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Function to fit the naive overall population model to the data. This model is going to estimate the subgroup treatment effects with the overall population treatment effect.

Usage

naivepop(resp, trt, data, resptype = c("survival", "binary"), status = NULL)

Arguments

resp

(string)
the response variable name.

trt

(string)
the treatment variable name. The treatment variable must be a factor with 2 levels where the first level is the control and the second one the treatment.

data

(data frame)
the data frame with the variables.

resptype

(string)
the type of data used. Can be "survival" or "binary".

status

(string)
only for "survival" resptype, the status variable name in survival data.

Value

List with fit, model, resptype, data.

Examples

naivepop("tt_pfs", "arm", example_data, "survival", "ev_pfs")
#> $fit
#> Call:
#> survival::coxph(formula = form_surv, data = data)
#> 
#>         coef exp(coef) se(coef)      z      p
#> arm1 -0.4051    0.6669   0.1291 -3.138 0.0017
#> 
#> Likelihood ratio test=10  on 1 df, p=0.001562
#> n= 1000, number of events= 247 
#> 
#> $model
#> [1] "naive_pop"
#> 
#> $resptype
#> [1] "survival"
#> 
#> $data
#>        id arm x_1 x_2 x_3 x_4 x_5 x_6 x_7 x_8 x_9 x_10      tt_pfs ev_pfs
#> 1       1   0   b   a   b   b   d   b   b   c   b    c 0.979498732      1
#> 2       2   0   b   b   a   a   d   a   a   b   a    c 3.476191848      0
#> 3       3   0   a   a   b   c   a   b   b   a   b    c 1.794663841      1
#> 4       4   0   a   a   a   c   a   b   b   c   b    c 0.019712920      1
#> 5       5   1   b   a   b   c   d   b   b   c   b    c 2.216765148      0
#> 6       6   1   a   b   b   c   a   a   a   c   a    a 2.324199624      0
#> 7       7   1   a   b   b   c   c   b   a   a   a    b 3.082556300      0
#> 8       8   1   b   a   a   a   d   b   b   a   b    b 1.250501391      0
#> 9       9   1   b   b   b   c   d   b   b   b   b    b 2.533054867      0
#> 10     10   0   a   b   b   c   c   b   b   c   b    c 2.321689305      0
#> 11     11   0   a   b   b   c   a   b   b   b   b    c 1.163695734      0
#> 12     12   0   a   a   a   b   c   a   a   b   b    a 2.327617746      0
#> 13     13   1   b   b   b   c   d   b   b   c   b    a 1.557345104      0
#> 14     14   0   b   a   b   c   d   b   a   b   b    b 3.279062328      0
#> 15     15   1   b   b   b   c   d   b   b   c   b    b 0.258456717      1
#> 16     16   1   b   b   b   c   c   a   b   b   b    b 2.994460463      0
#> 17     17   0   b   a   a   c   d   a   b   c   b    b 3.677546230      0
#> 18     18   1   b   a   b   b   d   b   a   a   a    c 3.174681265      0
#> 19     19   0   a   b   a   a   c   b   b   b   b    c 1.485011801      1
#> 20     20   0   a   b   b   a   b   b   a   b   b    a 2.513046296      0
#> 21     21   1   b   a   a   b   d   b   b   c   b    b 2.905220468      0
#> 22     22   1   b   b   b   a   a   b   b   c   b    c 1.395111958      1
#> 23     23   0   a   b   b   a   d   b   b   c   b    c 0.749298059      1
#> 24     24   1   b   b   b   b   d   b   b   c   b    c 0.411565826      1
#> 25     25   1   b   b   b   b   c   a   b   c   b    c 4.133184389      0
#> 26     26   0   b   a   b   b   d   b   a   a   b    c 2.605405316      0
#> 27     27   0   a   b   b   a   b   a   a   c   b    c 0.925607213      1
#> 28     28   1   a   b   b   a   d   b   b   c   b    a 1.415933688      0
#> 29     29   1   b   b   b   c   b   b   b   b   a    b 2.730121392      0
#> 30     30   1   a   b   a   a   a   b   b   b   b    c 1.834961029      0
#> 31     31   0   a   a   b   c   a   a   b   c   b    b 0.180409590      0
#> 32     32   1   b   b   b   c   c   b   b   b   b    a 3.609689554      0
#> 33     33   1   b   a   b   b   d   a   a   a   b    b 2.094657864      1
#> 34     34   1   a   b   b   b   b   a   a   c   b    b 3.682572402      0
#> 35     35   0   a   b   b   c   b   a   b   c   b    c 2.576083283      0
#> 36     36   1   a   b   b   b   b   b   b   c   b    c 1.204526777      0
#> 37     37   1   b   b   b   a   a   a   b   a   b    c 3.667869977      0
#> 38     38   0   a   b   b   b   c   a   a   b   b    b 3.092556613      1
#> 39     39   1   a   b   b   a   d   b   b   c   b    c 2.357560078      0
#> 40     40   1   b   b   b   b   c   b   b   a   a    c 0.036191869      1
#> 41     41   1   a   a   b   c   c   b   b   b   b    c 0.234841473      0
#> 42     42   0   a   a   b   b   d   a   a   c   b    c 0.587647308      1
#> 43     43   0   a   b   b   a   d   b   b   b   a    c 1.261205134      0
#> 44     44   1   b   b   b   c   d   a   a   c   b    a 1.249009087      0
#> 45     45   0   a   a   b   c   d   a   a   c   a    a 3.640314055      0
#> 46     46   1   a   b   a   c   c   b   b   b   a    a 1.243406125      0
#> 47     47   0   b   b   b   b   a   a   b   b   a    a 2.322889097      0
#> 48     48   0   a   a   b   b   b   b   b   c   b    c 1.823543570      0
#> 49     49   0   b   b   b   b   a   b   b   c   b    c 4.056354659      0
#> 50     50   0   b   b   b   b   a   a   a   b   b    c 1.341769347      0
#> 51     51   1   b   b   b   b   d   b   b   a   b    c 2.651151680      0
#> 52     52   0   b   b   a   a   d   a   b   c   b    a 1.298521998      0
#> 53     53   0   a   a   b   c   a   b   b   c   b    c 1.626243873      1
#> 54     54   0   b   a   b   c   b   a   a   a   a    b 2.452561401      0
#> 55     55   0   a   b   a   c   d   a   b   c   b    b 0.848998456      1
#> 56     56   0   a   b   b   b   d   a   b   b   b    c 1.400157230      0
#> 57     57   0   a   b   b   c   d   b   a   c   b    c 2.045072306      0
#> 58     58   0   b   a   a   c   c   a   b   a   b    c 2.610763836      0
#> 59     59   1   b   b   b   c   d   b   b   b   a    a 1.731573992      0
#> 60     60   0   a   a   b   c   a   b   a   a   a    b 1.719964435      0
#> 61     61   0   a   b   b   c   d   a   b   b   b    c 3.136375958      0
#> 62     62   0   b   a   a   c   d   b   b   c   b    c 1.955358932      1
#> 63     63   1   a   b   a   a   c   b   b   c   b    a 1.829136482      1
#> 64     64   0   a   b   b   b   d   a   b   c   b    b 3.734177186      0
#> 65     65   1   a   b   b   a   c   b   b   c   b    a 0.662259042      1
#> 66     66   1   b   b   b   b   c   b   a   a   b    c 2.747751379      0
#> 67     67   1   a   a   a   b   d   a   b   b   a    b 2.355779405      0
#> 68     68   1   b   b   b   c   a   a   a   c   b    c 1.255595290      0
#> 69     69   0   a   b   a   c   b   b   b   b   a    c 0.466405591      1
#> 70     70   1   b   b   b   c   c   a   a   a   b    c 2.561694645      0
#> 71     71   0   b   b   b   a   d   b   b   b   b    c 1.405106136      0
#> 72     72   0   b   b   b   c   c   b   b   b   b    c 1.997595510      0
#> 73     73   1   b   b   a   c   b   b   b   b   b    b 3.037549368      0
#> 74     74   1   b   b   b   a   c   b   b   c   b    b 2.753225398      1
#> 75     75   1   a   a   a   b   c   b   a   c   b    c 2.479194577      1
#> 76     76   1   a   a   b   b   d   b   b   b   b    c 2.681556612      1
#> 77     77   1   b   a   b   a   d   b   a   c   b    c 3.225931104      0
#> 78     78   1   a   b   b   c   d   b   b   b   b    b 1.841309082      1
#> 79     79   1   b   b   b   c   d   b   b   b   b    a 2.877211953      0
#> 80     80   1   b   b   b   a   b   b   b   b   a    a 2.292173580      0
#> 81     81   0   b   a   b   a   c   b   b   b   b    a 0.607461570      1
#> 82     82   1   b   a   b   c   a   a   a   a   b    b 3.014991436      0
#> 83     83   0   b   b   b   a   d   b   b   c   b    c 2.162697510      1
#> 84     84   1   a   b   b   a   b   a   b   b   b    b 3.274838086      1
#> 85     85   1   b   b   b   c   d   b   a   b   b    b 3.872389941      0
#> 86     86   0   b   a   a   b   d   b   b   c   a    c 2.251539409      1
#> 87     87   1   a   a   b   c   d   b   b   c   b    c 3.910779387      0
#> 88     88   0   a   a   b   a   d   a   b   b   b    b 3.095598311      1
#> 89     89   1   a   b   b   b   c   b   b   b   b    c 2.248697100      0
#> 90     90   1   b   b   b   a   c   a   b   c   b    b 2.294192665      0
#> 91     91   0   b   a   a   a   c   b   a   a   b    c 2.592737579      1
#> 92     92   0   b   b   b   c   d   a   a   c   b    a 2.265549472      0
#> 93     93   1   b   b   a   a   c   b   b   c   b    c 3.844342304      0
#> 94     94   0   a   a   b   b   c   a   a   a   a    b 0.790516156      1
#> 95     95   0   a   b   b   b   a   b   b   c   b    c 1.533211884      0
#> 96     96   0   a   b   a   b   c   b   b   b   b    b 2.352416722      1
#> 97     97   1   b   a   b   c   c   a   a   b   b    b 1.239632165      1
#> 98     98   0   a   a   b   a   d   a   b   a   b    c 3.413484766      0
#> 99     99   0   a   a   b   c   a   b   b   b   b    c 1.715824780      0
#> 100   100   0   b   a   a   a   d   b   a   c   b    c 3.606632369      0
#> 101   101   1   b   b   b   a   d   b   b   c   b    c 0.382010490      0
#> 102   102   0   a   b   a   b   d   a   a   a   b    a 3.751110080      0
#> 103   103   1   b   a   b   c   d   b   a   c   b    b 1.444109305      1
#> 104   104   0   a   a   b   c   c   b   a   c   b    b 1.650184458      0
#> 105   105   0   b   b   b   b   a   b   b   b   a    b 4.141721915      0
#> 106   106   0   b   a   b   a   d   b   b   c   b    c 2.987760139      0
#> 107   107   0   b   b   b   a   d   b   a   a   b    a 1.920696468      0
#> 108   108   1   b   b   b   a   d   a   a   c   b    c 1.493149543      0
#> 109   109   1   b   a   b   a   c   b   a   a   a    b 3.224818711      0
#> 110   110   1   a   a   a   a   d   b   b   c   b    c 3.804687148      0
#> 111   111   0   a   a   a   b   a   b   b   c   b    b 2.423242062      0
#> 112   112   0   a   a   b   a   c   a   b   b   a    b 1.179798517      1
#> 113   113   1   b   b   a   c   a   b   b   b   b    c 3.034114442      1
#> 114   114   0   a   b   b   a   d   b   b   c   b    b 3.536220474      0
#> 115   115   1   a   a   b   c   d   b   b   c   a    b 3.112235791      0
#> 116   116   1   b   b   b   a   c   a   b   a   b    c 1.042752681      1
#> 117   117   1   b   a   b   c   d   b   b   c   a    b 1.320373644      1
#> 118   118   1   a   b   b   b   a   b   b   c   b    b 1.425618873      0
#> 119   119   0   b   b   b   b   c   b   a   c   b    c 3.353897151      1
#> 120   120   0   a   b   b   a   d   b   b   c   b    b 1.268393170      1
#> 121   121   1   b   b   b   b   c   a   a   c   a    c 3.372124037      0
#> 122   122   1   a   a   b   a   c   b   b   c   b    b 2.387792409      0
#> 123   123   1   b   a   a   b   c   b   a   c   b    a 1.556245162      1
#> 124   124   1   b   a   b   a   d   b   b   c   b    a 2.296228510      0
#> 125   125   1   b   b   b   a   b   b   b   a   a    a 3.550667871      0
#> 126   126   0   a   a   b   a   b   b   a   b   b    c 1.215999609      0
#> 127   127   0   b   b   b   c   a   a   a   c   b    c 1.335441662      0
#> 128   128   0   a   b   a   c   d   b   b   b   b    c 1.359221741      0
#> 129   129   0   b   b   b   b   b   b   b   c   a    b 3.012353070      0
#> 130   130   0   a   b   b   b   c   b   b   c   b    b 2.798760954      1
#> 131   131   0   a   b   b   b   a   a   a   a   b    c 1.465784428      1
#> 132   132   0   b   b   b   c   d   a   b   c   b    b 3.165649739      0
#> 133   133   0   b   a   b   c   a   b   b   c   b    c 2.973984759      0
#> 134   134   1   a   b   b   a   d   b   b   a   a    b 0.873753598      0
#> 135   135   0   a   b   b   b   d   a   a   b   b    b 1.282714146      0
#> 136   136   1   b   b   b   b   a   a   a   a   a    c 1.421097437      0
#> 137   137   0   a   a   b   b   b   b   a   b   b    a 3.291128141      1
#> 138   138   1   b   a   a   c   d   b   b   b   b    a 3.434366958      0
#> 139   139   0   b   a   a   c   a   a   a   a   a    b 1.423858315      0
#> 140   140   0   a   a   a   a   d   b   b   a   b    a 1.442090895      1
#> 141   141   0   a   a   b   a   a   a   a   c   b    c 3.225628939      0
#> 142   142   0   a   b   b   b   d   b   a   a   b    b 1.425295888      0
#> 143   143   0   b   b   b   a   c   b   b   c   b    b 3.257421825      0
#> 144   144   0   b   b   b   b   d   a   a   a   a    b 0.208831749      1
#> 145   145   0   a   b   b   b   d   b   a   c   a    b 1.738549073      0
#> 146   146   0   b   b   b   c   d   b   b   c   b    b 3.420277860      0
#> 147   147   1   b   b   b   b   a   b   b   b   b    a 1.537073242      0
#> 148   148   1   a   a   b   b   a   a   b   c   b    c 2.187943666      0
#> 149   149   0   a   b   a   b   b   b   b   c   b    c 1.981761839      1
#> 150   150   1   b   b   b   a   d   b   a   b   b    a 3.889170438      0
#> 151   151   1   a   b   a   c   c   a   a   a   b    c 2.259858399      0
#> 152   152   0   a   b   b   c   d   a   b   a   a    a 2.736151236      0
#> 153   153   1   b   b   b   a   c   b   a   c   b    a 3.462722880      0
#> 154   154   1   b   b   b   a   b   b   a   c   b    c 3.647719519      0
#> 155   155   0   b   b   b   a   d   a   a   b   b    c 1.586994628      0
#> 156   156   0   a   b   b   c   c   a   a   c   b    b 1.735749720      1
#> 157   157   0   b   a   b   c   c   b   b   a   b    a 1.644806151      0
#> 158   158   1   a   b   b   c   c   a   b   c   b    b 1.881330444      0
#> 159   159   0   a   b   a   a   a   b   b   c   b    b 3.941598676      0
#> 160   160   0   a   b   b   b   c   b   b   c   a    c 1.024647409      1
#> 161   161   1   b   a   b   c   c   b   a   b   b    b 2.164948961      0
#> 162   162   1   b   b   a   b   b   a   a   c   b    b 1.573016535      0
#> 163   163   0   a   a   b   a   d   a   b   c   b    c 4.042076603      0
#> 164   164   1   a   a   b   c   a   b   b   c   b    c 2.308520972      0
#> 165   165   0   b   a   a   b   b   b   a   c   b    c 3.560321281      0
#> 166   166   1   b   b   b   c   d   a   a   b   b    c 3.821655032      0
#> 167   167   0   b   a   b   b   a   b   b   c   b    b 3.348169608      0
#> 168   168   0   a   b   b   a   b   b   b   c   b    c 0.855315494      1
#> 169   169   1   a   b   a   c   c   a   b   b   b    b 0.399445394      1
#> 170   170   1   a   a   b   a   c   b   a   c   a    b 2.754753920      0
#> 171   171   1   b   b   b   a   b   a   b   b   b    c 1.683824513      0
#> 172   172   0   b   b   b   a   a   b   a   c   b    a 0.664252100      1
#> 173   173   0   a   b   b   c   c   a   a   c   b    b 1.225418381      0
#> 174   174   0   b   b   a   b   d   a   a   c   a    b 2.052165401      0
#> 175   175   0   a   a   a   c   a   a   b   b   b    a 3.893238385      0
#> 176   176   1   b   b   b   a   d   b   b   a   b    b 2.719518226      0
#> 177   177   1   b   b   a   c   d   b   a   a   a    a 2.814086079      0
#> 178   178   0   a   a   b   b   c   a   b   b   b    a 3.125743607      0
#> 179   179   1   b   b   b   c   c   a   b   c   a    c 3.168227731      0
#> 180   180   1   a   b   b   c   d   a   a   b   a    a 3.946302453      0
#> 181   181   1   a   a   b   b   c   b   b   c   a    c 1.173344950      0
#> 182   182   0   b   a   b   c   a   b   b   c   b    b 2.429282547      1
#> 183   183   1   b   a   b   a   d   b   a   b   b    b 2.650199801      0
#> 184   184   1   a   b   b   c   d   a   b   a   b    c 2.476959355      0
#> 185   185   1   b   b   b   c   d   a   b   b   b    c 1.179992915      0
#> 186   186   0   b   b   b   c   d   a   b   b   b    b 2.234263673      0
#> 187   187   0   a   b   a   b   d   b   b   a   b    c 1.386127357      1
#> 188   188   1   a   a   b   b   d   b   b   b   b    a 3.194935179      0
#> 189   189   0   a   b   b   a   d   a   b   b   b    b 4.047532163      0
#> 190   190   0   a   a   a   a   d   a   a   b   b    c 4.049164846      0
#> 191   191   0   b   a   a   a   c   b   b   c   b    c 2.370213936      0
#> 192   192   0   b   a   b   c   c   a   b   b   b    c 2.175779457      0
#> 193   193   0   a   a   b   a   d   a   a   c   b    c 1.731241612      1
#> 194   194   1   b   b   b   c   d   a   a   b   a    b 2.952289037      0
#> 195   195   0   a   a   b   b   a   b   b   c   b    c 1.351545711      1
#> 196   196   1   a   a   b   c   b   b   b   c   b    c 3.402068211      0
#> 197   197   1   b   b   a   c   a   b   a   c   b    a 1.708395166      0
#> 198   198   0   b   b   b   b   d   b   b   b   b    b 1.837236536      0
#> 199   199   0   a   b   b   b   c   b   a   c   b    b 1.650132711      0
#> 200   200   0   b   b   b   a   b   b   a   c   a    c 1.964878347      0
#> 201   201   1   a   b   b   b   c   b   b   c   a    b 1.646174945      0
#> 202   202   0   a   b   b   b   d   b   b   c   a    b 1.867413208      1
#> 203   203   1   b   a   b   c   d   b   a   a   b    c 1.530580460      0
#> 204   204   0   b   b   b   a   c   b   b   a   b    b 1.939617895      1
#> 205   205   1   b   a   b   c   a   b   a   c   b    c 0.950205476      1
#> 206   206   0   a   b   b   c   a   b   b   c   b    c 2.584497682      0
#> 207   207   1   b   b   a   b   d   a   a   b   b    b 3.516620693      0
#> 208   208   1   b   b   b   c   a   a   b   b   b    c 0.325832215      1
#> 209   209   0   b   b   a   a   d   b   a   b   b    b 1.754429473      1
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#> 
#> attr(,"class")
#> [1] "bonsaiforest" "naivepop"