Read files created of the statistical spreadsheet 'jamovi' (https://www.jamovi.org)
Source:R/read_omv.R
read_omv.RdRead files created of the statistical spreadsheet 'jamovi' (https://www.jamovi.org)
Usage
read_omv(
fleInp = "",
useFlt = FALSE,
rmMsVl = FALSE,
sveAtt = TRUE,
getSyn = FALSE,
getHTM = FALSE
)Arguments
- fleInp
Name (including the path, if required) of the 'jamovi'-file to be read ("FILENAME.omv"; default: "")
- useFlt
Apply filters (remove the lines where the filter is set to 0; default: FALSE)?
- rmMsVl
Remove values defined as missing values (replace them with NA; default: FALSE)?
- sveAtt
Store attributes that are not required in the data set (if you want to write the same data set using write_omv; default: FALSE)?
- getSyn
Extract syntax from the analyses in the 'jamovi'-file and store it in the attribute "syntax" (default: FALSE)?
- getHTM
Store index.html in the attribute "HTML" (default: FALSE)?
Value
data frame (can be directly used with functions included in the R-package jmv and syntax from 'jamovi'; also compatible with the format of the
R-package foreign)
Examples
nmeInp <- system.file("extdata", "ToothGrowth.omv", package = "jmvReadWrite")
data <- jmvReadWrite::read_omv(fleInp = nmeInp)
str(data)
#> 'data.frame': 60 obs. of 16 variables:
#> $ Filter 1 : logi TRUE TRUE TRUE TRUE TRUE TRUE ...
#> ..- attr(*, "name")= chr "Filter 1"
#> ..- attr(*, "id")= int 18
#> ..- attr(*, "columnType")= chr "Filter"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr "logLen < 1.5"
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 78
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "filterNo")= int 0
#> ..- attr(*, "active")= logi FALSE
#> $ ID : chr "1" "2" "3" "4" ...
#> ..- attr(*, "jmv-id")= logi TRUE
#> ..- attr(*, "name")= chr "ID"
#> ..- attr(*, "id")= int 24
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Text"
#> ..- attr(*, "measureType")= chr "ID"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "string"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ logLen : num 0.623 1.061 0.863 0.763 0.806 ...
#> ..- attr(*, "jmv-desc")= chr "Trial with log10"
#> ..- attr(*, "name")= chr "logLen"
#> ..- attr(*, "id")= int 10
#> ..- attr(*, "columnType")= chr "Computed"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr "LOG10(len)"
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr "Trial with log10"
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ supp - Transform 1: Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
#> ..- attr(*, "values")= int [1:2] 1 2
#> ..- attr(*, "name")= chr "supp - Transform 1"
#> ..- attr(*, "id")= int 12
#> ..- attr(*, "columnType")= chr "Recoded"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr "RECODE(`supp`, IFMISS($source, NA, 1), MATCH($source, 'VC', 'OJ'))"
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 3
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 1
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi TRUE
#> $ len : num 4.2 11.5 7.3 5.8 6.4 10 11.2 11.2 5.2 7 ...
#> ..- attr(*, "name")= chr "len"
#> ..- attr(*, "id")= int 2
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "importName")= chr "len"
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ supp : Factor w/ 2 levels "OJ","VC": 2 2 2 2 2 2 2 2 2 2 ...
#> ..- attr(*, "name")= chr "supp"
#> ..- attr(*, "id")= int 3
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Text"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr "supp"
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi TRUE
#> $ dose : num 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 ...
#> ..- attr(*, "name")= chr "dose"
#> ..- attr(*, "id")= int 4
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 211
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "importName")= chr "dose"
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ dose2 : Ord.factor w/ 3 levels "0.5"<"1.0"<"2.0": 1 1 1 1 1 1 1 1 1 1 ...
#> ..- attr(*, "name")= chr "dose2"
#> ..- attr(*, "id")= int 31
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Text"
#> ..- attr(*, "measureType")= chr "Ordinal"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi TRUE
#> $ dose3 : Factor w/ 3 levels "500","1000","2000": 1 1 1 1 1 1 1 1 1 1 ...
#> ..- attr(*, "values")= int [1:3] 500 1000 2000
#> ..- attr(*, "name")= chr "dose3"
#> ..- attr(*, "id")= int 49
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi TRUE
#> $ Trial : Factor w/ 17 levels "A","B","C","D",..: 1 2 2 3 3 3 4 4 4 4 ...
#> ..- attr(*, "jmv-desc")= chr "Trial"
#> ..- attr(*, "name")= chr "Trial"
#> ..- attr(*, "id")= int 5
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Text"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr "Trial"
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi FALSE
#> $ Residuals : num -3.78 3.52 -0.68 -2.18 -1.58 ...
#> ..- attr(*, "jmv-desc")= chr "Residuals from ANOVA"
#> ..- attr(*, "name")= chr "Residuals"
#> ..- attr(*, "id")= int 32
#> ..- attr(*, "columnType")= chr "Output"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "outputAnalysisId")= int 2
#> ..- attr(*, "outputOptionName")= chr "residsOV"
#> ..- attr(*, "outputName")= chr "1"
#> ..- attr(*, "outputDesiredColumnName")= chr "Residuals"
#> ..- attr(*, "outputAssignedColumnName")= chr "Residuals"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr "Residuals from ANOVA"
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ J : num 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 ...
#> ..- attr(*, "name")= chr "J"
#> ..- attr(*, "id")= int 33
#> ..- attr(*, "columnType")= chr "Computed"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr "dose ^ 2"
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ K : num -1.64 2.01 -0.09 -0.84 -0.54 ...
#> ..- attr(*, "name")= chr "K"
#> ..- attr(*, "id")= int 34
#> ..- attr(*, "columnType")= chr "Computed"
#> ..- attr(*, "dataType")= chr "Decimal"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr "MEAN(dose, Residuals)"
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "number"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> $ L : int 1 2 3 4 5 6 7 8 9 10 ...
#> ..- attr(*, "name")= chr "L"
#> ..- attr(*, "id")= int 35
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")=List of 2
#> .. ..$ : chr "== 99"
#> .. ..$ : chr "== 88"
#> $ M : logi TRUE FALSE FALSE FALSE FALSE TRUE ...
#> ..- attr(*, "name")= chr "M"
#> ..- attr(*, "id")= int 55
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Nominal"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> ..- attr(*, "trimLevels")= logi TRUE
#> $ weights : int 1 1 1 1 1 1 1 1 1 1 ...
#> ..- attr(*, "name")= chr "weights"
#> ..- attr(*, "id")= int 36
#> ..- attr(*, "columnType")= chr "Data"
#> ..- attr(*, "dataType")= chr "Integer"
#> ..- attr(*, "measureType")= chr "Continuous"
#> ..- attr(*, "formula")= chr ""
#> ..- attr(*, "formulaMessage")= chr ""
#> ..- attr(*, "parentId")= int 0
#> ..- attr(*, "width")= int 100
#> ..- attr(*, "type")= chr "integer"
#> ..- attr(*, "importName")= chr ""
#> ..- attr(*, "description")= chr ""
#> ..- attr(*, "transform")= int 0
#> ..- attr(*, "edits")= list()
#> ..- attr(*, "missingValues")= list()
#> - attr(*, "fltLst")= chr "Filter 1"
#> - attr(*, "removedRows")= list()
#> - attr(*, "addedRows")= list()
#> - attr(*, "transforms")=List of 1
#> ..$ :List of 7
#> .. ..$ name : chr "Transform 1"
#> .. ..$ id : int 1
#> .. ..$ suffix : chr ""
#> .. ..$ formula :List of 1
#> .. .. ..$ : chr "MATCH($source, 'VC', 'OJ')"
#> .. ..$ formulaMessage:List of 1
#> .. .. ..$ : chr ""
#> .. ..$ measureType : chr "None"
#> .. ..$ description : chr ""
# shows the data frame including all jamovi attributes:
# 'data.frame': 60 obs. of 16 variables:
# $ Filter 1 : logi TRUE TRUE TRUE TRUE TRUE TRUE ...
# ..- attr(*, "name")= chr "Filter 1"
# ..- attr(*, "id")= int 18
# ..- attr(*, "columnType")= chr "Filter"
# ..- attr(*, "dataType")= chr "Integer"
# ..- attr(*, "measureType")= chr "Nominal"
# ..- attr(*, "formula")= chr "logLen < 1.5"
# ..- attr(*, "formulaMessage")= chr ""
# ..- attr(*, "parentId")= int 0
# ..- attr(*, "width")= int 78
# ..- attr(*, "type")= chr "integer"
# ..- attr(*, "importName")= chr ""
# ..- attr(*, "description")= chr ""
# ..- attr(*, "transform")= int 0
# ..- attr(*, "edits")= list()
# ..- attr(*, "missingValues")= list()
# ..- attr(*, "filterNo")= int 0
# ..- attr(*, "active")= logi FALSE
# ... (continued)
# getSyn requires jmvcore and RProtoBuf, and is thus not run here
if (FALSE) { # \dontrun{
data <- jmvReadWrite::read_omv(fleInp = nmeInp, getSyn = TRUE)
} # }
# if the syntax couldn't be extracted, an empty list - length = 0 - is returned,
# otherwise, the commands are shown and the first analysis is run, with the output
# from the second analysis being assigned to the variable result
if (length(attr(data, "syntax")) >= 1) {
print(attr(data, "syntax"))
if (nzchar(system.file(package = "jmv"))) {
# the print-function is only used to force devtools::run_examples() to show output
eval(parse(text = paste0("result = ", attr(data, "syntax")[1])))
# without assigning the output to a variable, the command would be:
# eval(parse(text = attr(data, "syntax")[1]))
print(names(result))
print(result$main)
# -> "main" "assump" "contrasts" "postHoc" "emm" "residsOV"
# (the names of the six output tables)
}
}