I am trying to move from long format data to wide format in order to do some correlation analyses.
But, dcast seems to create to rows for the first subject and splits the data across those two rows filling the created empty cells with NA.
The first 2 subjects were being duplicated when I was using alphanumeric subject codes, I went to numeric subject numbers and that has to down to only the first subject being duplicated.
the first few lines of the long format data frame:
Subject Age Gender R_PTA L_PTA BE_PTA Avg_PTA L_Aided_SII R_Aided_SII Best_Aided_SII L_Unaided_SII R_Unaided_SII Best_Unaided_SII L_SII_Diff R_SII_Diff
1 1 74 M 48.33 53.33 48.33 50.83 31 42 42 14 25 25 17 17
2 2 77 F 36.67 36.67 36.67 36.67 73 67 73 44 43 44 29 24
3 3 72 F 45.00 41.67 41.67 43.33 42 34 42 35 28 35 7 6
4 4 66 F 36.67 36.67 36.67 36.67 66 76 76 44 44 44 22 32
5 5 38 F 41.67 46.67 41.67 44.17 48 58 58 23 29 29 25 29
6 6 65 M 35.00 43.33 35.00 39.17 46 60 60 32 46 46 14 14
Best_SII_Diff rSII MoCA_Vis MoCA_Nam MoCA_Attn MoCA_Lang MoCA_Abst MoCA_Del_Rec MoCA_Ori MoCA_Tot PNT Semantic Aided PNT_Prop PNT_Prop_Mod
1 17 -0.4231157 5 3 6 2 2 2 6 26 0.971 0.029 Unaided 0.971 0.983
2 29 1.2739255 3 3 5 0 2 2 5 20 0.954 0.046 Unaided 0.960 0.966
3 7 -1.2777889 4 2 5 2 2 5 6 26 0.966 0.034 Unaided 0.960 0.982
4 32 1.5959701 5 3 6 3 2 5 6 30 0.983 0.017 Unaided 0.983 0.994
5 29 0.9492167 4 2 6 3 1 3 6 25 0.983 0.017 Unaided 0.983 0.994
6 14 -0.2936395 4 2 6 2 2 2 6 24 0.989 0.011 Unaided 0.989 0.994
PNT_S_Wt PNT_P_Wt
1 0.046 0.041
2 0.073 0.033
3 0.045 0.074
4 0.049 0.057
5 0.049 0.057
6 0.049 0.057
Creating varlist:
varlist <- list(colnames(subset(PNT_Data_All2, ,c(18:27,29:33))))
My dcast command:
Data_Wide <- dcast(as.data.table(PNT_Data_All2),Subject + Age + Gender + R_PTA + L_PTA + BE_PTA + Avg_PTA + L_Aided_SII + R_Aided_SII + Best_Aided_SII + L_Unaided_SII + R_Unaided_SII + Best_Unaided_SII + L_SII_Diff + R_SII_Diff + Best_SII_Diff + rSII ~ Aided, value.var=varlist)
The resulting first few lines of the wide format:
Subject Age Gender R_PTA L_PTA BE_PTA Avg_PTA L_Aided_SII R_Aided_SII Best_Aided_SII L_Unaided_SII R_Unaided_SII Best_Unaided_SII L_SII_Diff R_SII_Diff
1: 1 74 M 48.33 53.33 48.33 50.83 31 42 42 14 25 25 17 17
2: 1 74 M 48.33 53.33 48.33 50.83 31 42 42 14 25 25 17 17
3: 2 77 F 36.67 36.67 36.67 36.67 73 67 73 44 43 44 29 24
4: 3 72 F 45.00 41.67 41.67 43.33 42 34 42 35 28 35 7 6
5: 4 66 F 36.67 36.67 36.67 36.67 66 76 76 44 44 44 22 32
6: 5 38 F 41.67 46.67 41.67 44.17 48 58 58 23 29 29 25 29
Notice Subject 1 has 2 entries. All of the other subjects seem correct
Is this a problem with my command/arguments? A bug in dcast?
Edit 1: Through the process of elimination, the extra entries only appear when I include the "rSII" variable. This is a variable that is calculated from a previous step in the script:
PNT_Data_All$rSII <- stdres(lm(Best_Aided_SII ~ Best_Unaided_SII, data=PNT_Data_All))
PNT_Data_All <- PNT_Data_All[, colnames(PNT_Data_All)[c(1:17,34,18:33)]]
Is there something about that calculated variable that would mess up dcast for some subjects?
Edit 2 to add my workaround:
I ended up rounding the calculated variable to 3 digits after the decimal and that solved the problem. Everything is casting correctly now with no duplicates.
PNT_Data_All$rSII <- format(round(stdres(lm(Best_Aided_SII ~ Best_Unaided_SII, data=PNT_Data_All)),3),nsmall=3)
Related
I guess something similar should have been asked before, however I could only find an answer for python and SQL. So please notify me in the comments when this was also asked for R!
Data
Let's say we have a dataframe like this:
set.seed(1); df <- data.frame( position = 1:20,value = sample(seq(1,100), 20))
# In cause you do not get the same dataframe see the comment by #Ian Campbell - thanks!
position value
1 1 27
2 2 37
3 3 57
4 4 89
5 5 20
6 6 86
7 7 97
8 8 62
9 9 58
10 10 6
11 11 19
12 12 16
13 13 61
14 14 34
15 15 67
16 16 43
17 17 88
18 18 83
19 19 32
20 20 63
Goal
I'm interested in calculating the average value for n positions and subtract this from the average value of the next n positions, let's say n=5 for now.
What I tried
I now used this method, however when I apply this to a bigger dataframe it takes a huge amount of time, and hence wonder if there is a faster method for this.
calc <- function( pos ) {
this.five <- df %>% slice(pos:(pos+4))
next.five <- df %>% slice((pos+5):(pos+9))
differ = mean(this.five$value)- mean(next.five$value)
data.frame(dif= differ)
}
df %>%
group_by(position) %>%
do(calc(.$position))
That produces the following table:
position dif
<int> <dbl>
1 1 -15.8
2 2 9.40
3 3 37.6
4 4 38.8
5 5 37.4
6 6 22.4
7 7 4.20
8 8 -26.4
9 9 -31
10 10 -35.4
11 11 -22.4
12 12 -22.3
13 13 -0.733
14 14 15.5
15 15 -0.400
16 16 NaN
17 17 NaN
18 18 NaN
19 19 NaN
20 20 NaN
I suspect a data.table approach may be faster.
library(data.table)
setDT(df)
df[,c("roll.position","rollmean") := lapply(.SD,frollmean,n=5,fill=NA, align = "left")]
df[, result := rollmean[.I] - rollmean[.I + 5]]
df[,.(position,value,rollmean,result)]
# position value rollmean result
# 1: 1 27 46.0 -15.8
# 2: 2 37 57.8 9.4
# 3: 3 57 69.8 37.6
# 4: 4 89 70.8 38.8
# 5: 5 20 64.6 37.4
# 6: 6 86 61.8 22.4
# 7: 7 97 48.4 4.2
# 8: 8 62 32.2 -26.4
# 9: 9 58 32.0 -31.0
#10: 10 6 27.2 -35.4
#11: 11 19 39.4 -22.4
#12: 12 16 44.2 NA
#13: 13 61 58.6 NA
#14: 14 34 63.0 NA
#15: 15 67 62.6 NA
#16: 16 43 61.8 NA
#17: 17 88 NA NA
#18: 18 83 NA NA
#19: 19 32 NA NA
#20: 20 63 NA NA
Data
RNGkind(sample.kind = "Rounding")
set.seed(1); df <- data.frame( position = 1:20,value = sample(seq(1,100), 20))
RNGkind(sample.kind = "default")
Not sure if the title makes sense, but I am new to "R" and to say the least I am confused. As you can see in the code below I have multiple entries that have the same name. For example, time ON and sample 1 appears 3 times. I want to figure out how to calculate the average of the OD at time ON and sample 1. How do I go about doing this? I want to do this for all repeats in the data frame.
Thanks in advance! Hope my question makes sense.
> freednaod
time sample OD
1 ON 1 0.248
2 ON 1 0.245
3 ON 1 0.224
4 ON 2 0.262
5 ON 2 0.260
6 ON 2 0.255
7 ON 3 0.245
8 ON 3 0.249
9 ON 3 0.244
10 0 1 0.010
11 0 1 0.013
12 0 1 0.012
13 0 2 0.014
14 0 2 0.013
15 0 2 0.015
16 0 3 0.013
17 0 3 0.013
18 0 3 0.014
19 30 1 0.018
20 30 1 0.020
21 30 1 0.019
22 30 2 0.017
23 30 2 0.019
24 30 2 0.021
25 30 3 0.021
26 30 3 0.020
27 30 3 0.024
28 60 1 0.023
29 60 1 0.024
30 60 1 0.023
31 60 2 0.031
32 60 2 0.031
33 60 2 0.033
34 60 3 0.025
35 60 3 0.028
36 60 3 0.024
37 90 1 0.052
38 90 1 0.048
39 90 1 0.049
40 90 2 0.076
41 90 2 0.078
42 90 2 0.081
43 90 3 0.073
44 90 3 0.068
45 90 3 0.067
46 120 1 0.124
47 120 1 0.128
48 120 1 0.134
49 120 2 0.202
50 120 2 0.202
51 120 2 0.186
52 120 3 0.192
53 120 3 0.182
54 120 3 0.183
55 150 1 0.229
56 150 1 0.215
57 150 1 0.220
58 150 2 0.197
59 150 2 0.216
60 150 2 0.200
61 150 3 0.207
62 150 3 0.211
63 150 3 0.209
By converting the 'time' column to a factor with levels specified by the unique level, the output would be ordered in the same order as in the initial dataset
aggregate(OD~ sample + time, transform(freednaod,
time = factor(time, levels = unique(time))), mean)[c(2, 1, 3)]
Or using dplyr
library(dplyr)
freednaod %>%
group_by(time = factor(time, levels = unique(time)), sample) %>%
summarise(OD = mean(OD))
I've seen the answers about multiplying one matrix by another. But I have a single matrix, completely numerical.
As an example:
matrix = read.table(text =
"ID Mult t1 t2 t3 t4 t5
4 0.164 10 20 30 40 50
16 0.581 5 10 5 10 5
42 0.008 16 17 18 19 20
91 0.328 20 20 20 20 20
103 0.108 103 42 56 84 61",
h = T)
I want to multiply t1 through t5 by the multiplier, separately, and put the results in new columns in my matrix.
I would do it column by column, but for the fact that I have over 200 columns!
Hopefully, someone can suggest a more simple fix.
You could do:
df=read.table(text="ID Mult t1 t2 t3 t4 t5
4 0.164 10 20 30 40 50
16 0.581 5 10 5 10 5
42 0.008 16 17 18 19 20
91 0.328 20 20 20 20 20
103 0.108 103 42 56 84 61",h=T)
df[,c(paste0(colnames(df[,grepl("^t.*",colnames(df),perl = T)]),"bis"))]=df[,grepl("^t.*",colnames(df),perl = T)]*df$Mult
df[,grepl("^t.*",colnames(df),perl = T)] subsets df to only have the columns starting with "t"
df[,c(paste0(colnames(df[,grepl("^t.*",colnames(df),perl = T)]),"bis"))] take the colnames() of the previous subset, and concatenate them using paste0() with "bis" or any string to indicate the change. This creates the new columns which are filled with the results of the multiplication.
> df
ID Mult t1 t2 t3 t4 t5 t1bis t2bis t3bis t4bis t5bis
1 4 0.164 10 20 30 40 50 1.640 3.280 4.920 6.560 8.200
2 16 0.581 5 10 5 10 5 2.905 5.810 2.905 5.810 2.905
3 42 0.008 16 17 18 19 20 0.128 0.136 0.144 0.152 0.160
4 91 0.328 20 20 20 20 20 6.560 6.560 6.560 6.560 6.560
5 103 0.108 103 42 56 84 61 11.124 4.536 6.048 9.072 6.588
Some don't like loops, but I do sometimes. This is one of those times :)
mydf<-matrix
for (i in 3:length(mydf)){
mydf[,length(mydf)+1] <- mydf$Mult * mydf[i]
}
mydf
ID Mult t1 t2 t3 t4 t5 t1.1 t2.1 t3.1 t4.1 t5.1
1 4 0.164 10 20 30 40 50 1.640 3.280 4.920 6.560 8.200
2 16 0.581 5 10 5 10 5 2.905 5.810 2.905 5.810 2.905
3 42 0.008 16 17 18 19 20 0.128 0.136 0.144 0.152 0.160
4 91 0.328 20 20 20 20 20 6.560 6.560 6.560 6.560 6.560
5 103 0.108 103 42 56 84 61 11.124 4.536 6.048 9.072 6.588
I have two sets of panel data that I would like to merge. The problem is that, for each respective time interval, the variable which links the two data sets appears more frequently in the first data frame than the second. My objective is to add each row from the second data set to its corresponding row in the first data set, even if that necessitates copying said row multiple times in the same time interval. Specifically, I am working with basketball data from the NBA. The first data set is a panel of Player and Date while the second is one of Team (Tm) and Date. Thus, each Team entry should be copied multiple times per date, once for each player on that team who played that day. I could do this easily in excel, but the data frames are too large.
The result is 0 observations of 52 variables. I've experimented with bind, match, different versions of merge, and I've searched for everything I can think of; but, nothing seems to address this issue specifically. Disclaimer, I am very new to R.
Here is my code up until my road block:
HGwd = "~/Documents/Fantasy/Basketball"
library(plm)
library(mice)
library(VIM)
library(nnet)
library(tseries)
library(foreign)
library(ggplot2)
library(truncreg)
library(boot)
Pdata = read.csv("2015-16PlayerData.csv", header = T)
attach(Pdata)
Pdata$Age = as.numeric(as.character(Pdata$Age))
Pdata$Date = as.Date(Pdata$Date, '%m/%e/%Y')
names(Pdata)[8] = "OppTm"
Pdata$GS = as.factor(as.character(Pdata$GS))
Pdata$MP = as.numeric(as.character(Pdata$MP))
Pdata$FG = as.numeric(as.character(Pdata$FG))
Pdata$FGA = as.numeric(as.character(Pdata$FGA))
Pdata$X2P = as.numeric(as.character(Pdata$X2P))
Pdata$X2PA = as.numeric(as.character(Pdata$X2PA))
Pdata$X3P = as.numeric(as.character(Pdata$X3P))
Pdata$X3PA = as.numeric(as.character(Pdata$X3PA))
Pdata$FT = as.numeric(as.character(Pdata$FT))
Pdata$FTA = as.numeric(as.character(Pdata$FTA))
Pdata$ORB = as.numeric(as.character(Pdata$ORB))
Pdata$DRB = as.numeric(as.character(Pdata$DRB))
Pdata$TRB = as.numeric(as.character(Pdata$TRB))
Pdata$AST = as.numeric(as.character(Pdata$AST))
Pdata$STL = as.numeric(as.character(Pdata$STL))
Pdata$BLK = as.numeric(as.character(Pdata$BLK))
Pdata$TOV = as.numeric(as.character(Pdata$TOV))
Pdata$PF = as.numeric(as.character(Pdata$PF))
Pdata$PTS = as.numeric(as.character(Pdata$PTS))
PdataPD = plm.data(Pdata, index = c("Player", "Date"))
attach(PdataPD)
Tdata = read.csv("2015-16TeamData.csv", header = T)
attach(Tdata)
Tdata$Date = as.Date(Tdata$Date, '%m/%e/%Y')
names(Tdata)[3] = "OppTm"
Tdata$MP = as.numeric(as.character(Tdata$MP))
Tdata$FG = as.numeric(as.character(Tdata$FG))
Tdata$FGA = as.numeric(as.character(Tdata$FGA))
Tdata$X2P = as.numeric(as.character(Tdata$X2P))
Tdata$X2PA = as.numeric(as.character(Tdata$X2PA))
Tdata$X3P = as.numeric(as.character(Tdata$X3P))
Tdata$X3PA = as.numeric(as.character(Tdata$X3PA))
Tdata$FT = as.numeric(as.character(Tdata$FT))
Tdata$FTA = as.numeric(as.character(Tdata$FTA))
Tdata$PTS = as.numeric(as.character(Tdata$PTS))
Tdata$Opp.FG = as.numeric(as.character(Tdata$Opp.FG))
Tdata$Opp.FGA = as.numeric(as.character(Tdata$Opp.FGA))
Tdata$Opp.2P = as.numeric(as.character(Tdata$Opp.2P))
Tdata$Opp.2PA = as.numeric(as.character(Tdata$Opp.2PA))
Tdata$Opp.3P = as.numeric(as.character(Tdata$Opp.3P))
Tdata$Opp.3PA = as.numeric(as.character(Tdata$Opp.3PA))
Tdata$Opp.FT = as.numeric(as.character(Tdata$Opp.FT))
Tdata$Opp.FTA = as.numeric(as.character(Tdata$Opp.FTA))
Tdata$Opp.PTS = as.numeric(as.character(Tdata$Opp.PTS))
TdataPD = plm.data(Tdata, index = c("OppTm", "Date"))
attach(TdataPD)
PD = merge(PdataPD, TdataPD, by = "OppTm", all.x = TRUE)
attach(PD)
Any help on how to do this would be greatly appreciated!
EDIT
I've tweaked it a little from last night, but still nothing seems to do the trick. See the above, updated code for what I am currently using.
Here is the output for head(PdataPD):
Player Date Rk Pos Tm X..H OppTm W.L GS MP FG FGA FG. X2P
22408 Aaron Brooks 2015-10-27 817 G CHI CLE W 0 16 3 9 0.333 3
22144 Aaron Brooks 2015-10-28 553 G CHI # BRK W 0 16 5 9 0.556 3
21987 Aaron Brooks 2015-10-30 396 G CHI # DET L 0 18 2 6 0.333 1
21456 Aaron Brooks 2015-11-01 4687 G CHI ORL W 0 16 3 11 0.273 3
21152 Aaron Brooks 2015-11-03 4383 G CHI # CHO L 0 17 5 8 0.625 1
20805 Aaron Brooks 2015-11-05 4036 G CHI OKC W 0 13 4 8 0.500 3
X2PA X2P. X3P X3PA X3P. FT FTA FT. ORB DRB TRB AST STL BLK TOV PF PTS GmSc
22408 8 0.375 0 1 0.000 0 0 NA 0 2 2 0 0 0 2 1 6 -0.9
22144 3 1.000 2 6 0.333 0 0 NA 0 1 1 3 1 0 1 4 12 8.5
21987 2 0.500 1 4 0.250 0 0 NA 0 4 4 4 0 0 0 1 5 5.2
21456 6 0.500 0 5 0.000 0 0 NA 2 1 3 1 1 1 1 4 6 1.0
21152 3 0.333 4 5 0.800 0 0 NA 0 0 0 4 1 0 0 4 14 12.6
20805 5 0.600 1 3 0.333 0 0 NA 1 1 2 0 0 0 0 1 9 5.6
FPTS H.A
22408 7.50 H
22144 20.25 A
21987 16.50 A
21456 14.75 H
21152 24.00 A
20805 12.00 H
And for head(TdataPD):
OppTm Date Rk X Opp Result MP FG FGA FG. X2P X2PA X2P. X3P X3PA
2105 ATL 2015-10-27 71 DET L 94-106 240 37 82 0.451 29 55 0.527 8 27
2075 ATL 2015-10-29 41 # NYK W 112-101 240 42 83 0.506 32 59 0.542 10 24
2047 ATL 2015-10-30 13 CHO W 97-94 240 36 83 0.434 28 60 0.467 8 23
2025 ATL 2015-11-01 437 # CHO W 94-92 240 37 88 0.420 30 59 0.508 7 29
2001 ATL 2015-11-03 413 # MIA W 98-92 240 37 90 0.411 30 69 0.435 7 21
1973 ATL 2015-11-04 385 BRK W 101-87 240 37 76 0.487 29 54 0.537 8 22
X3P. FT FTA FT. PTS Opp.FG Opp.FGA Opp.FG. Opp.2P Opp.2PA Opp.2P. Opp.3P
2105 0.296 12 15 0.800 94 37 96 0.385 25 67 0.373 12
2075 0.417 18 26 0.692 112 38 93 0.409 32 64 0.500 6
2047 0.348 17 22 0.773 97 36 88 0.409 24 58 0.414 12
2025 0.241 13 14 0.929 94 32 86 0.372 18 49 0.367 14
2001 0.333 17 22 0.773 98 38 86 0.442 33 58 0.569 5
1973 0.364 19 24 0.792 101 36 83 0.434 31 62 0.500 5
Opp.3PA Opp.3P. Opp.FT Opp.FTA Opp.FT. Opp.PTS
2105 29 0.414 20 26 0.769 106
2075 29 0.207 19 21 0.905 101
2047 30 0.400 10 13 0.769 94
2025 37 0.378 14 15 0.933 92
2001 28 0.179 11 16 0.688 92
1973 21 0.238 10 13 0.769 87
If there is way to truncate the output from dput(head(___)), I am not familiar with it. It appears that simply erasing the excess characters would remove entire variables from the dataset.
It would help if you posted your data (or a working subset of it) and a little more detail on how you are trying to merge, but if I understand what you are trying to do, you want each final data record to have individual stats for each player on a particular date followed by the player's team's stats for that date. In this case, you should have a team column in the Player table that identifies the player's team, and then join the two tables on the composite key Date and Team by setting the by= attribute in merge:
merge(PData, TData, by=c("Date", "Team"))
The fact that the data frames are of different lengths doesn't matter--this is exactly what join/merge operations are for.
For an alternative to merge(), you might check out the dplyr package join functions at https://cran.r-project.org/web/packages/dplyr/vignettes/two-table.html
My question is similar to Fill region between two loess-smoothed lines in R with ggplot1
But I have two groups.
g1<-ggplot(NVIQ_predict,aes(cogn.age, predict, color=as.factor(NVIQ_predict$group)))+
geom_smooth(aes(x = cogn.age, y = upper,group=group),se=F)+
geom_line(aes(linetype = group), size = 0.8)+
geom_smooth(aes(x = cogn.age, y = lower,group=group),se=F)
I want to fill red and blue for each group.
I tried:
gg1 <- ggplot_build(g1)
df2 <- data.frame(x = gg1$data[[1]]$x,
ymin = gg1$data[[1]]$y,
ymax = gg1$data[[3]]$y)
g1 + geom_ribbon(data = df2, aes(x = x, ymin = ymin, ymax = ymax),fill = "grey", alpha = 0.4)
But it gave me the error: Aesthetics must either be length one, or the same length as the dataProblems
I get the same error every time my geom_ribbon() data and ggplot() data differ.
Can somebody help me with it? Thank you so much!
My data looks like:
> NVIQ_predict
cogn.age predict upper lower group
1 7 39.04942 86.68497 18.00000 1
2 8 38.34993 82.29627 18.00000 1
3 10 37.05174 74.31657 18.00000 1
4 11 36.45297 70.72421 18.00000 1
5 12 35.88770 67.39555 18.00000 1
6 13 35.35587 64.32920 18.00000 1
7 14 34.85738 61.52322 18.00000 1
8 16 33.95991 56.68024 18.00000 1
9 17 33.56057 54.63537 18.00000 1
10 18 33.19388 52.83504 18.00000 1
11 19 32.85958 51.27380 18.00000 1
12 20 32.55752 49.94791 18.00000 1
13 21 32.28766 48.85631 18.00000 1
14 24 31.67593 47.09206 18.00000 1
15 25 31.53239 46.91136 18.00000 1
16 28 31.28740 48.01764 18.00000 1
17 32 31.36627 50.55201 18.00000 1
18 35 31.73386 53.19630 18.00000 1
19 36 31.91487 54.22624 18.00000 1
20 37 32.13026 55.25721 18.00000 1
21 38 32.38237 56.26713 18.00000 1
22 40 32.98499 58.36229 18.00000 1
23 44 34.59044 62.80187 18.00000 1
24 45 35.06804 64.01951 18.00000 1
25 46 35.57110 65.31888 18.00000 1
26 47 36.09880 66.64696 17.93800 1
27 48 36.72294 67.60053 17.97550 1
28 49 37.39182 68.49995 18.03062 1
29 50 38.10376 69.35728 18.10675 1
30 51 38.85760 70.17693 18.18661 1
31 52 39.65347 70.95875 18.27524 1
32 53 40.49156 71.70261 18.38020 1
33 54 41.35332 72.44006 17.90682 1
34 59 46.37849 74.91802 18.63206 1
35 60 47.53897 75.66218 19.64432 1
36 61 48.74697 76.43933 20.82346 1
37 63 51.30607 78.02426 23.73535 1
38 71 63.43129 86.05467 40.43482 1
39 72 65.15618 87.44794 42.72704 1
40 73 66.92714 88.95324 45.01966 1
41 84 89.42079 114.27939 68.03834 1
42 85 91.73831 117.44007 69.83676 1
43 7 33.69504 54.03695 15.74588 2
44 8 34.99931 53.96500 18.00533 2
45 10 37.61963 54.05684 22.43516 2
46 11 38.93493 54.21969 24.60049 2
47 12 40.25315 54.45963 26.73027 2
48 13 41.57397 54.77581 28.82348 2
49 14 42.89710 55.16727 30.87982 2
50 16 45.54954 56.17193 34.88453 2
51 17 46.87877 56.78325 36.83632 2
52 18 48.21025 57.46656 38.75807 2
53 19 49.54461 58.22266 40.65330 2
54 20 50.88313 59.05509 42.52505 2
55 21 52.22789 59.97318 44.36944 2
56 24 56.24397 63.21832 49.26963 2
57 25 57.55394 64.33850 50.76938 2
58 28 61.45282 68.05043 54.85522 2
59 32 66.44875 72.85234 60.04517 2
60 35 69.96560 76.06171 63.86949 2
61 36 71.09268 77.06821 65.11714 2
62 37 72.19743 78.04559 66.34927 2
63 38 73.28041 78.99518 67.56565 2
64 40 75.37861 80.81593 69.94129 2
65 44 79.29028 84.20275 74.37780 2
66 45 80.20272 85.00888 75.39656 2
67 46 81.08645 85.80180 76.37110 2
68 47 81.93696 86.57689 77.29704 2
69 48 82.75920 87.34100 78.17739 2
70 49 83.55055 88.09165 79.00945 2
71 50 84.30962 88.82357 79.79567 2
72 51 85.03743 89.53669 80.53817 2
73 52 85.73757 90.23223 81.24291 2
74 53 86.41419 90.91607 81.91232 2
75 54 87.05716 91.58632 82.52800 2
76 59 89.75923 94.58218 84.93629 2
77 60 90.18557 95.05573 85.31541 2
78 61 90.58166 95.51469 85.64864 2
79 63 91.27115 96.31107 86.23124 2
80 71 92.40983 98.35031 86.46934 2
81 72 92.36362 98.52258 86.20465 2
82 73 92.27734 98.67161 85.88308 2
83 84 88.66150 98.84699 78.47602 2
84 85 88.08846 98.73625 77.44067 2
According to Gregor, I tried inherit.aes = FALSE, the error is gone. But my plot looks like:
We've got all the info we need. Now we just need to, ahem, connect the dots ;-)
First the input data:
NVIQ_predict <- read.table(text = "
id cogn.age predict upper lower group
1 7 39.04942 86.68497 18.00000 1
2 8 38.34993 82.29627 18.00000 1
3 10 37.05174 74.31657 18.00000 1
4 11 36.45297 70.72421 18.00000 1
5 12 35.88770 67.39555 18.00000 1
6 13 35.35587 64.32920 18.00000 1
7 14 34.85738 61.52322 18.00000 1
8 16 33.95991 56.68024 18.00000 1
9 17 33.56057 54.63537 18.00000 1
10 18 33.19388 52.83504 18.00000 1
11 19 32.85958 51.27380 18.00000 1
12 20 32.55752 49.94791 18.00000 1
13 21 32.28766 48.85631 18.00000 1
14 24 31.67593 47.09206 18.00000 1
15 25 31.53239 46.91136 18.00000 1
16 28 31.28740 48.01764 18.00000 1
17 32 31.36627 50.55201 18.00000 1
18 35 31.73386 53.19630 18.00000 1
19 36 31.91487 54.22624 18.00000 1
20 37 32.13026 55.25721 18.00000 1
21 38 32.38237 56.26713 18.00000 1
22 40 32.98499 58.36229 18.00000 1
23 44 34.59044 62.80187 18.00000 1
24 45 35.06804 64.01951 18.00000 1
25 46 35.57110 65.31888 18.00000 1
26 47 36.09880 66.64696 17.93800 1
27 48 36.72294 67.60053 17.97550 1
28 49 37.39182 68.49995 18.03062 1
29 50 38.10376 69.35728 18.10675 1
30 51 38.85760 70.17693 18.18661 1
31 52 39.65347 70.95875 18.27524 1
32 53 40.49156 71.70261 18.38020 1
33 54 41.35332 72.44006 17.90682 1
34 59 46.37849 74.91802 18.63206 1
35 60 47.53897 75.66218 19.64432 1
36 61 48.74697 76.43933 20.82346 1
37 63 51.30607 78.02426 23.73535 1
38 71 63.43129 86.05467 40.43482 1
39 72 65.15618 87.44794 42.72704 1
40 73 66.92714 88.95324 45.01966 1
41 84 89.42079 114.27939 68.03834 1
42 85 91.73831 117.44007 69.83676 1
43 7 33.69504 54.03695 15.74588 2
44 8 34.99931 53.96500 18.00533 2
45 10 37.61963 54.05684 22.43516 2
46 11 38.93493 54.21969 24.60049 2
47 12 40.25315 54.45963 26.73027 2
48 13 41.57397 54.77581 28.82348 2
49 14 42.89710 55.16727 30.87982 2
50 16 45.54954 56.17193 34.88453 2
51 17 46.87877 56.78325 36.83632 2
52 18 48.21025 57.46656 38.75807 2
53 19 49.54461 58.22266 40.65330 2
54 20 50.88313 59.05509 42.52505 2
55 21 52.22789 59.97318 44.36944 2
56 24 56.24397 63.21832 49.26963 2
57 25 57.55394 64.33850 50.76938 2
58 28 61.45282 68.05043 54.85522 2
59 32 66.44875 72.85234 60.04517 2
60 35 69.96560 76.06171 63.86949 2
61 36 71.09268 77.06821 65.11714 2
62 37 72.19743 78.04559 66.34927 2
63 38 73.28041 78.99518 67.56565 2
64 40 75.37861 80.81593 69.94129 2
65 44 79.29028 84.20275 74.37780 2
66 45 80.20272 85.00888 75.39656 2
67 46 81.08645 85.80180 76.37110 2
68 47 81.93696 86.57689 77.29704 2
69 48 82.75920 87.34100 78.17739 2
70 49 83.55055 88.09165 79.00945 2
71 50 84.30962 88.82357 79.79567 2
72 51 85.03743 89.53669 80.53817 2
73 52 85.73757 90.23223 81.24291 2
74 53 86.41419 90.91607 81.91232 2
75 54 87.05716 91.58632 82.52800 2
76 59 89.75923 94.58218 84.93629 2
77 60 90.18557 95.05573 85.31541 2
78 61 90.58166 95.51469 85.64864 2
79 63 91.27115 96.31107 86.23124 2
80 71 92.40983 98.35031 86.46934 2
81 72 92.36362 98.52258 86.20465 2
82 73 92.27734 98.67161 85.88308 2
83 84 88.66150 98.84699 78.47602 2
84 85 88.08846 98.73625 77.44067 2", header = TRUE)
NVIQ_predict$id <- NULL
Make sure the group column is a factor variable, so we can use it as a line type.
NVIQ_predict$group <- as.factor(NVIQ_predict$group)
Then build the plot.
library(ggplot2)
g1 <- ggplot(NVIQ_predict, aes(cogn.age, predict, color=group)) +
geom_smooth(aes(x = cogn.age, y = upper, group=group), method = loess, se = FALSE) +
geom_smooth(aes(x = cogn.age, y = lower, group=group), method = loess, se = FALSE) +
geom_line(aes(linetype = group), size = 0.8)
Finally, extract the (x,ymin) and (x,ymax) coordinates of the curves for group 1 as well as group 2. These pairs have identical x-coordinates, so connecting those points mimics shading the areas between both curves. This was explained in Fill region between two loess-smoothed lines in R with ggplot. The only difference here is that we need to be a bit more careful to select and connect the points that belong to the correct curves...
gp <- ggplot_build(g1)
d1 <- gp$data[[1]]
d2 <- gp$data[[2]]
df1 <- data.frame(x = d1[d1$group == 1,]$x,
ymin = d2[d2$group == 1,]$y,
ymax = d1[d1$group == 1,]$y)
df2 <- data.frame(x = d1[d1$group == 2,]$x,
ymin = d2[d2$group == 2,]$y,
ymax = d1[d1$group == 2,]$y)
g1 + geom_ribbon(data = df1, aes(x = x, ymin = ymin, ymax = ymax), inherit.aes = FALSE, fill = "grey", alpha = 0.4) +
geom_ribbon(data = df2, aes(x = x, ymin = ymin, ymax = ymax), inherit.aes = FALSE, fill = "grey", alpha = 0.4)
The result looks like this: