorMale 6
Obstruction No 715 (81.2) 17 (63.0) 0.026 obstruct.factorNo 7
Yes 166 (18.8) 10 (37.0) obstruct.factorYes 8
The strcture of data shows the factor variables to have more than 1 level
> str(colon_s[c(explanatory, dependent)])
'data.frame': 929 obs. of 5 variables:
$ age : num 43 63 71 66 69 57 77 54 46 68 ...
..- attr(*, "label")= chr "Age (years)"
$ age.factor : Factor w/ 3 levels "<40 years","40-59 years",..: 2 3 3 3 3 2 3 2 2 3 ...
..- attr(*, "label")= chr "Age"
$ sex.factor : Factor w/ 2 levels "Female","Male": 2 2 1 1 2 1 2 2 2 1 ...
..- attr(*, "label")= chr "Sex"
$ obstruct.factor: Factor w/ 2 levels "No","Yes": NA 1 1 2 1 1 1 1 1 1 ...
..- attr(*, "label")= chr "Obstruction"
$ perfor.factor : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 1 1 1 1 1 ...
..- attr(*, "label")= chr "Perforation"
Regarding selection of factor variables with the condition mentioned, we could use
library(dplyr)
colon_s_sub <- colon_s %>%
select(where(~ is.factor(.x) && nlevels(.x) > 1 && all(table(.x) > 0) &
sum(complete.cases(.x)) > 0))
I have some output from the vegan function specaccum. It is a list of 8 objects of varying lengths;
> str(SPECIES)
List of 8
$ call : language specaccum(comm = PRETEND.DATA, method = "rarefaction")
$ method : chr "rarefaction"
$ sites : num [1:5] 1 2 3 4 5
$ richness : num [1:5] 20.9 34.5 42.8 47.4 50
$ sd : num [1:5] 1.51 2.02 1.87 1.35 0
$ perm : NULL
$ individuals: num [1:5] 25 50 75 100 125
$ freq : num [1:50] 1 2 3 2 4 3 3 3 4 2 ...
- attr(*, "class")= chr "specaccum"
I want to extract three of the lists ('richness', 'sd' and 'individuals') and convert them to columns in a data frame. I have developed a workaround;
SPECIES.rich <- data.frame(SPECIES[["richness"]])
SPECIES.sd <- data.frame(SPECIES[["sd"]])
SPECIES.individuals <- data.frame(SPECIES[["individuals"]])
SPECIES.df <- cbind(SPECIES.rich, SPECIES.sd, SPECIES.individuals)
But this seems clumsy and protracted. I wonder if anyone could suggest a neater solution? (Should I be looking at something with lapply??) Thanks!
Example data to generate the specaccum output;
Set.Seed(100)
PRETEND.DATA <- matrix(sample(0:1, 250, replace = TRUE), 5, 50)
library(vegan)
SPECIES <- specaccum(PRETEND.DATA, method = "rarefaction")
We can concatenate the names in a vector and extract it
SPECIES.df <- data.frame(SPECIES[c("richness", "sd", "individuals")])
Another alternative, similar to akrun, is:
ctoc1 = as.data.frame(cbind(SPECIES$richness, SPECIES$sd, SPECIES$individuals))
Please note that in both cases (my answer and akrun) you will get an error if the lengths of the columns do not match.
e.g.: SPECIES.df <- data.frame(SPECIES[c( "sd", "freq")])
Error in data.frame(richness = c(20.5549865665613, 33.5688503093388, 41.4708434700877, :
arguments imply differing number of rows:7, 47
If so, remember to use length() function :
length(SPECIES$sd) <- 47 # this will add NAs to increase the column length.
SPECIES.df <- data.frame(SPECIES[c("sd", "freq")])
SPECIES.df # dataframe with 2 columns and 7 rows.
I am using the ggmcmc package to produce a summary pdf file of rjags package output using the ggmcmc() function. However, I get the following error message:
> ggmcmc(x, file = "Model0-output.pdf")
Plotting histograms
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 160, 164
When I check the structure of the input dataframe I created with the ggs() function, everything looks to be correct.
> str(x)
'data.frame': 240000 obs. of 4 variables:
$ Iteration: int 1 2 3 4 5 6 7 8 9 10 ...
$ Chain : int 1 1 1 1 1 1 1 1 1 1 ...
$ Parameter: Factor w/ 32 levels "N[1]","N[2]",..: 1 1 1 1 1 1 1 1 1 1 ...
$ value : num 96 87 76 79 89 95 85 78 86 89 ...
- attr(*, "nChains")= int 3
- attr(*, "nParameters")= int 32
- attr(*, "nIterations")= int 2500
- attr(*, "nBurnin")= num 2000
- attr(*, "nThin")= num 2
- attr(*, "description")= chr "postout0"
- attr(*, "parallel")= logi FALSE
Can anyone help me identify where the error is being caused and how I can correct it? Am I missing something obvious?
ggmcmc 0.5.1 solves the calculation of the number of bins in a different manner that it did it in previous versions. Previous versions relied on ggplot2:::bin, whereas 0.5.1 computes the bins and their binwidth by itself.
It is likely your case that the range of some of the parameters was so extreme that rounding errors would make some of them have one more or one less bins, therefore producing this error.
When working on a hierarchical/multilevel/panel dataset, it may be very useful to adopt a package which returns the within- and between-group standard deviations of the available variables.
This is something that with the following data in Stata can be easily done through the command
xtsum, i(momid)
I made a research, but I cannot find any R package which can do that..
edit:
Just to fix ideas, an example of hierarchical dataset could be this:
son_id mom_id hispanic mom_smoke son_birthweigth
1 1 1 1 3950
2 1 1 0 3890
3 1 1 0 3990
1 2 0 1 4200
2 2 0 1 4120
1 3 0 0 2975
2 3 0 1 2980
The "multilevel" structure is given by the fact that each mother (higher level) has two or more sons (lower level). Hence, each mother defines a group of observations.
Accordingly, each dataset variable can vary either between and within mothers or only between mothers. birtweigth varies among mothers, but also within the same mother. Instead, hispanic is fixed for the same mother.
For example, the within-mother variance of son_birthweigth is:
# mom1 means
bwt_mean1 <- (3950+3890+3990)/3
bwt_mean2 <- (4200+4120)/2
bwt_mean3 <- (2975+2980)/2
# Within-mother variance for birthweigth
((3950-bwt_mean1)^2 + (3890-bwt_mean1)^2 + (3990-bwt_mean1)^2 +
(4200-bwt_mean2)^2 + (4120-bwt_mean2)^2 +
(2975-bwt_mean3)^2 + (2980-bwt_mean3)^2)/(7-1)
While the between-mother variance is:
# overall mean of birthweigth:
# mean <- sum(data$son_birthweigth)/length(data$son_birthweigth)
mean <- (3950+3890+3990+4200+4120+2975+2980)/7
# within variance:
((bwt_mean1-mean)^2 + (bwt_mean2-mean)^2 + (bwt_mean3-mean)^2)/(3-1)
I don't know what your stata command should reproduce, but to answer the second part of question about
hierarchical structure , it is easy to do this with list.
For example, you define a structure like this:
tree = list(
"var1" = list(
"panel" = list(type ='p',mean = 1,sd=0)
,"cluster" = list(type = 'c',value = c(5,8,10)))
,"var2" = list(
"panel" = list(type ='p',mean = 2,sd=0.5)
,"cluster" = list(type="c",value =c(1,2)))
)
To create this lapply is convinent to work with list
tree <- lapply(list('var1','var2'),function(x){
ll <- list(panel= list(type ='p',mean = rnorm(1),sd=0), ## I use symbol here not name
cluster= list(type = 'c',value = rnorm(3))) ## R prefer symbols
})
names(tree) <-c('var1','var2')
You can view he structure with str
str(tree)
List of 2
$ var1:List of 2
..$ panel :List of 3
.. ..$ type: chr "p"
.. ..$ mean: num 0.284
.. ..$ sd : num 0
..$ cluster:List of 2
.. ..$ type : chr "c"
.. ..$ value: num [1:3] 0.0722 -0.9413 0.6649
$ var2:List of 2
..$ panel :List of 3
.. ..$ type: chr "p"
.. ..$ mean: num -0.144
.. ..$ sd : num 0
..$ cluster:List of 2
.. ..$ type : chr "c"
.. ..$ value: num [1:3] -0.595 -1.795 -0.439
Edit after OP clarification
I think that package reshape2 is what you want. I will demonstrate this here.
The idea here is in order to do the multilevel analysis we need to reshape the data.
First to divide the variables into two groups :identifier and measured variables.
library(reshape2)
dat.m <- melt(dat,id.vars=c('son_id','mom_id')) ## other columns are measured
str(dat.m)
'data.frame': 21 obs. of 4 variables:
$ son_id : Factor w/ 3 levels "1","2","3": 1 2 3 1 2 1 2 1 2 3 ...
$ mom_id : Factor w/ 3 levels "1","2","3": 1 1 1 2 2 3 3 1 1 1 ...
$ variable: Factor w/ 3 levels "hispanic","mom_smoke",..: 1 1 1 1 1 1 1 2 2 2 ...
$ value : num 1 1 1 0 0 0 0 1 0 0 ..
Once your have data in "moten" form , you can "cast" to rearrange it in the shape that you want:
# mom1 means for all variable
acast(dat.m,variable~mom_id,mean)
1 2 3
hispanic 1.0000000 0 0.0
mom_smoke 0.3333333 1 0.5
son_birthweigth 3943.3333333 4160 2977.5
# Within-mother variance for birthweigth
acast(dat.m,variable~mom_id,function(x) sum((x-mean(x))^2))
1 2 3
hispanic 0.0000000 0 0.0
mom_smoke 0.6666667 0 0.5
son_birthweigth 5066.6666667 3200 12.5
## overall mean of each variable
acast(dat.m,variable~.,mean)
[,1]
hispanic 0.4285714
mom_smoke 0.5714286
son_birthweigth 3729.2857143
I know this question is four years old, but recently I wanted to do the same in R and came up with the following function. It depends on dplyr and tibble. Where: df is the dataframe, columns is a numerical vector to subset the dataframe and individuals is the column with the individuals.
xtsumR<-function(df,columns,individuals){
df<-dplyr::arrange_(df,individuals)
panel<-tibble::tibble()
for (i in columns){
v<-df %>% dplyr::group_by_() %>%
dplyr::summarize_(
mean=mean(df[[i]]),
sd=sd(df[[i]]),
min=min(df[[i]]),
max=max(df[[i]])
)
v<-tibble::add_column(v,variacao="overal",.before=-1)
v2<-aggregate(df[[i]],list(df[[individuals]]),"mean")[[2]]
sdB<-sd(v2)
varW<-df[[i]]-rep(v2,each=12) #
varW<-varW+mean(df[[i]])
sdW<-sd(varW)
minB<-min(v2)
maxB<-max(v2)
minW<-min(varW)
maxW<-max(varW)
v<-rbind(v,c("between",NA,sdB,minB,maxB),c("within",NA,sdW,minW,maxW))
panel<-rbind(panel,v)
}
var<-rep(names(df)[columns])
n1<-rep(NA,length(columns))
n2<-rep(NA,length(columns))
var<-c(rbind(var,n1,n1))
panel$var<-var
panel<-panel[c(6,1:5)]
names(panel)<-c("variable","variation","mean","standard.deviation","min","max")
panel[3:6]<-as.numeric(unlist(panel[3:6]))
panel[3:6]<-round(unlist(panel[3:6]),2)
return(panel)
}