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rpietro / NSQIPageComplications

Analysis of surgical complications using the NSQIP data set
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VMI - incvars - missing data visualization #22

Closed mworni closed 12 years ago

mworni commented 12 years ago

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

rpietro commented 12 years ago

all that message means is that you don't have a column called age_groups -- if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

mworni commented 12 years ago

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years | 70-79

years |

|-------------|-------------|-------------|-------------|-------------| | 39060 | 16298 | 15837 | 12312 | 9149 | | 0.387 | 0.162 | 0.157 | 0.122 | 0.091 |

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called age_groups -- if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

mworni commented 12 years ago

just realized that when I was creating the subset even after recoding my variables that the created age_group variable did not arrive in the new dataset.

Is it possible that age_group is not really attached to the nsqip.data dataset?

On Sun, Jul 1, 2012 at 10:09 AM, Mathias Worni mathiasworni@gmail.comwrote:

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years |

70-79 years |

|-------------|-------------|-------------|-------------|-------------| | 39060 | 16298 | 15837 | 12312 | 9149 | | 0.387 | 0.162 | 0.157 | 0.122 | 0.091 |

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called age_groups

if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

rpietro commented 12 years ago

so, i found that the variable wasn't there through names(nsqip.data) and View(nsqip.data) and so the problem was not with the subset since it wasn't there from the beginning. most important thing now is to track where the variable is and where it was lost. would start by opening the original (very first) dataset in a spreadsheet and checking

On Sun, Jul 1, 2012 at 4:23 AM, mworni < reply@reply.github.com

wrote:

just realized that when I was creating the subset even after recoding my variables that the created age_group variable did not arrive in the new dataset.

Is it possible that age_group is not really attached to the nsqip.data dataset?

On Sun, Jul 1, 2012 at 10:09 AM, Mathias Worni <mathiasworni@gmail.com

wrote:

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years |

70-79 years |

|-------------|-------------|-------------|-------------|-------------| | 39060 | 16298 | 15837 | 12312 | 9149 | | 0.387 | 0.162 | 0.157 | 0.122 | 0.091 |

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called age_groups

if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6691896

mworni commented 12 years ago

I created this variable in the "variable recoding" section of the script. It does not exist in the very original dataset.

On Sun, Jul 1, 2012 at 1:35 PM, Ricardo Pietrobon < reply@reply.github.com

wrote:

so, i found that the variable wasn't there through names(nsqip.data) and View(nsqip.data) and so the problem was not with the subset since it wasn't there from the beginning. most important thing now is to track where the variable is and where it was lost. would start by opening the original (very first) dataset in a spreadsheet and checking

On Sun, Jul 1, 2012 at 4:23 AM, mworni < reply@reply.github.com

wrote:

just realized that when I was creating the subset even after recoding my variables that the created age_group variable did not arrive in the new dataset.

Is it possible that age_group is not really attached to the nsqip.data dataset?

On Sun, Jul 1, 2012 at 10:09 AM, Mathias Worni <mathiasworni@gmail.com

wrote:

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years |

70-79 years |

|-------------|-------------|-------------|-------------|-------------| | 39060 | 16298 | 15837 | 12312 | 9149 | | 0.387 | 0.162 | 0.157 | 0.122 | 0.091 |

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called

age_groups

if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6691896

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6692771

rpietro commented 12 years ago

this is getting hard -- i can't organize the file because we are working at the same time, and withe file as is it is taking me forever because there is a bunch of stuff that needs to be distributed across different files. here is what i suggest:

  1. will wait for you to stop working at night and then i will come in and re-organize everything
  2. at the level where we are, it might be easier for you to learn github since then we won't have any other file conflicts. but this will take time, and so will leave that decision up to you. i'm fine with whatever you might decide

On Sun, Jul 1, 2012 at 7:39 AM, mworni < reply@reply.github.com

wrote:

I created this variable in the "variable recoding" section of the script. It does not exist in the very original dataset.

On Sun, Jul 1, 2012 at 1:35 PM, Ricardo Pietrobon < reply@reply.github.com

wrote:

so, i found that the variable wasn't there through names(nsqip.data) and View(nsqip.data) and so the problem was not with the subset since it wasn't there from the beginning. most important thing now is to track where the variable is and where it was lost. would start by opening the original (very first) dataset in a spreadsheet and checking

On Sun, Jul 1, 2012 at 4:23 AM, mworni < reply@reply.github.com

wrote:

just realized that when I was creating the subset even after recoding my variables that the created age_group variable did not arrive in the new dataset.

Is it possible that age_group is not really attached to the nsqip.data dataset?

On Sun, Jul 1, 2012 at 10:09 AM, Mathias Worni <mathiasworni@gmail.com

wrote:

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years |

70-79 years |

|-------------|-------------|-------------|-------------|-------------| | 39060 | 16298 | 15837 | 12312 | 9149 | | 0.387 | 0.162 | 0.157 | 0.122 | 0.091 |

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called

age_groups

if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6691896

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6692771

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6692796

rpietro commented 12 years ago

thought a bit more about this. if i change the file structure now, with you coming back to the clinic, we risk confusing you. so, let's leave as is. let me know if the changes we discussed today fixed the issue. it seems like the real problem was really just the missing variable, which we might have fixed through the detaching of the data

On Sun, Jul 1, 2012 at 9:34 AM, Ricardo Pietrobon pietr007@gmail.comwrote:

this is getting hard -- i can't organize the file because we are working at the same time, and withe file as is it is taking me forever because there is a bunch of stuff that needs to be distributed across different files. here is what i suggest:

  1. will wait for you to stop working at night and then i will come in and re-organize everything
  2. at the level where we are, it might be easier for you to learn github since then we won't have any other file conflicts. but this will take time, and so will leave that decision up to you. i'm fine with whatever you might decide

On Sun, Jul 1, 2012 at 7:39 AM, mworni < reply@reply.github.com

wrote:

I created this variable in the "variable recoding" section of the script. It does not exist in the very original dataset.

On Sun, Jul 1, 2012 at 1:35 PM, Ricardo Pietrobon < reply@reply.github.com

wrote:

so, i found that the variable wasn't there through names(nsqip.data) and View(nsqip.data) and so the problem was not with the subset since it wasn't there from the beginning. most important thing now is to track where the variable is and where it was lost. would start by opening the original (very first) dataset in a spreadsheet and checking

On Sun, Jul 1, 2012 at 4:23 AM, mworni < reply@reply.github.com

wrote:

just realized that when I was creating the subset even after recoding my variables that the created age_group variable did not arrive in the new dataset.

Is it possible that age_group is not really attached to the nsqip.data dataset?

On Sun, Jul 1, 2012 at 10:09 AM, Mathias Worni < mathiasworni@gmail.com

wrote:

Don't understand - when I use the

CrossTable(age_groups, missing.include=TRUE)

Cell Contents ------------------------- N N / Table Total

Total Observations in Table: 100829

        | 18-39 years | 40-49 years | 50-59 years | 60-69 years
------------- ------------- ------------- ------------- ------------- 39060 16298 15837 12312
9149
0.387 0.162 0.157 0.122
0.091

|-------------|-------------|-------------|-------------|-------------|

        | 80-89 years |   90+ years |
        |-------------|-------------|
        |        6890 |        1283 |
        |       0.068 |       0.013 |
        |-------------|-------------|

I get a result - but when I use it in the incvars command - it doesn't work. The age_groups variable does exist.

On Sun, Jul 1, 2012 at 6:36 AM, Ricardo Pietrobon < reply@reply.github.com

wrote:

all that message means is that you don't have a column called

age_groups

if you do names(nsqip.data) you will see that this is true. not sure where that variable is. there are other variables in that column that also aren't in your data set

btw, would comment the stuff you don't use all the time, like the install.package stuff -- takes centuries to run

On Fri, Jun 29, 2012 at 7:35 AM, mworni < reply@reply.github.com

wrote:

Ricardo - I started to play with VMI. I got some code to insert for the script. See page 3 of the "VIM imputation GUI" document I saved on the shared gdrive folder for the code in orginal.

incvars <- c(paste(c("age_groups", "diabetes", "alcoholuse", "chronicpulmonary", "decreasedfunction", "acutepulmonary", "chroniccardiac", "acutecardiac", "hypertension", "pvd", "renal", "acutecognitive", "cerebrovascular", "preopinfectedwound", "chronicsteroids", "preopalbumincateg", "bleedingdisorder", "totalwrvuquartile", "incisionalwoundclass", "optimequartile", "anesthesiaonlytimequartile", "ascites", "esophvarices"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) Fehler in [.data.frame(nsqip.data, , incvars) : undefined columns selected

I know that the mistake comes up because of "age_groups" because when I take this variable out, I don't get the error message anymore - but I don't know why this happens. I tried to reclass age_groups to missing - but this didn't help.

Any idea?

Btw. same happens here when I add preopsepsisclass to the incvars command beldow.

CrossTable(preopsepsisclass, missing.include=TRUE) incvars <- c(paste(c("bmiclass", "bmi", "highasa", "residentpresent", "preophospitallos"))) nsqip.data[, incvars] <- log10(nsqip.data[, incvars] + 1) aggr(nsqip.data[, incvars], numbers=TRUE, prop=c(TRUE, FALSE))

Reply to this email directly or view it on GitHub: https://github.com/rpietro/NSQIPageComplications/issues/22

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6690953

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6691896

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https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6692771

Reply to this email directly or view it on GitHub:

https://github.com/rpietro/NSQIPageComplications/issues/22#issuecomment-6692796