[R] spaghetti plot - urgent

[Rosa Oliveira]

Thanks for the tip! Ulrik, I've solved the problem with a different
code....

Best ;)

Ulrik Stervbo <ulrik.stervbo at gmail.com> escreveu em qua, 19/07/2017 às
20:28 :

> Hi Rosa,
>
> You pass a vector to ggplot, which expects a data.frame. I am sure you
> meant to do this:
>
> point7$y_point7 <- point7$beta0_7 + point7$beta1_7*point7$time + point7
> $epsilon_7
>
> ggplot(point7, aes(time, y_point7)) + geom_line()
>
> HTH
> Ulrik
>
>
> On Wed, 19 Jul 2017 at 20:37 Rosa Oliveira <rosita21 at gmail.com> wrote:
>
>> Hi everyone,
>>
>> I’m trying to do a spaghetti plot and I know I’m doing all wrong, It must
>> be.
>>
>> What I need:
>>
>> 15 subjects, each with measurements over 5 different times (t1, ..., t5),
>> and the variable that I need to represent in the spaguetti plot is given by:
>>
>> PCR = b0 + b1 * ti + epsilon
>>
>> B0, - baseline of each subject
>> B1 - trajectory of each subject over time (so multiply by t)
>> Epsilon - error associated with each subject
>>
>> Regression model with mixed effects.
>>
>> Thus, I generated b0, b1, epsilon and time created sequence.
>>
>> But I need to do spaguetti plot of the outcome and I can not understand
>> how much I search the publications.
>>
>> Sorry for the stupidity, but I do not even know how to do it and I need
>> it with the utmost urgency to finish a publication proposal :(
>>
>> Follows what I tried to do :( :( :(
>>
>>
>> library(ggplot2)
>> library(reshape)
>> library(lattice)
>> library(gtable)
>> library(grid)
>>
>>
>> set.seed(9027)
>>
>> n.longitudinal.observations  = 5                          # number of PCR
>> measures (per subject) in the hospital period
>> subjects                             = 15                      # Number
>> of simulations (1 per subject in the study)
>>
>> beta0_7_gerar                      = rnorm(subjects, mean = 1, sd = .5)
>> beta0_7                                =
>> as.data.frame(matrix(beta0_7_gerar,nrow=subjects,ncol=1))      # beta 0 -
>> input variable used to calculate PCR (the outcome)
>> beta1_7_gerar                     = rnorm(subjects, mean = -1, sd = .5)
>> beta1_7                               =
>> as.data.frame(matrix(beta1_7_gerar,nrow=subjects,ncol=1) )      # beta 1 -
>> input variable used to calculate PCR (the outcome)
>>
>> tj_gerar                                = seq.int(1,
>> n.longitudinal.observations, 1)
>> epsilon_7_gerar                  = rnorm(5*subjects, mean = 0, sd = .1)
>> epsilon_7                             =
>> as.data.frame(matrix(epsilon_7_gerar,nrow=subjects,ncol=1) )   # epsilon_7
>> - input variable used to calculate PCR (the outcome) - associated with each
>> subject
>>
>> tj                                          =
>> as.data.frame(matrix(tj_gerar,nrow=subjects,ncol=1) )                   #
>> time
>>
>> point7 <- cbind(beta0_7, beta1_7, tj, epsilon_7)
>> point7
>> point7 <- as.data.frame(point7)
>>
>> colnames(point7) = c("beta0_7","beta1_7","time", "epsilon_7")
>>
>>
>> y_point7 <- point7$beta0_7 + point7$beta1_7*point7$time + point7
>> $epsilon_7             (the outcome of the study - PCR)
>> y_point7
>>
>> require(ggplot2)
>>
>> png('test.png')
>> p = ggplot(y_point7, aes(time, y_point7)) + geom_line()
>> print(p)
>> dev.off()
>> savehistory()
>>
>>
>>
>>
>>
>>
>> OR:
>>
>> In the last part I also tried:
>>
>>
>> ID = rep(1:3, each = 5)
>>
>>
>> point7 <- cbind(ID,beta0_7, beta1_7, tj, epsilon_7)
>> point7
>> point7 <- as.data.frame(point7)
>>
>> colnames(point7) = c("ID","beta0_7","beta1_7","time", "epsilon_7")
>>
>>
>>
>>
>>
>> y_point7 <- point7$beta0_7 + point7$beta1_7*point7$time + point7
>> $epsilon_7
>> y_point7
>>
>> crp7 <- y_point7
>>
>> head(point7, n = 15)
>>
>>
>> ggplot(aes(x = tj_gerar, y = crp7), data = point7) +
>>   geom_line(aes(group = ID), color = "gray") +
>>   geom_smooth(aes(group = 1), method = "lm", size = 3, color = "red", se
>> = FALSE) +
>>   theme_bw()
>>
>> But none of these worked :(
>>
>> I was looking to have something like:
>>
>>
>> Being the outcome PCR and the year the times (1, 2, 3, 4, 5).
>>
>> Can someone help me please?
>>
>>
>> Thanks,
>>
>> Best Rosa
>>
>>
>>
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>
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