NMdata FAQ
-Built 2024-10-30 using NMdata 0.1.7.911.
+Built 2024-10-30 using NMdata 0.1.7.912.
This vignette is still under development. Please make sure to see latest version available here.
diff --git a/articles/NMdata-cheat.html b/articles/NMdata-cheat.html
index 6b55607c..c2e72275 100644
--- a/articles/NMdata-cheat.html
+++ b/articles/NMdata-cheat.html
@@ -38,7 +38,7 @@
@@ -141,7 +141,7 @@ NMdata Cheatsheet
-
@@ -479,7 +479,7 @@ Built 2024-10-30 using NMdata 0.1.7.911.
+Built 2024-10-30 using NMdata 0.1.7.912.
Please make sure to see latest version available here.
This cheat sheet is intented to provide an overview and remind of command names. Please refer to other vignettes for more details on @@ -323,10 +323,10 @@
Debugging input data (and contr res.debug$tables #> source name nrow ncol nid filetype file.mtime #> <char> <char> <int> <int> <int> <char> <POSc> -#> 1: input pkdata.csv 1502 23 150 csv 2024-10-30 15:00:48 +#> 1: input pkdata.csv 1502 23 150 csv 2024-10-30 21:04:49 #> file.logtime file has.col.row #> <char> <char> <lgcl> -#> 1: 2024-10-30 15:00:48.498617 nonmem/../derived/pkdata.csv TRUE +#> 1: 2024-10-30 21:04:49.131507 nonmem/../derived/pkdata.csv TRUE #> has.col.id #> <lgcl> #> 1: TRUE
Traceability#> [1] "NMdata-cheat.Rmd" #> #> $CreationTime -#> [1] "2024-10-30 15:00:48.498617" +#> [1] "2024-10-30 21:04:49.131507" #> #> $writtenTo #> [1] "derived/pkdata.rds derived/pkdata.csv" diff --git a/articles/NMscanData.html b/articles/NMscanData.html index 11854f25..a69909a2 100644 --- a/articles/NMscanData.html +++ b/articles/NMscanData.html @@ -38,7 +38,7 @@
NMscanData: Find And Combine All Output And -
Built 2024-10-30 using NMdata 0.1.7.911.
+Built 2024-10-30 using NMdata 0.1.7.912.
Please make sure to see latest vignette version available here.
Objectives
@@ -192,7 +192,7 @@ Introduction
library(NMdata)
-#> NMdata 0.1.7.911. Browse NMdata documentation at
+#> NMdata 0.1.7.912. Browse NMdata documentation at
#> https://nmautoverse.github.io/NMdata/
## not necessary for NMdata to run, but we use thse in the examples
library(data.table)
diff --git a/articles/ParameterTables.html b/articles/ParameterTables.html
index 2de8e455..96ff7fc1 100644
--- a/articles/ParameterTables.html
+++ b/articles/ParameterTables.html
@@ -38,7 +38,7 @@
library(NMdata)
-#> NMdata 0.1.7.911. Browse NMdata documentation at
+#> NMdata 0.1.7.912. Browse NMdata documentation at
#> https://nmautoverse.github.io/NMdata/
## not necessary for NMdata to run, but we use thse in the examples
library(data.table)
diff --git a/articles/ParameterTables.html b/articles/ParameterTables.html
index 2de8e455..96ff7fc1 100644
--- a/articles/ParameterTables.html
+++ b/articles/ParameterTables.html
@@ -38,7 +38,7 @@
Citation
Delff P (2024). NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling. -R package version 0.1.7.911, https://nmautoverse.github.io/NMdata/. +R package version 0.1.7.912, https://nmautoverse.github.io/NMdata/.
@Manual{,
title = {NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling},
author = {Philip Delff},
year = {2024},
- note = {R package version 0.1.7.911},
+ note = {R package version 0.1.7.912},
url = {https://nmautoverse.github.io/NMdata/},
}
diff --git a/index.html b/index.html
index 7658686d..834e0d96 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
@@ -225,14 +225,16 @@ Meta analysis made really easyGet the most recent version
If your archive has not been updated since July 2021, you may not find NMdata if you try to install with install.packages (option 1). In that case you have two other options. You can explicitly select CRAN for the installation. Or if you should want a version that has not yet reached CRAN, installing from Github is easy too.
## Option 2: Install explicitly from CRAN
-install.packages("NMdata",repos="https://cloud.r-project.org")
-library(NMdata)
-
-## Option 3: Install from github
-library(remotes)
-install_github("nmautoverse/NMdata")
-library(NMdata)
+## Option 1: Install from your default repository
+install.packages("NMdata")
+
+## Option 2: Install explicitly from CRAN
+install.packages("NMdata",repos="https://cloud.r-project.org")
+
+## Option 3: Install from github
+library(remotes)
+install_github("nmautoverse/NMdata")If you use the Github version, you may want to see the FAQ for how to install specific releases from Github (ensuring reproducibility).
diff --git a/news/index.html b/news/index.html
index 04070810..b2d68201 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
diff --git a/pkgdown.yml b/pkgdown.yml
index 6b44395d..13bb5889 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
NMdata-FAQ: NMdata-FAQ.html
NMscanData: NMscanData.html
ParameterTables: ParameterTables.html
-last_built: 2024-10-30T15:00Z
+last_built: 2024-10-30T21:04Z
urls:
reference: https://nmautoverse.github.io/NMdata/reference
article: https://nmautoverse.github.io/NMdata/articles
diff --git a/reference/NMapplyFilters.html b/reference/NMapplyFilters.html
index 39dff0fc..f089bd84 100644
--- a/reference/NMapplyFilters.html
+++ b/reference/NMapplyFilters.html
@@ -17,7 +17,7 @@
diff --git a/reference/NMcheckColnames.html b/reference/NMcheckColnames.html
index 5a69a6d6..5d008697 100644
--- a/reference/NMcheckColnames.html
+++ b/reference/NMcheckColnames.html
@@ -22,7 +22,7 @@
diff --git a/reference/NMcheckData.html b/reference/NMcheckData.html
index 1cb595ad..54300872 100644
--- a/reference/NMcheckData.html
+++ b/reference/NMcheckData.html
@@ -19,7 +19,7 @@
diff --git a/reference/NMcheckDataFile.html b/reference/NMcheckDataFile.html
index 90432c6c..78926e02 100644
--- a/reference/NMcheckDataFile.html
+++ b/reference/NMcheckDataFile.html
@@ -19,7 +19,7 @@
diff --git a/reference/NMcode2R.html b/reference/NMcode2R.html
index 83cf2071..7e580ee1 100644
--- a/reference/NMcode2R.html
+++ b/reference/NMcode2R.html
@@ -17,7 +17,7 @@
diff --git a/reference/NMdataConf.html b/reference/NMdataConf.html
index b55a7d76..719b3279 100644
--- a/reference/NMdataConf.html
+++ b/reference/NMdataConf.html
@@ -22,7 +22,7 @@
@@ -273,7 +273,7 @@ Examples
#> return(as.data.frame(list())) #> UseMethod("as.data.frame") #> } -#> <bytecode: 0x56495af3f848> +#> <bytecode: 0x5623e779f9c0> #> <environment: namespace:base> #> #> $check.time @@ -311,32 +311,32 @@Examples
#> { #> fnExtension(file, ext = ".ext") #> } -#> <bytecode: 0x56495af601e8> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e777f100> +#> <environment: 0x5623e779c4c0> #> #> $file.cov #> function (file) #> { #> fnExtension(file, ext = ".cov") #> } -#> <bytecode: 0x56495af5fb20> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e777f7c8> +#> <environment: 0x5623e779c4c0> #> #> $file.phi #> function (file) #> { #> fnExtension(file, ext = ".phi") #> } -#> <bytecode: 0x56495af5f458> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e777fe90> +#> <environment: 0x5623e779c4c0> #> #> $file.shk #> function (file) #> { #> fnExtension(file, ext = ".shk") #> } -#> <bytecode: 0x56495af5ed90> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e7780558> +#> <environment: 0x5623e779c4c0> #> #> $file.mod #> function (file) @@ -350,8 +350,8 @@Examples
#> } #> ctl #> } -#> <bytecode: 0x56495af5e6c8> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e777cdf0> +#> <environment: 0x5623e779c4c0> #> #> $file.data #> [1] "extract" @@ -362,8 +362,8 @@Examples
#> $modelname #> function (file) #> fnExtension(basename(file), "") -#> <bytecode: 0x56495af61688> -#> <environment: 0x56495af42d48> +#> <bytecode: 0x5623e777dc60> +#> <environment: 0x5623e779c4c0> #> #> $nc #> [1] 64 diff --git a/reference/NMdataConfOptions.html b/reference/NMdataConfOptions.html index e5e9137c..1010896a 100644 --- a/reference/NMdataConfOptions.html +++ b/reference/NMdataConfOptions.html @@ -17,7 +17,7 @@ diff --git a/reference/NMdataDecideOption.html b/reference/NMdataDecideOption.html index d4110b98..86354911 100644 --- a/reference/NMdataDecideOption.html +++ b/reference/NMdataDecideOption.html @@ -17,7 +17,7 @@ diff --git a/reference/NMdataGetOption.html b/reference/NMdataGetOption.html index 815010f2..43fbdefb 100644 --- a/reference/NMdataGetOption.html +++ b/reference/NMdataGetOption.html @@ -17,7 +17,7 @@ diff --git a/reference/NMdataOperations.html b/reference/NMdataOperations.html index 07f86573..d15ffd7f 100644 --- a/reference/NMdataOperations.html +++ b/reference/NMdataOperations.html @@ -17,7 +17,7 @@ diff --git a/reference/NMexpandDoses.html b/reference/NMexpandDoses.html index 7398ca1f..b43044a3 100644 --- a/reference/NMexpandDoses.html +++ b/reference/NMexpandDoses.html @@ -19,7 +19,7 @@ diff --git a/reference/NMextractDataFile.html b/reference/NMextractDataFile.html index 6d709b8f..4c6c2a82 100644 --- a/reference/NMextractDataFile.html +++ b/reference/NMextractDataFile.html @@ -21,7 +21,7 @@ diff --git a/reference/NMextractText.html b/reference/NMextractText.html index b74c05fd..c8bbbb3e 100644 --- a/reference/NMextractText.html +++ b/reference/NMextractText.html @@ -19,7 +19,7 @@ diff --git a/reference/NMgenText.html b/reference/NMgenText.html index ab3b65dd..eae27f4d 100644 --- a/reference/NMgenText.html +++ b/reference/NMgenText.html @@ -23,7 +23,7 @@ diff --git a/reference/NMinfo.html b/reference/NMinfo.html index 5554a1a3..52f51403 100644 --- a/reference/NMinfo.html +++ b/reference/NMinfo.html @@ -18,7 +18,7 @@ diff --git a/reference/NMisNumeric.html b/reference/NMisNumeric.html index 7b4fa817..6cf2be4b 100644 --- a/reference/NMisNumeric.html +++ b/reference/NMisNumeric.html @@ -20,7 +20,7 @@ diff --git a/reference/NMorderColumns.html b/reference/NMorderColumns.html index 485d1273..e0f5a53b 100644 --- a/reference/NMorderColumns.html +++ b/reference/NMorderColumns.html @@ -19,7 +19,7 @@ diff --git a/reference/NMreadCov.html b/reference/NMreadCov.html index 1fe3f54c..63d6d96e 100644 --- a/reference/NMreadCov.html +++ b/reference/NMreadCov.html @@ -17,7 +17,7 @@ diff --git a/reference/NMreadCsv.html b/reference/NMreadCsv.html index ead83940..e28d2125 100644 --- a/reference/NMreadCsv.html +++ b/reference/NMreadCsv.html @@ -18,7 +18,7 @@ diff --git a/reference/NMreadExt.html b/reference/NMreadExt.html index 9c9f216e..d46c6458 100644 --- a/reference/NMreadExt.html +++ b/reference/NMreadExt.html @@ -17,7 +17,7 @@ diff --git a/reference/NMreadParsText.html b/reference/NMreadParsText.html index 32641ca7..3aafef67 100644 --- a/reference/NMreadParsText.html +++ b/reference/NMreadParsText.html @@ -22,7 +22,7 @@ @@ -193,6 +193,10 @@Arguments
Deprecated. Use `format.sigma`.
+
Value
+data.frame with parameter names and fields read from comments
+Details
Off-diagonal omega and sigma elements will only be diff --git a/reference/NMreadPhi.html b/reference/NMreadPhi.html index 85cbb4c4..ff1416f4 100644 --- a/reference/NMreadPhi.html +++ b/reference/NMreadPhi.html @@ -17,7 +17,7 @@
Arguments
NMdataConf. +
+
Value
+data.frame relating parameters to variable names
+Details
`NMrelate()` processes $PRED, $PK and $ERROR sections. It diff --git a/reference/NMreplaceDataFile.html b/reference/NMreplaceDataFile.html index 15575812..506e504e 100644 --- a/reference/NMreplaceDataFile.html +++ b/reference/NMreplaceDataFile.html @@ -17,7 +17,7 @@
Examples
#> [1] "example.R" #> #> $dataCreate$CreationTime -#> [1] "2024-10-30 15:00:35 UTC" +#> [1] "2024-10-30 21:04:36 UTC" #> #> $dataCreate$description #> [1] "Example data" diff --git a/reference/NMtransInp.html b/reference/NMtransInp.html index 8b9e950c..349d05cc 100644 --- a/reference/NMtransInp.html +++ b/reference/NMtransInp.html @@ -17,7 +17,7 @@ diff --git a/reference/NMwriteData.html b/reference/NMwriteData.html index e3a1861b..5a5b0eda 100644 --- a/reference/NMwriteData.html +++ b/reference/NMwriteData.html @@ -23,7 +23,7 @@ diff --git a/reference/NMwriteSection.html b/reference/NMwriteSection.html index 9f6c1906..0c0f72fd 100644 --- a/reference/NMwriteSection.html +++ b/reference/NMwriteSection.html @@ -18,7 +18,7 @@ diff --git a/reference/addOmegaCorr.html b/reference/addOmegaCorr.html index 31f792a4..249cd356 100644 --- a/reference/addOmegaCorr.html +++ b/reference/addOmegaCorr.html @@ -17,7 +17,7 @@ diff --git a/reference/addTAPD.html b/reference/addTAPD.html index 38e6fdc7..332e5334 100644 --- a/reference/addTAPD.html +++ b/reference/addTAPD.html @@ -19,7 +19,7 @@ diff --git a/reference/cc.html b/reference/cc.html index 12707df2..91978a79 100644 --- a/reference/cc.html +++ b/reference/cc.html @@ -19,7 +19,7 @@ diff --git a/reference/checkColRow.html b/reference/checkColRow.html index 8ad93cd6..18efe453 100644 --- a/reference/checkColRow.html +++ b/reference/checkColRow.html @@ -20,7 +20,7 @@ diff --git a/reference/cl.html b/reference/cl.html index 0c0c4383..0080ecb5 100644 --- a/reference/cl.html +++ b/reference/cl.html @@ -18,7 +18,7 @@ diff --git a/reference/cleanSpaces.html b/reference/cleanSpaces.html index ec7e8bab..f8eaf97b 100644 --- a/reference/cleanSpaces.html +++ b/reference/cleanSpaces.html @@ -17,7 +17,7 @@ diff --git a/reference/colLabels.html b/reference/colLabels.html index 86368f78..e19c515a 100644 --- a/reference/colLabels.html +++ b/reference/colLabels.html @@ -17,7 +17,7 @@ @@ -95,6 +95,10 @@Arguments
See `?compareCols`
+
Value
+A data.frame with variable and their labels
+See also
compareCols NMinfo
Arguments
`replace` as regular expressions. +
+
Value
+a data.frame
+Examples
diff --git a/reference/egdt.html b/reference/egdt.html index f06ebb09..2c13aaf9 100644 --- a/reference/egdt.html +++ b/reference/egdt.html @@ -17,7 +17,7 @@Arguments
should be considered missing? Default is empty strings and strings only containing white spaces (`na.pattern="^ *$"`). + +vector of same class as `x`