Closed edvbb closed 4 years ago
MvZeijl1986
commented
4 years ago I have the same problem running an old script that used to work. I think it has something to do with the introduction of surv_fit. Now I use an old method for plotting the reference patients I want:
fit1 <- survfit(cox_model, newdata = newdata, data = df)
plot( fit1, main = "Title", xlab = "Months", ylab = "Survival probability", col = c("#5DC863FF", "#21908CFF","#3B528BFF", "#440154FF")
kassambara
commented
4 years ago Now, you need to specify the argument data in ggsurvplot(). The data should be same as the one used to compute survfit(). The following example works on my computer:
library("survival")
# Fit cox ph
#%%%%%%%%%%%%%
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung)
res.cox
# Survival curves by sex after adjusting by age and wt.loss
#%%%%%%%%%%%%%%%%%%%%%%%%
# we construct a new data frame with two rows,
# one for each value of sex; the other covariates are fixed to their average values
# Create the new data
new_df <- with(lung,
data.frame(sex = c(1, 2),
age = rep(mean(age, na.rm = TRUE), 2),
wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2)
)
)
new_df
# Survival curves with new data
#%%%%%%%%%%%%%%%%%%%%%%%%%%%
library(survminer)
fit <- survfit(res.cox, newdata = new_df)
ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv")Unfortunately, when I your example this also gives:
Error: object of type 'symbol' is not subsettable
I run: Rstudio - Version 1.2.1578 R - Version 3.6.1 (2019-07-05) -- "Action of the Toes" Survival - Version 3.1.8 Survminer - Version 0.4.6
edvbb
commented
4 years ago I can not re-Install the latest dev version
devtools::install_github("kassambara/survminer", build_vignettes = FALSE)
and get the error after
ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv") 
tpjoe
commented
4 years ago Now, you need to specify the argument
datain ggsurvplot(). The data should be same as the one used to computesurvfit(). The following example works on my computer:library("survival") # Fit cox ph #%%%%%%%%%%%%% res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung) res.cox # Survival curves by sex after adjusting by age and wt.loss #%%%%%%%%%%%%%%%%%%%%%%%% # we construct a new data frame with two rows, # one for each value of sex; the other covariates are fixed to their average values # Create the new data new_df <- with(lung, data.frame(sex = c(1, 2), age = rep(mean(age, na.rm = TRUE), 2), wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2) ) ) new_df # Survival curves with new data #%%%%%%%%%%%%%%%%%%%%%%%%%%% library(survminer) fit <- survfit(res.cox, newdata = new_df) ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2", censor = FALSE, surv.median.line = "hv")
I seem to have a similar problem with the new updates as well. The test code provided above also doesn't work for me. I got a similar error message as @MvZeijl1986 Session Info: Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS R version 3.6.1 (2019-07-05) survival_3.1-8 survminer_0.4.6
pacificasommers
commented
4 years ago I get the same error "Error: object of type 'symbol' is not subsettable" using the following code.
However, if I substitute the function surv_fit() for survfit(), no error occurs, but the plot is of all strata combined, instead of by sex. How can I separate these out by sex when using surv_fit?
library("survival")
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung)
new_df <- with(lung,
data.frame(sex = c(1, 2),
age = rep(mean(age, na.rm = TRUE), 2),
wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2)
)
)
library(survminer)
fit <- survfit(res.cox, newdata = new_df, data = lung)
ggsurvplot(fit, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv")Ubuntu 18.04.4 LTS (Bionic Beaver) R version 3.6.2 (2019-12-12) survminer_0.4.6.999 survival_3.1-8
manuelmateus16
commented
4 years ago I am also experiencing the same error "Error: object of type 'symbol' is not subsettable".
library(survminer)
library(survival)
res.cox <- coxph(Surv(tstart, tstop, Falecido) ~ Idade_no_diagnostico + Nr_cirurgias_acumuladas + Severidade, data=analise_survival_extended_Cox_PH)
fit <- survfit(res.cox, data=analise_survival_extended_Cox_PH)
ggsurvplot(fit, data=analise_survival_extended_Cox_PH)Session info R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.4 survminer_0.4.6 survival_3.1-8
Has anyone found a solution to overcome this error?
Thank you.
Rackdos
commented
4 years ago Hi! I have the same problem.. Has anyone managed to solve it?
edvbb
commented
4 years ago Now i do it with ggplot2
ALL CODE
library("survival")
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung)
res.cox# Survival curves by sex after adjusting by age and wt.loss
#%%%%%%%%%%%%%%%%%%%%%%%%
# we construct a new data frame with two rows,
# one for each value of sex; the other covariates are fixed to their average values
# Create the new data
sex_df <- with(lung,
data.frame(sex = c(1, 2),
age = rep(mean(age, na.rm = TRUE), 2),
wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2)
)
)
sex_df# Survival curves
library("ggplot2")
fit <- survfit(res.cox, newdata = sex_df)
dat = data.frame(surv = fit$surv,lower= fit$lower, upper = fit$upper,time= fit$time)
library(reshape2)
data = melt(dat, id="time")
library(tidyr)
data_wide <- data %>%
separate(col = variable, into = c("type", "sex"), sep = "\\.") %>%
spread(key = type, value = value)
g <- ggplot(data = data_wide) +
geom_line(aes(x = time, y = surv, group = sex, colour = sex),
size = 3.5,
linetype = 1) +
geom_ribbon(aes(x = time, ymin = lower, ymax = upper, group = sex, fill = sex),
alpha = 0.5) +
scale_colour_manual(values = c("#E7B800", "#2E9FDF", 'red')) +
scale_fill_manual(values = c("#E7B800", "#2E9FDF", 'red')) +
scale_x_continuous(limits = c(0, 840),
breaks = seq(0, 840, 120)) +
theme(legend.position = "top",
axis.text = element_text(size = 20),
axis.title = element_text(size = 20),
legend.text = element_text(size = 40),
legend.key.size = unit(3, "line"),
legend.title = element_blank()) +
ylab("Surv prob") +
geom_segment(aes(x = 0, y = 0.5, xend = max(q1$`50`), yend =0.5), color="grey50",
linetype="dashed", size=1.5)
q1 = as.data.frame(quantile(fit, conf.int = F))
for (i in 1:length(q1$`50`)) {
g = g + geom_segment(x = q1$`50`[i], y = 0, xend = q1$`50`[i], yend = 0.5,
color="grey50", linetype="dashed", size=1.5)
}
gThis issue is due to a recent change in the survival package. In older versions of the survival package, the function survfit(res.cox) returns an object of class survfit.cox. The class has been changed to survfitcox in the current survival package version.
Will be fixed in few minutes, thanks
kassambara
commented
4 years ago fixed in the latest dev version now (devtools::install_github("kassambara/survminer", build_vignettes = FALSE)), thanks.
Please let me know if it works for you so that we can close this issue.
library("survival")
# Fit cox ph
#%%%%%%%%%%%%%
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung)
res.cox
#> Call:
#> coxph(formula = Surv(time, status) ~ age + sex + wt.loss, data = lung)
#>
#> coef exp(coef) se(coef) z p
#> age 0.0200882 1.0202913 0.0096644 2.079 0.0377
#> sex -0.5210319 0.5939074 0.1743541 -2.988 0.0028
#> wt.loss 0.0007596 1.0007599 0.0061934 0.123 0.9024
#>
#> Likelihood ratio test=14.67 on 3 df, p=0.002122
#> n= 214, number of events= 152
#> (14 observations deleted due to missingness)
# Survival curves by sex after adjusting by age and wt.loss
#%%%%%%%%%%%%%%%%%%%%%%%%
# we construct a new data frame with two rows,
# one for each value of sex; the other covariates are fixed to their average values
# Create the new data
new_df <- with(lung,
data.frame(sex = c(1, 2),
age = rep(mean(age, na.rm = TRUE), 2),
wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2)
)
)
new_df
#> sex age wt.loss
#> 1 1 62.44737 9.831776
#> 2 2 62.44737 9.831776
# Survival curves with new data
#%%%%%%%%%%%%%%%%%%%%%%%%%%%
library(survminer)
#> Le chargement a nécessité le package : ggplot2
#> Le chargement a nécessité le package : ggpubr
fit <- survfit(res.cox, newdata = new_df)
ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv")
Created on 2020-05-16 by the reprex package (v0.3.0.9001)
Rackdos
commented
4 years ago Thank you so much for your time, I tried downloaded last version and I tried to run tour script, but I have the same problem. [image: image.png]
Il giorno sab 16 mag 2020 alle ore 16:44 Alboukadel KASSAMBARA < notifications@github.com> ha scritto:
fixed in the latest dev version now (devtools::install_github("kassambara/survminer", build_vignettes = FALSE)), thanks.
Please let me know if it works for you so that we can close this issue.
library("survival")
Fit cox ph
%%%%%%%%%%%%%
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung) res.cox
> Call:
> coxph(formula = Surv(time, status) ~ age + sex + wt.loss, data = lung)
>
> coef exp(coef) se(coef) z p
> age 0.0200882 1.0202913 0.0096644 2.079 0.0377
> sex -0.5210319 0.5939074 0.1743541 -2.988 0.0028
> wt.loss 0.0007596 1.0007599 0.0061934 0.123 0.9024
>
> Likelihood ratio test=14.67 on 3 df, p=0.002122
> n= 214, number of events= 152
> (14 observations deleted due to missingness)
Survival curves by sex after adjusting by age and wt.loss
%%%%%%%%%%%%%%%%%%%%%%%%
we construct a new data frame with two rows,
one for each value of sex; the other covariates are fixed to their average values
Create the new data
new_df <- with(lung,
data.frame(sex = c(1, 2), age = rep(mean(age, na.rm = TRUE), 2), wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2) )) new_df
> sex age wt.loss
> 1 1 62.44737 9.831776
> 2 2 62.44737 9.831776
Survival curves with new data
%%%%%%%%%%%%%%%%%%%%%%%%%%%
library(survminer)
> Le chargement a nécessité le package : ggplot2
> Le chargement a nécessité le package : ggpubr
fit <- survfit(res.cox, newdata = new_df)
ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv")Created on 2020-05-16 by the reprex package https://reprex.tidyverse.org (v0.3.0.9001)
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kassambara/survminer/issues/441#issuecomment-629656951, or unsubscribe https://github.com/notifications/unsubscribe-auth/APMO74LBNY5NDEURFFFN3L3RR2RFNANCNFSM4KIZ2KRQ .
kassambara
commented
4 years ago Please, provide your session infos. Here is mine:
library("survival")
library(survminer)
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 3.5.0 (2018-04-23)
#> os macOS Sierra 10.12.6
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate fr_FR.UTF-8
#> ctype fr_FR.UTF-8
#> tz Europe/Paris
#> date 2020-05-16
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
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#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.5.2)
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#> broom 0.5.5 2020-02-29 [1] CRAN (R 3.5.2)
#> callr 3.4.2 2020-02-12 [1] CRAN (R 3.5.2)
#> car 3.0-7 2020-03-11 [1] CRAN (R 3.5.2)
#> carData 3.0-3 2019-11-16 [1] CRAN (R 3.5.2)
#> cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.5.0)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 3.5.2)
#> colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.5.2)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
#> curl 4.3 2019-12-02 [1] CRAN (R 3.5.2)
#> data.table 1.12.8 2019-12-09 [1] CRAN (R 3.5.2)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
#> devtools 2.2.2 2020-02-17 [1] CRAN (R 3.5.2)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 3.5.2)
#> dplyr 0.8.99.9003 2020-05-16 [1] Github (tidyverse/dplyr@b4bc434)
#> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.5.2)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.5.2)
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#> ggplot2 * 3.3.0.9000 2020-05-16 [1] Github (tidyverse/ggplot2@e3fbccc)
#> ggpubr * 0.3.0.999 2020-05-16 [1] local (kassambara/ggpubr@73d0ff6)
#> ggsignif 0.6.0 2019-08-08 [1] CRAN (R 3.5.2)
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#> gtable 0.3.0 2019-03-25 [1] CRAN (R 3.5.2)
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#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.5.2)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
#> Matrix 1.2-14 2018-04-13 [1] CRAN (R 3.5.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.0)
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#> processx 3.4.2 2020-02-09 [1] CRAN (R 3.5.2)
#> ps 1.3.2 2020-02-13 [1] CRAN (R 3.5.2)
#> purrr 0.3.3 2019-10-18 [1] CRAN (R 3.5.2)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 3.5.2)
#> Rcpp 1.0.4 2020-03-17 [1] CRAN (R 3.5.2)
#> readxl 1.3.1 2019-03-13 [1] CRAN (R 3.5.2)
#> remotes 2.1.1 2020-02-15 [1] CRAN (R 3.5.2)
#> reprex 0.3.0.9001 2020-05-16 [1] Github (tidyverse/reprex@a019cc4)
#> rio 0.5.16 2018-11-26 [1] CRAN (R 3.5.0)
#> rlang 0.4.6.9000 2020-05-16 [1] Github (tidyverse/rlang@683f7a5)
#> rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.5.2)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
#> rstatix 0.5.0.999 2020-05-16 [1] Github (kassambara/rstatix@f762514)
#> scales 1.1.0 2019-11-18 [1] CRAN (R 3.5.2)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
#> stringi 1.4.6 2020-02-17 [1] CRAN (R 3.5.2)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.2)
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#>
#> [1] /Library/Frameworks/R.framework/Versions/3.5/Resources/libraryCreated on 2020-05-16 by the reprex package (v0.3.0.9001)
Rackdos
commented
4 years ago devtools::session_info() ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.0.0 (2020-04-24) os macOS Catalina 10.15.3 system x86_64, darwin17.0 ui RStudio language (EN) collate it_IT.UTF-8 ctype it_IT.UTF-8 tz Europe/Rome date 2020-05-16
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ! package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
broom 0.5.6 2020-04-20 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
car 3.0-7 2020-03-11 [1] CRAN (R 4.0.0)
carData 3.0-3 2019-11-16 [1] CRAN (R 4.0.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0)
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devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
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dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
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fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
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forcats 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
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ggsignif 0.6.0 2019-08-08 [1] CRAN (R 4.0.0)
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gmodels * 2.18.1 2018-06-25 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.0)
haven 2.2.0 2019-11-08 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
km.ci 0.5-2 2009-08-30 [1] CRAN (R 4.0.0)
KMsurv 0.1-5 2012-12-03 [1] CRAN (R 4.0.0)
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nlme 3.1-147 2020-04-13 [1] CRAN (R 4.0.0)
openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.0)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
psych 1.9.12.31 2020-01-08 [1] CRAN (R 4.0.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
readxl * 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
rio 0.5.16 2018-11-26 [1] CRAN (R 4.0.0)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rstatix 0.5.0 2020-04-28 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
survival * 3.1-12 2020-04-10 [1] CRAN (R 4.0.0)
V survminer * 0.4.6 2020-05-16 [1] Github (kassambara/survminer@e828309) survMisc 0.5.5 2018-07-05 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyr 1.0.3 2020-05-07 [1] CRAN (R 4.0.0)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
vcd * 1.4-7 2020-04-02 [1] CRAN (R 4.0.0)
vctrs 0.3.0 2020-05-11 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
zip 2.0.4 2019-09-01 [1] CRAN (R 4.0.0)
zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
V ── Loaded and on-disk version mismatch.
Il giorno sab 16 mag 2020 alle ore 16:44 Alboukadel KASSAMBARA < notifications@github.com> ha scritto:
fixed in the latest dev version now (devtools::install_github("kassambara/survminer", build_vignettes = FALSE)), thanks.
Please let me know if it works for you so that we can close this issue.
library("survival")
Fit cox ph
%%%%%%%%%%%%%
res.cox <- coxph(Surv(time, status) ~ age + sex + wt.loss, data = lung) res.cox
> Call:
> coxph(formula = Surv(time, status) ~ age + sex + wt.loss, data = lung)
>
> coef exp(coef) se(coef) z p
> age 0.0200882 1.0202913 0.0096644 2.079 0.0377
> sex -0.5210319 0.5939074 0.1743541 -2.988 0.0028
> wt.loss 0.0007596 1.0007599 0.0061934 0.123 0.9024
>
> Likelihood ratio test=14.67 on 3 df, p=0.002122
> n= 214, number of events= 152
> (14 observations deleted due to missingness)
Survival curves by sex after adjusting by age and wt.loss
%%%%%%%%%%%%%%%%%%%%%%%%
we construct a new data frame with two rows,
one for each value of sex; the other covariates are fixed to their average values
Create the new data
new_df <- with(lung,
data.frame(sex = c(1, 2), age = rep(mean(age, na.rm = TRUE), 2), wt.loss = rep(mean(wt.loss, na.rm = TRUE), 2) )) new_df
> sex age wt.loss
> 1 1 62.44737 9.831776
> 2 2 62.44737 9.831776
Survival curves with new data
%%%%%%%%%%%%%%%%%%%%%%%%%%%
library(survminer)
> Le chargement a nécessité le package : ggplot2
> Le chargement a nécessité le package : ggpubr
fit <- survfit(res.cox, newdata = new_df)
ggsurvplot(fit, data = new_df, conf.int = TRUE, palette = "Dark2",
censor = FALSE, surv.median.line = "hv")Created on 2020-05-16 by the reprex package https://reprex.tidyverse.org (v0.3.0.9001)
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kassambara/survminer/issues/441#issuecomment-629656951, or unsubscribe https://github.com/notifications/unsubscribe-auth/APMO74LBNY5NDEURFFFN3L3RR2RFNANCNFSM4KIZ2KRQ .
kassambara
commented
4 years ago I can see that you don't have the latest dev version of survminer (0.4.6.999).
Please re-start your R session and install the dev version using devtools::install_github("kassambara/survminer", build_vignettes = FALSE).
Rackdos
commented
4 years ago You’re right! sorry! It perfectly works! Thank You so much!
Il giorno sab 16 mag 2020 alle 17:20 Alboukadel KASSAMBARA < notifications@github.com> ha scritto:
I can see that you don't have the latest dev version of survminer (0.4.6.999).
Please re-start your R session and install the dev version using devtools::install_github("kassambara/survminer", build_vignettes = FALSE).
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kassambara/survminer/issues/441#issuecomment-629662485, or unsubscribe https://github.com/notifications/unsubscribe-auth/APMO74KEDH5A66PQYXJCOZLRR2VNHANCNFSM4KIZ2KRQ .
kassambara
commented
4 years ago thank you for the test and feedback; so we can now close this issue
Marsus1972
commented
4 years ago Hi,
I also have problems with survminer, couldnt load it with R 4.0.0 and now i've tried with 3.6.1 but then it says below:
"Error: package 'ggpubr' could not be loaded In addition: Warning message: package 'ggpubr' was built under R version 3.6.2"
I cant find 3.6.2 now when 4.0.0 is out ...
What should I do?
Many thanks for reply
Loading required package: ggpubr Error: package or namespace load failed for 'ggpubr' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'Rcpp' Error: package 'ggpubr' could not be loaded In addition: Warning message: package 'ggpubr' was built under R version 3.6.2
devtools::session_info()
- Session info ------------------------------------------------------------- setting value
version R version 3.6.1 (2019-07-05) os macOS Catalina 10.15.2
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate C
ctype C
tz Europe/Stockholm
date 2020-05-17
Marsus1972
commented
4 years ago And ggsurvplot is not available for neither version 3.6.1 nor 4.0.0. Any hints how to overcome this?
kassambara
commented
4 years ago please consider restarting your r session, and then:
1) install ggpubr 2) install the survminer dev version
Marsus1972
commented
4 years ago yes thanks a lot, now it worked!!
RobertJamesMann
commented
4 years ago Hi,
Thank you for the help on this feed - helped recover original error.
However, since installing ggpubr and installed survminer dev version I get the following:
Error: Failed to install 'survminer' from GitHub: (converted from warning) cannot remove prior installation of package ‘rlang’
Please could you assist, greatly appreciated.
mmbautista
commented
4 years ago Hi,
I have installed the lastest survminer package 0.4.6.999 using the code below: devtools::install_github("kassambara/survminer", build_vignettes = FALSE)
However, once I load the package, the following error occurred:
library(survminer)
Error: package or namespace load failed for ‘survminer’ in get(method, envir = home):
lazy-load database 'C:/Users/jcaba/Documents/R/win-library/4.0/survminer/R/survminer.rdb' is corrupt
In addition: Warning messages:
1: In .registerS3method(fin[i, 1], fin[i, 2], fin[i, 3], fin[i, 4], :
restarting interrupted promise evaluation
2: In get(method, envir = home) :
restarting interrupted promise evaluation
3: In get(method, envir = home) : internal error -3 in R_decompress1Would really appreciate an advice, thank you!
I can not visualize new data in cox model We can see this example How to plot Cox model with ggsurvplot()?
It used to work, now no and I get
Error in .get_data(fit, data = data, complain = FALSE) : Thedataargument should be provided either to ggsurvfit or survfit.Or if I use
I get
Error: object of type 'symbol' is not subsettablesurvminer_0.4.6