johnschwenck/bp

An R package for analyzing blood pressure data

bp's Issues

bp_hist() with bp_children and bp_preg data

with the bp_children data processed such as

children_proc <- process_data(bp_children, sbp = 'sbp', dbp = 'dbp', id = 'id', visit = 'visit)

and run the bp_hist() function

bp_hist(children_proc)

I get the following error...
Error in eval(predvars, data, env) : object 'DAY_OF_WEEK' not found

bp_report plots fine to a file, but the screen output is extremely strange

In running the example in ?bp_reportl I discovered that when the output is directed to the screen, multiple windows are opened, many plots are made and eventually things are plotted on top of each other. Complete chaos! Looks like the plot calls are being duplicated. It goes on for more than 3 minutes but does eventually quit w/o error.

This is really hard to describe so I made a screen recording. I'm sending the first minute to John's e-mail since it is so big.

Plotting to a file works correctly and quickly.

Thanks!

R > sessionInfo()
R Under development (unstable) (2021-03-04 r80062)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bp_1.0.1

loaded via a namespace (and not attached):
 [1] fansi_0.4.2      assertthat_0.2.1 dplyr_1.0.4      crayon_1.4.1     utf8_1.1.4       grid_4.1.0      
 [7] R6_2.5.0         DBI_1.1.1        lifecycle_1.0.0  gtable_0.3.0     magrittr_2.0.1   scales_1.1.1    
[13] ggplot2_3.3.3    pillar_1.5.0     rlang_0.4.10     generics_0.1.0   vctrs_0.3.6      ellipsis_0.3.1  
[19] glue_1.4.2       purrr_0.3.4      munsell_0.5.0    compiler_4.1.0   pkgconfig_2.0.3  colorspace_2.0-0
[25] tidyselect_1.1.0 tibble_3.1.0    

Aggregate does not seem to work

Hey,
I was testing the packages and noticed that the aggregate feature does not seem to work.
See reprex below, with data points well below the 3 min threshold.
The output seems to be the same, no matter if I include 'agg = TRUE' or not.

Please let me know if I missed anything obvious.

Thanks!

Edit: Improved reprex to have side by side example with agg = F and agg = T

library(bp)

data_raw_reprex<-tibble::tribble(
  ~DATE.TIME, ~SYST, ~DIAST,  ~HR,
  "2022-06-28 17:01:56", "129",   "76", "86",
  "2022-06-28 17:02:46", "138",   "76", "83",
  "2022-06-28 17:03:40", "130",   "66", "80",
  "2022-06-29 15:11:07", "127",   "77", "75",
  "2022-06-29 15:12:00", "124",   "79", "76",
  "2022-06-29 15:12:50", "127",   "76", "76",
  "2022-06-30 14:03:22", "134",   "81", "74",
  "2022-06-30 14:04:18", "139",   "81", "72",
  "2022-06-30 14:05:17", "130",   "77", "74",
  "2022-06-30 18:59:43", "734",   "74", "72",
  "2022-06-30 19:00:33", "131",   "78", "73",
  "2022-06-30 19:01:31", "146",   "72", "74",
  "2022-06-30 19:02:28", "125",   "73", "72"
)

data_proc_agg_F<-process_data(data_raw_reprex,
                              sbp = 'syst',
                              dbp = 'diast',
                              date_time = 'date.time',
                              hr = 'hr')
#> 1 values that exceeded the SUL or SLL thresholds were coerced to NA.
#> DATE column created from DATE_TIME column.
#> No PP column found or specified. Automatically generated from SBP and DBP columns.
#> No RPP column found or specified. Automatically generated from SBP and HR columns.
#> No MAP column found or specified. Automatically generated from SBP and DBP columns.

bp_report(data_proc_agg_F, save_report = 0)
#> Report not saved to a file. To save, specify save_report = TRUE.

data_proc_agg_T<-process_data(data_raw_reprex,
                        sbp = 'syst',
                        dbp = 'diast',
                        date_time = 'date.time',
                        hr = 'hr',
                        agg = TRUE,
                        agg_thresh = '5',
                        collapse_df = TRUE)
#> 1 values that exceeded the SUL or SLL thresholds were coerced to NA.
#> DATE column created from DATE_TIME column.
#> No PP column found or specified. Automatically generated from SBP and DBP columns.
#> No RPP column found or specified. Automatically generated from SBP and HR columns.
#> No MAP column found or specified. Automatically generated from SBP and DBP columns.

bp_report(data_proc_agg_T, save_report = 0)
#> Report not saved to a file. To save, specify save_report = TRUE.

^{Created on 2022-07-02 by the reprex package (v2.0.1)}

dip_class_plot Error

Hi,

I am trying to re-create the plots I have seen in your publication using bp_hypnos data that is already in bp package. I installed bp package with vignettes. However, when I use either dip_class_plot(hypnos_proc) or dip_class_plot(hypnos_proc, subj = 70417), I get the following error:

Error in check_aesthetics():
! Aesthetics must be either length 1 or the same as the data (1): colour, shape, x and y
Run rlang::last_error() to see where the error occurred.

Do you know any work around this issue? I tried debugging, but it did not solve the issue as I am not much experienced with R.

process_data() documentation, an OMRON script

I finally figured out what I needed to do to preprocess a data table from my OMRON blood pressure cuff for the process_data() function. It worked, but would have been quicker with concise documentation by output field of the expected input. Eg; 'required', 'optional', and 'calculated'. Maybe I missed it, but a table would be very nice.

Here's a link to the preprocessor script I ended up with, in case someone else is wrangling OMRON data: https://github.com/chasbecker/bp/blob/main/main.R

bp_scatter() subj parameter does not behave as expected

I have the bp_hypnos data processed such as...

hypnos_proc <- process_data(bp_hypnos, bp_type = 'abpm', sbp = "syst", dbp = "DIAST", date_time = "date.time", id = "id", wake = "wake", visit = "visit", hr = "hr", map = "map", rpp = "rpp", pp = "pp", ToD_int = c(5, 13, 18, 23))

We have the following different ID's we can use in the subj argument of the bp_scatter function...
70417, 70422, 70424, 70435,70439

When running the code with all the subjects selected bp_scatter(data = hypnos_proc, subj = c(70417, 70422, 70424, 70435,70439)) and none of the subjects selected bp_scatter(data = hypnos_proc, subj = NULL), I would expect the same plot to be produced, but this is not the case.

Moreover, the following warning occurs,
Warning message: In ID == subj : longer object length is not a multiple of shorter object length
but this only happens when more than 2 subjects are selected, that is bp_scatter(data = hypnos_proc, subj = c(70424, 70435)) would not produce the warning, but bp_scatter(data = hypnos_proc, subj = c(70424, 70435, 70439)) would produce the warning.

bp_hist function gives undefined columns selected

bp installed with devtools::install_github("johnschwenck/bp")

I have import my data into data frame bp, and if I run:

bp_proc <- process_data(bp, sbp = 'SYS', dbp = 'DIA', hr = 'PUL', date_time = 'DT')
head(bp_proc)

The result is for process_data is:

No PP column found. Automatically generated from SBP and DBP columns.
No MAP column found. Automatically generated from SBP and DBP columns.
NOTE: Created DATE column from DATE_TIME column

and head gives:

        DATE           DATE_TIME HOUR SBP DBP BP_CLASS HR       MAP PP
1 2021-06-20 2021-06-20 09:53:00    9 114  75   Normal 61  88.00000 39
2 2021-06-20 2021-06-20 09:47:00    9 123  78 Elevated 61  93.00000 45
3 2021-06-18 2021-06-18 20:46:00   20 125  84 IDH - S1 64  97.66667 41
4 2021-06-18 2021-06-18 20:40:00   20 133  87  Stage 1 64 102.33333 46
5 2021-06-17 2021-06-17 19:17:00   19 116  81 IDH - S1 66  92.66667 35
6 2021-06-17 2021-06-17 19:11:00   19 132  85  Stage 1 62 100.66667 47
  SBP_CATEGORY DBP_CATEGORY ID GROUP TIME_OF_DAY DAY_OF_WEEK BP_TYPE
1       Normal       Normal  1     1     Morning         Sun    HBPM
2     Elevated       Normal  1     1     Morning         Sun    HBPM
3     Elevated      Stage 1  1     1     Evening         Fri    HBPM
4      Stage 1      Stage 1  1     1     Evening         Fri    HBPM
5       Normal      Stage 1  1     1     Evening         Thu    HBPM
6      Stage 1      Stage 1  1     1     Evening         Thu    HBPM

The names function gives:

> names(bp_proc)
 [1] "DATE"         "DATE_TIME"    "HOUR"         "SBP"          "DBP"
 [6] "BP_CLASS"     "HR"           "MAP"          "PP"           "SBP_CATEGORY"
[11] "DBP_CATEGORY" "ID"           "GROUP"        "TIME_OF_DAY"  "DAY_OF_WEEK"
[16] "BP_TYPE"

If I run bp_hist(bp_proc) I get:

Error in `[.data.frame`(SBP_ToD, , c(3, 1, 2, 4, 5)) :
  undefined columns selected

This also happens with the version installed with install.packages("bp").

What am I doing wrong?

thanks,
Chris

Missing DATE_TIME-plot when executing bp_ts_plot()

First: Many thanks for this great package!
Just tried it with some own values, and received a perfect bp-Report ( bp_report() ). As I used the bp_ts_plots() function it only resulted in the BP-by-hour-plot, omitting the the BP-by-DATE_TIME-plot (for a series of >150 values from approx. a month's period). Perhaps my fault (as I didn't have read the complete manual, just the vignette) or some issue?
Keep up your great work!