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RE: [NMusers] [Suggest] NONMEM adds UTF-8 support for csv files

From: STANDING, Joseph (GREAT ORMOND STREET HOSPITAL FOR CHILDREN NHS FOUNDATION TRU <joseph.standing_at_nhs.net>
Date: Tue, 5 Jun 2018 13:44:19 +0000

Dear Mark,

Here is another workaround: abandon the use of Microsoft Excel (and all possible Microsoft products) since this behaviour - new "improved" version that you paid for - actually makes your life harder. I have also encountered problems with Excel helpfully changing date format or time zones without being asked - great of you are collating data recorded in different time zones. If you must visualise your data in a spreadsheet just use libre office, or some other open source solution, but in general all data manipulations should be done in R not in a spreadsheet, so any changes to the data are traceable.

About 5 years ago I wiped Windows, installed Linux, and have never looked back. RStudio, NONMEM, LaTex and all sensible software work just the same, yet your computer now lasts much longer and runs faster because it is not clogged up with inefficient operating system software. If you are submitting to one of those backward journals that does not provide a LaTex template, simply write your paper in Rmarkdown and output as a Word doc (equations even come out OK these days).

Much of the above goes for Mac operating system too unfortunately. Upgrade the operating system and NONMEM stops working, students have had terrible problems. If you must have a Mac because you like paying twice the price for a metal case, wipe the operating system and put linux on. I can highly recommend Lubuntu.

BW,

Joe





________________________________________
From: owner-nmusers_at_globomaxnm.com [owner-nmusers_at_globomaxnm.com] on behalf of Sebastien Bihorel [sebastien.bihorel_at_cognigencorp.com]
Sent: 04 June 2018 14:04
To: Mark Tepeck
Cc: nmusers_at_globomaxnm.com
Subject: Re: [NMusers] [Suggest] NONMEM adds UTF-8 support for csv files

Hi,

Two things:
- NONMEM does not require ID to be the first variable in $INPUT
- the headers of your csv file do not have to match the variable names used in $INPUT

So you have 2 easy workarounds for your issue:
- as previously pointed out, you can use another first variable... a deletion flag variable or a study variable are as good candidates as ID for the 1st column of your data.
- rename your ID variable as NMID in your csv file (or any alphanumeric combo that do not start with ID for that matter)

Sebastien

________________________________
From: "Mark Tepeck" <mark.tepeck_at_gmail.com>
To: "Nick Holford" <n.holford_at_auckland.ac.nz>, nmusers_at_globomaxnm.com
Sent: Monday, June 4, 2018 7:52:28 AM
Subject: Re: [NMusers] [Suggest] NONMEM adds UTF-8 support for csv files

Hi All,

Unfortunately, the latest release of MS Excel 2017 (build 9330.2087 for office 365) becomes more restrictive on SYLK files, which is apparently a step-back update, but really a typical Microsoft behavior ☹. Even you agree to continue with the warning messages, the latest Excel will end up with a blank sheet. Using #ID is a practical workaround for this situation but definitely not the most intuitive one. On the other hand, even most NONMEM users are already used to some ‘tricks’, this issue still costs unnecessary efforts and deepens the learning curve for NONMEM newbies. Personally, it is surprising to see a well-maintained software lack support for UTF-8 csv files, which are now well supported by all major csv viewers, e.g. Editpad, Notepad++, open office, MS office. If this is a small fix for NONMEM, I sincerely hope that it could become true. This feature might potentially streamline NONMEM runs without adding # , as well as make NONMEM learning more fun.

Thank you,

Mark

On Mon, Jun 4, 2018 at 1:15 AM, Nick Holford <n.holford_at_auckland.ac.nz<mailto:n.holford_at_auckland.ac.nz>> wrote:
Hi,
Excel can open files with ID as the first column header. You just have to agree to continue when Excel shows its warning messages.
Personally I use #ID as the first column header which avoids the Excel warnings and also means I don’t need to specify an IGNORE character in NM-TRAN because # is the default.
Best wishes,
Nick

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Read the question, answer the question, attempt all questions

From: owner-nmusers_at_globomaxnm.com<mailto:owner-nmusers_at_globomaxnm.com> <owner-nmusers_at_globomaxnm.com<mailto:owner-nmusers_at_globomaxnm.com>> On Behalf Of HUI, Ka Ho
Sent: Monday, June 4, 2018 4:48 AM
To: Mark Tepeck <mark.tepeck_at_gmail.com<mailto:mark.tepeck_at_gmail.com>>; nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>
Subject: [FORGED] [NMusers] 回覆: [NMusers] [Suggest] NONMEM adds UTF-8 support for csv files

Dear Mark

Does it work if you don't put "ID" as the first column? Back to the days when I frequently used Excel, this had been the solution for me.

Matthew

------ 原有訊息------
寄件者: Mark Tepeck
日期: 2018年6月4日週一 10:41
收件者: nmusers_at_globomaxnm.com<mailto:nmusers_at_globomaxnm.com>;
副本:
主旨:[NMusers] [Suggest] NONMEM adds UTF-8 support for csv files

Hi NONMEM Users,

As a PK scientist, I often manipulate csv files with Microsoft Excel, R, and NONMEM. As some of you may have seen, if the first record in a csv file is a string “ID”, Microsoft Excel would mistake it as an SYLK file which cannot be opened normally by Excel. One workaround is to use any strings other than ID, e.g. id, '‘ID’. However, this may cause new problems in some scenarios. Another potential solution is to use the R function readr::write_excel_csv ('dataframe.csv') to output a csv file with UTF-8 Byte order mark. Unfortunately, this csv file turned out to become unreadable for NONMEM although Excel likes it. Since waiting for bug fixing of Excel by Microsoft is not optimistic, I would truly appreciate it if NONMEM can add UTF-8 support.

Thank you,

Mark Tepeck



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Received on Tue Jun 05 2018 - 09:44:19 EDT

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