Https://tutorials.pumas.ai/

[Abhiram]

Attempting to load from PharmaDatasets…
PharmaDatasets method failed: ArgumentError(“Could not find “pumas\\analysis_data\\warfarin_pkpd_FOCEI_2cpt” dataset. Did you mean one of the following?\n\n - “pumas_tutorials\\wide_data”\n - “pumas_tutorials\\iv_sd_final_target_format”\n - “pumas_tutorials\\po_sd_1”\n - “psptutorials\\basics_p2_mould\\sec12.7.1”\n - “psptutorials\\basics_p2_mould\\sec12.3.1”\n - “psptutorials\\basics_p2_mould\\sec12.6.5”\n”)

Attempting to load from local file…
Trying: C:\Users\Abhiram\VSCODE\WARFARIN\warfarin_data.csv
File not found at this location
Trying: C:\Users\Abhiram\warfarin_data.csv
File not found at this location
Trying: C:\Users\Abhiram\Downloads\warfarin_data.csv
File not found at this location
Trying: warfarin_data.csv
File not found at this location

======================================================================

COULD NOT LOAD DATA FROM ANY SOURCE

SOLUTION OPTIONS:

1. USE PHARMADATASETS (Easiest):
   The Warfarin dataset should be available in PharmaDatasets.
   If not installed, run:
   using Pkg; Pkg.add(“PharmaDatasets”)

2. DOWNLOAD THE FILE:
   Download warfarin data from:
   https://github.com/PumasAI/PumasTutorials.jl/tree/master/data

3. CREATE YOUR OWN DATA:
   Check the required format in the documentation

4. CHECK YOUR FILE LOCATION:
   Current working directory: C:\Users\Abhiram
   List files here: readdir(pwd())
   ERROR: Cannot proceed without data. Please follow solutions above.
   Stacktrace:
   [1] error(s::String)
   @ Base .\error.jl:35
   [2] top-level scope
   @ .\Untitled-2:87

caused by: ArgumentError: Could not find “pumas\analysis_data\warfarin_pkpd_FOCEI_2cpt” dataset. Did you mean one of the following?

• “pumas_tutorials\wide_data”
• “pumas_tutorials\iv_sd_final_target_format”
• “pumas_tutorials\po_sd_1”
• “psptutorials\basics_p2_mould\sec12.7.1”
• “psptutorials\basics_p2_mould\sec12.3.1”
• “psptutorials\basics_p2_mould\sec12.6.5”

Stacktrace:
[1] _dataset_path(query::String)
@ PharmaDatasets .\none:138
[2] dataset (repeats 2 times)
@ .\none:151 [inlined]
[3] top-level scope
@ .\Untitled-2:29

Im doing Module 4: Population PK and PK/PD Modeling with Pumas (Compartmental PK model)
im facing the the above arror pls help to resolve

[patrick]

Hello!

Let us see if we can get to the bottom of this.

Is it correct that you are doing the fitting tutorial? Can you verify exactly what tutorial and what code you run?

Is it in this line?

```

warfarin_data = dataset(“pumas/warfarin_nonmem”)
```
?

Also, can I ask what version of Pumas your are using?

Thanks!
Patrick

[Abhiram]

Hello Patrick,

I’m on module 4 (image attached)

warfarin_df = dataset(“pumas/warfarin_nonmem”). This is the dataset I’m using.

I’m using Pumas2.7.0

I’m running code for :

1. Finding individual parameters.
2. Finding PK parameters
3. Goodness of Fit.

Thanks!
Abhiram.

[patrick]

This confuses me, because your initial error says you’re trying to load a different dataset? If I copy your exact code I get a unicode error because I think discourse is converting the double ticks, but I get

julia> using PharmaDatasets

julia> warfarin_df = dataset(“pumas/warfarin_nonmem”)
ERROR: ParseError:
# Error @ REPL[2]:1:23
warfarin_df = dataset(“pumas/warfarin_nonmem”)
#                     ╙ ── unknown unicode character '“'
Stacktrace:
 [1] top-level scope
   @ none:1

julia> warfarin_df = dataset("pumas/warfarin_nonmem")
515×9 DataFrame
 Row │ id     time     evid   amt      dvid   dv       wtbl     age    sex
     │ Int64  Float64  Int64  Float64  Int64  Float64  Float64  Int64  String1
─────┼─────────────────────────────────────────────────────────────────────────
   1 │     1      0.0      1    100.0      0      0.0     66.7     50  M
   2 │     1      0.5      0      0.0      1      0.0     66.7     50  M
   3 │     1      1.0      0      0.0      1      1.9     66.7     50  M
   4 │     1      2.0      0      0.0      1      3.3     66.7     50  M
   5 │     1      3.0      0      0.0      1      6.6     66.7     50  M
   6 │     1      6.0      0      0.0      1      9.1     66.7     50  M
   7 │     1      9.0      0      0.0      1     10.8     66.7     50  M
   8 │     1     12.0      0      0.0      1      8.6     66.7     50  M
   9 │     1     24.0      0      0.0      1      5.6     66.7     50  M
  ⋮  │   ⋮       ⋮       ⋮       ⋮       ⋮       ⋮        ⋮       ⋮       ⋮
 507 │    33     36.0      0      0.0      2     32.0     66.7     50  M
 508 │    33     48.0      0      0.0      1      6.4     66.7     50  M
 509 │    33     48.0      0      0.0      2     26.0     66.7     50  M
 510 │    33     72.0      0      0.0      1      4.8     66.7     50  M
 511 │    33     72.0      0      0.0      2     22.0     66.7     50  M
 512 │    33     96.0      0      0.0      1      3.1     66.7     50  M
 513 │    33     96.0      0      0.0      2     28.0     66.7     50  M
 514 │    33    120.0      0      0.0      1      2.5     66.7     50  M
 515 │    33    120.0      0      0.0      2     33.0     66.7     50  M
                                                               497 rows omitted

This is with Pumas v2.7.0

[srg808]

I am having a similar issue. I am trying to access a dataset in PharmaDatasets.jl called CLIstemCell. However, when trying to activate the package in DeepPumas v0.9.0 on the desktop client, it is not able to find it and I get the following:

ERROR: ArgumentError: Package PharmaDatasets not found in current path.
- Run `import Pkg; Pkg.add("PharmaDatasets")` to install the PharmaDatasets package.

When I try to add it, I get the following errror:

(Unit 1 Case Study) pkg> add PharmaDatasets
ERROR: The following package names could not be resolved:
 * Pharmadatasets (not found in project, manifest or registry)
Suggestions: ZarrDatasets SpatialDatasets CuratedDatasets FatDatasets PyGDatasets GraphDatasets VegaDatasets PlasmoDataPlots GraphMLDatasets NLIDatasets GRIBDatasets PlasmaWaves HCIDatasets ChartParsers MetopDatasets CDFDatasets