rpsych

R: Why am I receiving a "Number of categories should be increased in order to count frequencies" warning from psycho::alpha()?


I received the following error when passing a data.frame with 3 (moderately skewed) numeric vectors and no missing values to psych::alpha():

Number of categories should be increased in order to count frequencies.

Looking through ?alpha documentation, it looks like I should be able to adjust this with the max argument:

max: the number of categories/item to consider if reporting category frequencies. Defaults to 10, passed to link{response.frequencies}

This description is unclear to me, but I guessed if I set this to a number exceeding the count of unique values of any column in my data, it should go away...but it doesn't.

Any ideas what is causing this warning? Somehow this appears in several posts on here but not directly addressing the cause of the error. Example data and code to reproduce the issue are below.

library(psych)

# Default argument values
alpha(df)

# Changing max
alpha(df, max = 100)
df <- structure(list(x1 = c(0.560264465798536, 0.933211877385453, 0.979830303833817, 
-0.139011930926932, -0.651814621858942, 0.513646039350172, -0.372104063168755, 
0.793356598040359, 0.513646039350172, -1.35109101858441, 0.746738171591994, 
0.0940802013148908, -0.232248783823662, -0.372104063168755, -1.67742000372296, 
-0.232248783823662, 0.793356598040359, 0.280553907108349, 0.839975024488723, 
-0.185630357375297, 0.140698627763255, 0.70011974514363, 0.373790760005078, 
-0.0457750780302031, 0.933211877385453, -0.791669901204036, 0.513646039350172, 
-0.41872248961712, -1.21123573923932, 0.653501318695266, 0.839975024488723, 
0.467027612901807, -0.884906754100765, 0.606882892246901, 0.886593450937088, 
0.280553907108349, 0.606882892246901, 0.746738171591994, 0.513646039350172, 
0.327172333556713, -3.21582807651899, 0.560264465798536, -0.0923935044785677, 
0.606882892246901, -0.278867210272026, 0.606882892246901, -0.325485636720391, 
0.0474617748665261, -0.511959342513849, -0.278867210272026, 0.746738171591994, 
0.979830303833817, -3.26244650296736, -2.60978853269025, 0.327172333556713, 
0.839975024488723, -0.0923935044785677, 0.606882892246901, 0.0940802013148908, 
0.233935480659984, -0.325485636720391, 0.420409186453442, 0.513646039350172, 
-0.139011930926932, -0.185630357375297, -0.41872248961712, 0.187317054211619, 
-0.325485636720391, -2.51655167979353, -2.79626223848371, -0.139011930926932, 
0.933211877385453, -0.558577768962213, -1.53756472437787, -1.30447259213605, 
-0.372104063168755, 0.233935480659984, 0.420409186453442, -2.2834595475517, 
0.280553907108349, 0.979830303833817, 0.979830303833817, 0.886593450937088, 
0.327172333556713, 0.839975024488723, -1.67742000372296, -0.139011930926932, 
0.140698627763255, -1.44432787148114, 0.979830303833817, -0.0457750780302031, 
0.000843348418161536, 0.560264465798536, 0.606882892246901, 0.0940802013148908, 
0.979830303833817, -1.16461731279095, 0.979830303833817, 0.140698627763255, 
-2.93611751782881), x2 = c(0.136902564711936, 0.717047589790198, 
0.910429264816285, 0.407636909748458, 0.794400259800633, 0.523665914764111, 
0.136902564711936, 0.83307659480585, 0.523665914764111, -0.0951554453193692, 
-2.76382256067938, 0.0208735596962833, 0.0595498947015008, 0.368960574743241, 
-0.0564791103141517, -0.0951554453193692, 0.717047589790198, 
0.407636909748458, 0.83307659480585, -0.0951554453193692, 0.601018584774546, 
0.639694919779763, -0.636624135392414, 0.0595498947015008, 0.871752929811068, 
-1.4875035055072, 0.407636909748458, 0.175578899717153, -1.02338748544459, 
0.0595498947015008, 0.871752929811068, 0.562342249769328, -0.0564791103141517, 
0.639694919779763, 0.755723924795415, 0.523665914764111, 0.562342249769328, 
0.368960574743241, 0.717047589790198, 0.407636909748458, -2.57044088565329, 
0.523665914764111, -0.0564791103141517, 0.755723924795415, -0.0178027753089342, 
0.717047589790198, -0.133831780324587, 0.136902564711936, -0.0564791103141517, 
-1.99029586057503, 0.67837125478498, 0.910429264816285, -2.53176455064807, 
-2.10632486559068, 0.368960574743241, 0.794400259800633, 0.330284239738023, 
-0.288537120345457, 0.523665914764111, 0.368960574743241, -0.172508115329804, 
0.523665914764111, 0.523665914764111, 0.910429264816285, -0.0564791103141517, 
0.446313244753676, 0.523665914764111, 0.0982262297067184, -2.18367753560111, 
-2.33838287562198, -0.0564791103141517, 0.83307659480585, -0.327213455350674, 
-1.79691418554894, -2.91852790070025, -1.99029586057503, 0.252931569727588, 
0.484989579758893, -1.02338748544459, 0.175578899717153, 0.910429264816285, 
0.910429264816285, 0.910429264816285, 0.330284239738023, -2.87985156569503, 
-1.25544549547589, 0.523665914764111, 0.523665914764111, -1.06206382044981, 
0.910429264816285, 0.562342249769328, -0.0951554453193692, -2.87985156569503, 
0.717047589790198, 0.0208735596962833, 0.83307659480585, -0.365889790355891, 
0.910429264816285, 0.910429264816285, 0.562342249769328), x3 = c(0.376284465894342, 
0.74833264743926, 0.93435673821172, -0.367811897195496, 0.794838670132375, 
0.469296511280572, 0.0507423070425382, 0.701826624746145, 0.469296511280572, 
-1.34443837375091, 0.701826624746145, 0.329778443201227, 0.283272420508112, 
-0.50732996527484, -2.08853473684074, -0.367811897195496, 0.84134469282549, 
0.469296511280572, 0.887850715518605, -0.0887757610368065, 0.469296511280572, 
0.376284465894342, -1.99552269145451, -0.0422697383436916, 0.887850715518605, 
-0.693354056047299, 0.283272420508112, -0.274799851809266, -1.15841428297845, 
-0.925884169512874, 0.701826624746145, 0.329778443201227, -0.228293829116151, 
0.608814579359916, 0.84134469282549, -0.228293829116151, 0.701826624746145, 
0.701826624746145, 0.74833264743926, 0.283272420508112, -3.25118530416862, 
0.469296511280572, -0.0422697383436916, 0.84134469282549, -0.181787806423036, 
0.562308556666801, -0.181787806423036, 0.00423628434942329, 0.236766397814997, 
-0.321305874502381, 0.655320602053031, 0.93435673821172, -3.2046792814755, 
-2.8791371226237, 0.236766397814997, 0.701826624746145, -0.460823942581726, 
0.236766397814997, -0.135281783729921, 0.236766397814997, -0.135281783729921, 
0.608814579359916, 0.469296511280572, -1.34443837375091, -0.181787806423036, 
-0.135281783729921, 0.329778443201227, 0.0972483297356525, -3.01865519070304, 
-2.8791371226237, 0.469296511280572, 0.84134469282549, -1.06540223759222, 
-2.22805280492009, -0.832872124126644, 0.143754352428767, -0.135281783729921, 
0.422790488587457, -0.925884169512874, 0.562308556666801, 0.887850715518605, 
0.93435673821172, 0.93435673821172, 0.283272420508112, 0.794838670132375, 
-1.39094439644402, -0.181787806423036, -1.6234745099096, -1.25142632836468, 
0.93435673821172, 0.74833264743926, 0.701826624746145, 0.422790488587457, 
0.701826624746145, -0.181787806423036, 0.887850715518605, -1.29793235105779, 
0.93435673821172, 0.562308556666801, -2.64660700915812)), row.names = c(NA, 
-100L), class = c("tbl_df", "tbl", "data.frame"))

Solution

  • The alpha() function calls "response.frequencies()" (line 82) which calls "responseFrequency()" which counts the number of unique items in your dataframe. Based on the docs I thought you would have 3 categories, but according to this function you actually have 142. This is very unintuitive, but if you set max = 142 you get the "Non missing response frequency for each item" output and you don't get the warning:

    library(psych)
    
    df <- structure(list(x1 = c(0.560264465798536, 0.933211877385453, 0.979830303833817, 
                                -0.139011930926932, -0.651814621858942, 0.513646039350172, -0.372104063168755, 
                                0.793356598040359, 0.513646039350172, -1.35109101858441, 0.746738171591994, 
                                0.0940802013148908, -0.232248783823662, -0.372104063168755, -1.67742000372296, 
                                -0.232248783823662, 0.793356598040359, 0.280553907108349, 0.839975024488723, 
                                -0.185630357375297, 0.140698627763255, 0.70011974514363, 0.373790760005078, 
                                -0.0457750780302031, 0.933211877385453, -0.791669901204036, 0.513646039350172, 
                                -0.41872248961712, -1.21123573923932, 0.653501318695266, 0.839975024488723, 
                                0.467027612901807, -0.884906754100765, 0.606882892246901, 0.886593450937088, 
                                0.280553907108349, 0.606882892246901, 0.746738171591994, 0.513646039350172, 
                                0.327172333556713, -3.21582807651899, 0.560264465798536, -0.0923935044785677, 
                                0.606882892246901, -0.278867210272026, 0.606882892246901, -0.325485636720391, 
                                0.0474617748665261, -0.511959342513849, -0.278867210272026, 0.746738171591994, 
                                0.979830303833817, -3.26244650296736, -2.60978853269025, 0.327172333556713, 
                                0.839975024488723, -0.0923935044785677, 0.606882892246901, 0.0940802013148908, 
                                0.233935480659984, -0.325485636720391, 0.420409186453442, 0.513646039350172, 
                                -0.139011930926932, -0.185630357375297, -0.41872248961712, 0.187317054211619, 
                                -0.325485636720391, -2.51655167979353, -2.79626223848371, -0.139011930926932, 
                                0.933211877385453, -0.558577768962213, -1.53756472437787, -1.30447259213605, 
                                -0.372104063168755, 0.233935480659984, 0.420409186453442, -2.2834595475517, 
                                0.280553907108349, 0.979830303833817, 0.979830303833817, 0.886593450937088, 
                                0.327172333556713, 0.839975024488723, -1.67742000372296, -0.139011930926932, 
                                0.140698627763255, -1.44432787148114, 0.979830303833817, -0.0457750780302031, 
                                0.000843348418161536, 0.560264465798536, 0.606882892246901, 0.0940802013148908, 
                                0.979830303833817, -1.16461731279095, 0.979830303833817, 0.140698627763255, 
                                -2.93611751782881), x2 = c(0.136902564711936, 0.717047589790198, 
                                                           0.910429264816285, 0.407636909748458, 0.794400259800633, 0.523665914764111, 
                                                           0.136902564711936, 0.83307659480585, 0.523665914764111, -0.0951554453193692, 
                                                           -2.76382256067938, 0.0208735596962833, 0.0595498947015008, 0.368960574743241, 
                                                           -0.0564791103141517, -0.0951554453193692, 0.717047589790198, 
                                                           0.407636909748458, 0.83307659480585, -0.0951554453193692, 0.601018584774546, 
                                                           0.639694919779763, -0.636624135392414, 0.0595498947015008, 0.871752929811068, 
                                                           -1.4875035055072, 0.407636909748458, 0.175578899717153, -1.02338748544459, 
                                                           0.0595498947015008, 0.871752929811068, 0.562342249769328, -0.0564791103141517, 
                                                           0.639694919779763, 0.755723924795415, 0.523665914764111, 0.562342249769328, 
                                                           0.368960574743241, 0.717047589790198, 0.407636909748458, -2.57044088565329, 
                                                           0.523665914764111, -0.0564791103141517, 0.755723924795415, -0.0178027753089342, 
                                                           0.717047589790198, -0.133831780324587, 0.136902564711936, -0.0564791103141517, 
                                                           -1.99029586057503, 0.67837125478498, 0.910429264816285, -2.53176455064807, 
                                                           -2.10632486559068, 0.368960574743241, 0.794400259800633, 0.330284239738023, 
                                                           -0.288537120345457, 0.523665914764111, 0.368960574743241, -0.172508115329804, 
                                                           0.523665914764111, 0.523665914764111, 0.910429264816285, -0.0564791103141517, 
                                                           0.446313244753676, 0.523665914764111, 0.0982262297067184, -2.18367753560111, 
                                                           -2.33838287562198, -0.0564791103141517, 0.83307659480585, -0.327213455350674, 
                                                           -1.79691418554894, -2.91852790070025, -1.99029586057503, 0.252931569727588, 
                                                           0.484989579758893, -1.02338748544459, 0.175578899717153, 0.910429264816285, 
                                                           0.910429264816285, 0.910429264816285, 0.330284239738023, -2.87985156569503, 
                                                           -1.25544549547589, 0.523665914764111, 0.523665914764111, -1.06206382044981, 
                                                           0.910429264816285, 0.562342249769328, -0.0951554453193692, -2.87985156569503, 
                                                           0.717047589790198, 0.0208735596962833, 0.83307659480585, -0.365889790355891, 
                                                           0.910429264816285, 0.910429264816285, 0.562342249769328), x3 = c(0.376284465894342, 
                                                                                                                            0.74833264743926, 0.93435673821172, -0.367811897195496, 0.794838670132375, 
                                                                                                                            0.469296511280572, 0.0507423070425382, 0.701826624746145, 0.469296511280572, 
                                                                                                                            -1.34443837375091, 0.701826624746145, 0.329778443201227, 0.283272420508112, 
                                                                                                                            -0.50732996527484, -2.08853473684074, -0.367811897195496, 0.84134469282549, 
                                                                                                                            0.469296511280572, 0.887850715518605, -0.0887757610368065, 0.469296511280572, 
                                                                                                                            0.376284465894342, -1.99552269145451, -0.0422697383436916, 0.887850715518605, 
                                                                                                                            -0.693354056047299, 0.283272420508112, -0.274799851809266, -1.15841428297845, 
                                                                                                                            -0.925884169512874, 0.701826624746145, 0.329778443201227, -0.228293829116151, 
                                                                                                                            0.608814579359916, 0.84134469282549, -0.228293829116151, 0.701826624746145, 
                                                                                                                            0.701826624746145, 0.74833264743926, 0.283272420508112, -3.25118530416862, 
                                                                                                                            0.469296511280572, -0.0422697383436916, 0.84134469282549, -0.181787806423036, 
                                                                                                                            0.562308556666801, -0.181787806423036, 0.00423628434942329, 0.236766397814997, 
                                                                                                                            -0.321305874502381, 0.655320602053031, 0.93435673821172, -3.2046792814755, 
                                                                                                                            -2.8791371226237, 0.236766397814997, 0.701826624746145, -0.460823942581726, 
                                                                                                                            0.236766397814997, -0.135281783729921, 0.236766397814997, -0.135281783729921, 
                                                                                                                            0.608814579359916, 0.469296511280572, -1.34443837375091, -0.181787806423036, 
                                                                                                                            -0.135281783729921, 0.329778443201227, 0.0972483297356525, -3.01865519070304, 
                                                                                                                            -2.8791371226237, 0.469296511280572, 0.84134469282549, -1.06540223759222, 
                                                                                                                            -2.22805280492009, -0.832872124126644, 0.143754352428767, -0.135281783729921, 
                                                                                                                            0.422790488587457, -0.925884169512874, 0.562308556666801, 0.887850715518605, 
                                                                                                                            0.93435673821172, 0.93435673821172, 0.283272420508112, 0.794838670132375, 
                                                                                                                            -1.39094439644402, -0.181787806423036, -1.6234745099096, -1.25142632836468, 
                                                                                                                            0.93435673821172, 0.74833264743926, 0.701826624746145, 0.422790488587457, 
                                                                                                                            0.701826624746145, -0.181787806423036, 0.887850715518605, -1.29793235105779, 
                                                                                                                            0.93435673821172, 0.562308556666801, -2.64660700915812)), row.names = c(NA, 
                                                                                                                                                                                                    -100L), class = c("tbl_df", "tbl", "data.frame"))
    
    # Default argument values
    alpha(df)
    #> Number of categories should be increased  in order to count frequencies.
    #> 
    #> Reliability analysis   
    #> Call: alpha(x = df)
    #> 
    #>   raw_alpha std.alpha G6(smc) average_r S/N   ase   mean   sd median_r
    #>       0.87      0.87    0.86      0.69 6.8 0.023 -0.056 0.91     0.61
    #> 
    #>     95% confidence boundaries 
    #>          lower alpha upper
    #> Feldt     0.82  0.87  0.91
    #> Duhachek  0.83  0.87  0.92
    #> 
    #>  Reliability if an item is dropped:
    #>    raw_alpha std.alpha G6(smc) average_r  S/N alpha se var.r med.r
    #> x1      0.74      0.74    0.59      0.59  2.8    0.052    NA  0.59
    #> x2      0.94      0.94    0.89      0.89 15.5    0.012    NA  0.89
    #> x3      0.76      0.76    0.61      0.61  3.1    0.048    NA  0.61
    #> 
    #>  Item statistics 
    #>      n raw.r std.r r.cor r.drop   mean sd
    #> x1 100  0.93  0.93  0.93   0.84 -0.068  1
    #> x2 100  0.82  0.82  0.64   0.62 -0.014  1
    #> x3 100  0.92  0.92  0.91   0.82 -0.086  1
    
    # Changing max
    length(unique(unlist(df)))
    #> 142
    alpha(df, max=142)
    #> 
    #> Reliability analysis   
    #> Call: alpha(x = df, max = 142)
    #> 
    #>   raw_alpha std.alpha G6(smc) average_r S/N   ase   mean   sd median_r
    #>       0.87      0.87    0.86      0.69 6.8 0.023 -0.056 0.91     0.61
    #> 
    #>     95% confidence boundaries 
    #>          lower alpha upper
    #> Feldt     0.82  0.87  0.91
    #> Duhachek  0.83  0.87  0.92
    #> 
    #>  Reliability if an item is dropped:
    #>    raw_alpha std.alpha G6(smc) average_r  S/N alpha se var.r med.r
    #> x1      0.74      0.74    0.59      0.59  2.8    0.052    NA  0.59
    #> x2      0.94      0.94    0.89      0.89 15.5    0.012    NA  0.89
    #> x3      0.76      0.76    0.61      0.61  3.1    0.048    NA  0.61
    #> 
    #>  Item statistics 
    #>      n raw.r std.r r.cor r.drop   mean sd
    #> x1 100  0.93  0.93  0.93   0.84 -0.068  1
    #> x2 100  0.82  0.82  0.64   0.62 -0.014  1
    #> x3 100  0.92  0.92  0.91   0.82 -0.086  1
    #> 
    #> Non missing response frequency for each item
    #>    -3.26244650296736 -3.25118530416862 -3.21582807651899 -3.2046792814755
    #> x1              0.01              0.00              0.01             0.00
    #> x2              0.00              0.00              0.00             0.00
    #> x3              0.00              0.01              0.00             0.01
    #>    -3.01865519070304 -2.93611751782881 -2.91852790070025 -2.87985156569503
    #> x1              0.00              0.01              0.00              0.00
    #> x2              0.00              0.00              0.01              0.02
    #> x3              0.01              0.00              0.00              0.00
    #>    -2.8791371226237 -2.79626223848371 -2.76382256067938 -2.64660700915812
    #> x1             0.00              0.01              0.00              0.00
    #> x2             0.00              0.00              0.01              0.00
    #> x3             0.02              0.00              0.00              0.01
    #>    -2.60978853269025 -2.57044088565329 -2.53176455064807 -2.51655167979353
    #> x1              0.01              0.00              0.00              0.01
    #> x2              0.00              0.01              0.01              0.00
    #> x3              0.00              0.00              0.00              0.00
    #>    -2.33838287562198 -2.2834595475517 -2.22805280492009 -2.18367753560111
    #> x1              0.00             0.01              0.00              0.00
    #> x2              0.01             0.00              0.00              0.01
    #> x3              0.00             0.00              0.01              0.00
    #>    -2.10632486559068 -2.08853473684074 -1.99552269145451 -1.99029586057503
    #> x1              0.00              0.00              0.00              0.00
    #> x2              0.01              0.00              0.00              0.02
    #> x3              0.00              0.01              0.01              0.00
    #>    -1.79691418554894 -1.67742000372296 -1.6234745099096 -1.53756472437787
    #> x1              0.00              0.02             0.00              0.01
    #> x2              0.01              0.00             0.00              0.00
    #> x3              0.00              0.00             0.01              0.00
    #>    -1.4875035055072 -1.44432787148114 -1.39094439644402 -1.35109101858441
    #> x1             0.00              0.01              0.00              0.01
    #> x2             0.01              0.00              0.00              0.00
    #> x3             0.00              0.00              0.01              0.00
    #>    -1.34443837375091 -1.30447259213605 -1.29793235105779 -1.25544549547589
    #> x1              0.00              0.01              0.00              0.00
    #> x2              0.00              0.00              0.00              0.01
    #> x3              0.02              0.00              0.01              0.00
    #>    -1.25142632836468 -1.21123573923932 -1.16461731279095 -1.15841428297845
    #> x1              0.00              0.01              0.01              0.00
    #> x2              0.00              0.00              0.00              0.00
    #> x3              0.01              0.00              0.00              0.01
    #>    -1.06540223759222 -1.06206382044981 -1.02338748544459 -0.925884169512874
    #> x1              0.00              0.00              0.00               0.00
    #> x2              0.00              0.01              0.02               0.00
    #> x3              0.01              0.00              0.00               0.02
    #>    -0.884906754100765 -0.832872124126644 -0.791669901204036 -0.693354056047299
    #> x1               0.01               0.00               0.01               0.00
    #> x2               0.00               0.00               0.00               0.00
    #> x3               0.00               0.01               0.00               0.01
    #>    -0.651814621858942 -0.636624135392414 -0.558577768962213 -0.511959342513849
    #> x1               0.01               0.00               0.01               0.01
    #> x2               0.00               0.01               0.00               0.00
    #> x3               0.00               0.00               0.00               0.00
    #>    -0.50732996527484 -0.460823942581726 -0.41872248961712 -0.372104063168755
    #> x1              0.00               0.00              0.02               0.03
    #> x2              0.00               0.00              0.00               0.00
    #> x3              0.01               0.01              0.00               0.00
    #>    -0.367811897195496 -0.365889790355891 -0.327213455350674 -0.325485636720391
    #> x1               0.00               0.00               0.00               0.03
    #> x2               0.00               0.01               0.01               0.00
    #> x3               0.02               0.00               0.00               0.00
    #>    -0.321305874502381 -0.288537120345457 -0.278867210272026 -0.274799851809266
    #> x1               0.00               0.00               0.02               0.00
    #> x2               0.00               0.01               0.00               0.00
    #> x3               0.01               0.00               0.00               0.01
    #>    -0.232248783823662 -0.228293829116151 -0.185630357375297 -0.181787806423036
    #> x1               0.02               0.00               0.02               0.00
    #> x2               0.00               0.00               0.00               0.00
    #> x3               0.00               0.02               0.00               0.05
    #>    -0.172508115329804 -0.139011930926932 -0.135281783729921 -0.133831780324587
    #> x1               0.00               0.04               0.00               0.00
    #> x2               0.01               0.00               0.00               0.01
    #> x3               0.00               0.00               0.04               0.00
    #>    -0.0951554453193692 -0.0923935044785677 -0.0887757610368065
    #> x1                0.00                0.02                0.00
    #> x2                0.04                0.00                0.00
    #> x3                0.00                0.00                0.01
    #>    -0.0564791103141517 -0.0457750780302031 -0.0422697383436916
    #> x1                0.00                0.02                0.00
    #> x2                0.06                0.00                0.00
    #> x3                0.00                0.00                0.02
    #>    -0.0178027753089342 0.000843348418161536 0.00423628434942329
    #> x1                0.00                 0.01                0.00
    #> x2                0.01                 0.00                0.00
    #> x3                0.00                 0.00                0.01
    #>    0.0208735596962833 0.0474617748665261 0.0507423070425382 0.0595498947015008
    #> x1               0.00               0.01               0.00               0.00
    #> x2               0.02               0.00               0.00               0.03
    #> x3               0.00               0.00               0.01               0.00
    #>    0.0940802013148908 0.0972483297356525 0.0982262297067184 0.136902564711936
    #> x1               0.03               0.00               0.00              0.00
    #> x2               0.00               0.00               0.01              0.03
    #> x3               0.00               0.01               0.00              0.00
    #>    0.140698627763255 0.143754352428767 0.175578899717153 0.187317054211619
    #> x1              0.03              0.00              0.00              0.01
    #> x2              0.00              0.00              0.02              0.00
    #> x3              0.00              0.01              0.00              0.00
    #>    0.233935480659984 0.236766397814997 0.252931569727588 0.280553907108349
    #> x1              0.02              0.00              0.00              0.03
    #> x2              0.00              0.00              0.01              0.00
    #> x3              0.00              0.04              0.00              0.00
    #>    0.283272420508112 0.327172333556713 0.329778443201227 0.330284239738023
    #> x1              0.00              0.03              0.00              0.00
    #> x2              0.00              0.00              0.00              0.02
    #> x3              0.04              0.00              0.03              0.00
    #>    0.368960574743241 0.373790760005078 0.376284465894342 0.407636909748458
    #> x1              0.00              0.01              0.00              0.00
    #> x2              0.04              0.00              0.00              0.04
    #> x3              0.00              0.00              0.02              0.00
    #>    0.420409186453442 0.422790488587457 0.446313244753676 0.467027612901807
    #> x1              0.02              0.00              0.00              0.01
    #> x2              0.00              0.00              0.01              0.00
    #> x3              0.00              0.02              0.00              0.00
    #>    0.469296511280572 0.484989579758893 0.513646039350172 0.523665914764111
    #> x1              0.00              0.00              0.05               0.0
    #> x2              0.00              0.01              0.00               0.1
    #> x3              0.07              0.00              0.00               0.0
    #>    0.560264465798536 0.562308556666801 0.562342249769328 0.601018584774546
    #> x1              0.03              0.00              0.00              0.00
    #> x2              0.00              0.00              0.04              0.01
    #> x3              0.00              0.03              0.00              0.00
    #>    0.606882892246901 0.608814579359916 0.639694919779763 0.653501318695266
    #> x1              0.06              0.00              0.00              0.01
    #> x2              0.00              0.00              0.02              0.00
    #> x3              0.00              0.02              0.00              0.00
    #>    0.655320602053031 0.67837125478498 0.70011974514363 0.701826624746145
    #> x1              0.00             0.00             0.01              0.00
    #> x2              0.00             0.01             0.00              0.00
    #> x3              0.01             0.00             0.00              0.08
    #>    0.717047589790198 0.746738171591994 0.74833264743926 0.755723924795415
    #> x1              0.00              0.03             0.00              0.00
    #> x2              0.05              0.00             0.00              0.02
    #> x3              0.00              0.00             0.03              0.00
    #>    0.793356598040359 0.794400259800633 0.794838670132375 0.83307659480585
    #> x1              0.02              0.00              0.00             0.00
    #> x2              0.00              0.02              0.00             0.04
    #> x3              0.00              0.00              0.02             0.00
    #>    0.839975024488723 0.84134469282549 0.871752929811068 0.886593450937088
    #> x1              0.04             0.00              0.00              0.02
    #> x2              0.00             0.00              0.02              0.00
    #> x3              0.00             0.04              0.00              0.00
    #>    0.887850715518605 0.910429264816285 0.933211877385453 0.93435673821172
    #> x1              0.00              0.00              0.03             0.00
    #> x2              0.00              0.09              0.00             0.00
    #> x3              0.04              0.00              0.00             0.06
    #>    0.979830303833817 miss
    #> x1              0.07    0
    #> x2              0.00    0
    #> x3              0.00    0
    

    If you use a smaller set unique values, such as 'survey' data where responses are represented as integers in the [1,5] interval, it is easier to see what the response frequencies section of the output is doing:

    # Using 'survey' data
    df2 <- data.frame(x1 = sample(1:5, 100, replace = TRUE),
                      x2 = sample(1:5, 100, replace = TRUE),
                      x3 = sample(1:5, 100, replace = TRUE))
    alpha(df2, max=5)
    #> Warning in alpha(df2, max = 5): Some items were negatively correlated with the total scale and probably 
    #> should be reversed.  
    #> To do this, run the function again with the 'check.keys=TRUE' option
    #> Some items ( x1 ) were negatively correlated with the total scale and 
    #> probably should be reversed.  
    #> To do this, run the function again with the 'check.keys=TRUE' option
    #> 
    #> Reliability analysis   
    #> Call: alpha(x = df2, max = 5)
    #> 
    #>   raw_alpha std.alpha G6(smc) average_r   S/N  ase mean   sd median_r
    #>      0.026     0.027   0.057    0.0091 0.028 0.17  2.9 0.84   -0.042
    #> 
    #>     95% confidence boundaries 
    #>          lower alpha upper
    #> Feldt    -0.36  0.03  0.32
    #> Duhachek -0.30  0.03  0.36
    #> 
    #>  Reliability if an item is dropped:
    #>    raw_alpha std.alpha G6(smc) average_r   S/N alpha se var.r  med.r
    #> x1     0.340     0.341   0.205     0.205  0.52     0.13    NA  0.205
    #> x2    -0.087    -0.087  -0.042    -0.042 -0.08     0.22    NA -0.042
    #> x3    -0.315    -0.315  -0.136    -0.136 -0.24     0.26    NA -0.136
    #> 
    #>  Item statistics 
    #>      n raw.r std.r r.cor r.drop mean  sd
    #> x1 100  0.47  0.47 -0.38 -0.116  3.0 1.4
    #> x2 100  0.63  0.61  0.31  0.048  2.9 1.5
    #> x3 100  0.66  0.67  0.49  0.128  2.9 1.4
    #> 
    #> Non missing response frequency for each item
    #>       1    2    3    4    5 miss
    #> x1 0.21 0.21 0.18 0.21 0.19    0
    #> x2 0.23 0.25 0.14 0.17 0.21    0
    #> x3 0.21 0.22 0.16 0.25 0.16    0
    

    Created on 2022-08-19 by the reprex package (v2.0.1)