ddediu
commented
5 years ago Hi Gustavo, I tried to reproduce it and everything seems to work fine? Which version of AdhereR are you using and on which platform? Best, Dan
Closed gustavorps closed 5 years ago
ddediu
commented
5 years ago Hi Gustavo, I tried to reproduce it and everything seems to work fine? Which version of AdhereR are you using and on which platform? Best, Dan
gustavorps
commented
5 years ago Hello @ddediu
I'm using rstudio.cloud
version commandplatform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 5.2
year 2018
month 12
day 20
svn rev 75870
language R
version.string R version 3.5.2 (2018-12-20)
nickname Eggshell Igloo sessionInfo() functionR version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readr_1.3.1 AdhereR_0.4.1 stringr_1.4.0 R.utils_2.8.0 R.oo_1.22.0 R.methodsS3_1.7.1
[7] read.dbc_1.0.5 optparse_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 cellranger_1.1.0 pillar_1.4.1 later_0.8.0 compiler_3.5.2
[6] colourpicker_1.0 shinyjs_1.0 shinyWidgets_0.4.8 forcats_0.4.0 tools_3.5.2
[11] highlight_0.4.7.2 digest_0.6.19 bit_1.1-14 viridisLite_0.3.0 tibble_2.1.3
[16] jsonlite_1.6 RSQLite_2.1.1 memoise_1.1.0 pkgconfig_2.0.2 rlang_0.3.4
[21] shiny_1.3.2 DBI_1.0.0 curl_3.3 haven_2.1.0 xfun_0.7
[26] xml2_1.2.0 RMariaDB_1.0.6 knitr_1.23 readODS_1.6.7 htmlwidgets_1.3
[31] hms_0.4.2 bit64_0.9-7 getopt_1.20.3 data.table_1.12.2 R6_2.4.0
[36] readxl_1.3.1 clipr_0.6.0 blob_1.1.1 magrittr_1.5 scales_1.0.0
[41] promises_1.0.1 htmltools_0.3.6 colorspace_1.4-1 xtable_1.8-4 mime_0.6
[46] httpuv_1.5.1 V8_2.2 stringi_1.4.3 miniUI_0.1.1.1 munsell_0.5.0
[51] crayon_1.3.4 # Load the AdhereR library:
library(AdhereR);
library(readr)
MyExamplePats <- read_csv("/cloud/project/MyExamplePats.csv")
# https://cran.r-project.org/web/packages/AdhereR/vignettes/AdhereR-overview.html#the-simple-cmas
knitr::kable(MyExamplePats, caption = "<a name=\"Table-1\"></a>**Table 1.** Medication events for two example patients");
# Create an object "cma0" of the most basic CMA type, "CMA0":
cma0v1 <- CMA0(
data=MyExamplePats, # use the two selected patients
ID.colname="PATIENT_ID", # the name of the column containing the IDs
event.date.colname="DATE", # the name of the column containing the event date
event.duration.colname="DURATION", # the name of the column containing the duration
event.daily.dose.colname="PERDAY", # the name of the column containing the dosage
medication.class.colname="CATEGORY", # the name of the column containing the category
followup.window.start=0, # FUW start in days since earliest event
observation.window.start=0, # OW start in days since earliest event
observation.window.duration=365*2, # OW duration in days
date.format="%d/%m/%Y"); # date format (mm/dd/yyyy)
# Plot the object (CMA0 shows the actual event data only):
plot(cma0v1, # the object to plot
align.all.patients=FALSE); # align all patients for easier comparison| PATIENT_ID| DURATION|DATE | PERDAY|CATEGORY |
|----------:|--------:|:----------|------:|:----------|
| 1| 30|20/06/2016 | 1|Coquetel A |
| 1| 60|11/07/2016 | 1|Coquetel A |
| 1| 60|21/09/2016 | 1|Coquetel A |
| 1| 60|14/02/2017 | 1|Coquetel A |
| 1| 60|20/03/2017 | 1|Coquetel A |
| 1| 60|04/09/2017 | 1|Coquetel A |
| 1| 60|13/12/2017 | 1|Coquetel A |
| 1| 30|06/03/2018 | 1|Coquetel A |
| 1| 30|17/04/2018 | 1|Coquetel A |
| 1| 60|23/05/2018 | 1|Coquetel A |
| 1| 30|20/06/2018 | 1|Coquetel A |
| 1| 60|15/08/2018 | 1|Coquetel A |
| 1| 60|18/10/2018 | 1|Coquetel A |
| 1| 30|26/11/2018 | 1|Coquetel A |
| 1| 60|18/01/2019 | 1|Coquetel A |
| 1| 60|18/03/2019 | 1|Coquetel A |
>
> # Create an object "cma0" of the most basic CMA type, "CMA0":
> cma0v1 <- CMA0(
+ data=ExamplePatsPatricia, # use the two selected patients
+ ID.colname="PATIENT_ID", # the name of the column containing the IDs
+ event.date.colname="DATE", # the name of the column containing the event date
+ event.duration.colname="DURATION", # the name of the column containing the duration
+ event.daily.dose.colname="PERDAY", # the name of the column containing the dosage
+ medication.class.colname="CATEGORY", # the name of the column containing the category
+ followup.window.start=0, # FUW start in days since earliest event
+ observation.window.start=0, # OW start in days since earliest event
+ observation.window.duration=365*2, # OW duration in days
+ date.format="%d/%m/%Y"); # date format (mm/dd/yyyy)
>
> # Plot the object (CMA0 shows the actual event data only):
> plot(cma0v1, # the object to plot
+ align.all.patients=FALSE); # align all patients for easier comparison
Error in rect(adh.plot.space[2] + as.numeric(cma$data$.FU.START.DATE[s[1]] - :
cannot mix zero-length and non-zero-length coordinatesHi again,
I've been trying for the past few hours to install AdhereR in a 3.5.2 environment on Rstudio.cloud but reader fails (which means that readODS fails which means that I can't install AdhereR) --> how did you manage to do it???
Dan
gustavorps
commented
5 years ago Hi again,
I've been trying for the past few hours to install AdhereR in a 3.5.2 environment on Rstudio.cloud but reader fails (which means that readODS fails which means that I can't install AdhereR) --> how did you manage to do it???
Dan
Sorry for the delay @ddediu
On the console:
install.packages("AdhereR")or
Menu > Tools > Install Packages...
ddediu
commented
5 years ago Hi,
yes, sure, I know how to do that :p but it turns out the issue was that I selected by mistake R 3.2.5 which is on a much-too-old OS for all packages to compile :)
So, now I did compile AdhereR under the right version of R (3.5.3) and ran your code on your data, but the plotting works just fine (I am using AdhereR 0.5)
So, what do we do differently?
Best, Dan
gustavorps
commented
5 years ago Good question. What we do differently?
I create a project from zero on rstudio.cloud execute these steps:
test.Rinstall.packages(c("AdhereR", "knitr", "readr"))MyExamplePats <- read_csv("/cloud/project/MyExamplePats.csv")by
MyExamplePats <- read_csv("https://gist.githubusercontent.com/gustavorps/0168f8c776c9943fc3960f8e76cf710a/raw/982353596f83127545fa9e37ac7cedfc89af3e44/MyExamplePats.csv")Still getting the error
Error in rect(adh.plot.space[2] + as.numeric(cma$data$.FU.START.DATE[s[1]] - :
cannot mix zero-length and non-zero-length coordinatesYou can access the project in this link
ddediu
commented
5 years ago Hi,
thanks for sharing your project: I just tested it with your code and the issue is... the bloody tibble returned by read_csv() :)
The work-around for now is very simple (I added it to you code): simply as.data.frame(MyExamplePats) when you call CMA0, but I will fix it in the future version of the package as well...
You can see that I don't use tibble myself, so I didn't think about it, so thanks a lot for finding this bug!
Best,
Dan
ddediu
commented
5 years ago Fixed in the next release (force the data parameter to CMAx() to data.frame)...
chemjong
commented
5 years ago Hi, thanks for sharing your project: I just tested it with your code and the issue is... the bloody
tibblereturned byread_csv():) The work-around for now is very simple (I added it to you code): simplyas.data.frame(MyExamplePats)when you callCMA0, but I will fix it in the future version of the package as well... You can see that I don't usetibblemyself, so I didn't think about it, so thanks a lot for finding this bug! Best, Dan
I still have the same error coming up.
ddediu
commented
5 years ago Hi, can you please give a bit more details (maybe even share a minimal reproducible dataset + code) so I can debug it? Thanks, Dan
Dataset
MyExamplePatsCode
Error