harrelfe / rmsb Goto Github PK

Warning message:
“'survival::survConcordance.fit' is deprecated.
Use 'concordancefit' instead.
See help("Deprecated")”

library(rms)
#> Loading required package: Hmisc
#> Loading required package: lattice
#> Loading required package: survival
#> Loading required package: Formula
#> Loading required package: ggplot2
#> 
#> Attaching package: 'Hmisc'
#> The following objects are masked from 'package:base':
#> 
#>     format.pval, units
#> Loading required package: SparseM
#> 
#> Attaching package: 'SparseM'
#> The following object is masked from 'package:base':
#> 
#>     backsolve
library(Hmisc)
library(rmsb)
#> Warning: package 'rmsb' was built under R version 4.1.0

DAT<-readRDS("C:/Users/Alberto/Desktop/caterina bayes/datos", refhook = NULL)

DAT$RR_PAC5<-DAT$RR_PAC4
DAT$RR_PAC5[DAT$RR_PAC5==1]<-0
DAT$RR_PAC5[DAT$RR_PAC5==2]<-1
DAT$RR_PAC5[DAT$RR_PAC5==3]<-2
DAT$RR_PAC5<-factor(DAT$RR_PAC5)

dd<-datadist(DAT)
options(datadist='dd')
bsix2 <- blrm(HE6  ~ cir * rcs(Age,3)+ linf+ RR_PAC5 + Esquema2+Estadio3  + pol(EORTC), 
             ~  pol(EORTC), cppo=function(y) y, data=DAT, file='C:/Users/Alberto/Desktop/caterina bayes/mod_finalint.rds') 
bsix2
#> Frequencies of Missing Values Due to Each Variable
#>      HE6      cir      Age     linf  RR_PAC5 Esquema2 Estadio3    EORTC 
#>        0        0        0        0        0        0        0        2 
#> 
#> Constrained Partial Proportional Odds Ordinal Logistic Model
#>  
#>  blrm(formula = HE6 ~ cir * rcs(Age, 3) + linf + RR_PAC5 + Esquema2 + 
#>      Estadio3 + pol(EORTC), ppo = ~pol(EORTC), cppo = function(y) y, 
#>      data = DAT, file = "C:/Users/Alberto/Desktop/caterina bayes/mod_finalint.rds")
#>  
#>  
#>  Frequencies of Responses
#>  
#>     0  8.3 16.7   25 33.3 41.7   50 58.3 66.7   75 83.3 91.7  100 
#>     5    1    4    1    9    2   43   18   35   20   48    8   23 
#>  
#>  
#>                    Mixed Calibration/             Discrimination               Rank Discrim.    
#>                Discrimination Indexes                    Indexes                     Indexes    
#>     Obs217    LOO log L-458.6+/-12.05    g   1.15 [0.896, 1.414]    C   0.651 [0.629, 0.671]    
#>  Draws4000     LOO IC    917.2+/-24.1    gp 0.228 [0.188, 0.269]    Dxy 0.301 [0.258, 0.342]    
#>    Chains4    Effective p27.62+/-2.08    EV  0.177 [0.119, 0.23]                                
#>     p   13     B 0.214 [0.203, 0.225]    v   1.18 [0.634, 1.712]                                
#>                                          vp 0.042 [0.029, 0.055]                                
#>  
#>                 Mode Beta Mean Beta Median Beta S.E.   Lower   Upper  
#>  cir=1          -0.3048   -0.2117   -0.2311     2.5772 -5.4525  4.6297
#>  Age             0.0781    0.0814    0.0810     0.0422 -0.0042  0.1628
#>  Age'           -0.1145   -0.1195   -0.1186     0.0529 -0.2267 -0.0194
#>  linf            0.2816    0.2868    0.2916     0.3336 -0.3699  0.9325
#>  RR_PAC5=1      -0.5909   -0.5951   -0.5896     0.3487 -1.2717  0.0925
#>  RR_PAC5=2      -0.7137   -0.7289   -0.7364     0.3644 -1.4355 -0.0187
#>  Esquema2       -0.0156   -0.0222   -0.0305     0.3128 -0.6002  0.6123
#>  Estadio3=1      0.0299    0.0286    0.0284     0.3145 -0.5739  0.6349
#>  Estadio3=2     -0.3872   -0.4075   -0.4141     0.5537 -1.5124  0.6412
#>  EORTC           0.2385    0.2528    0.2524     0.0980  0.0573  0.4420
#>  EORTC^2        -0.0013   -0.0014   -0.0014     0.0007 -0.0028 -0.0001
#>  cir=1 * Age    -0.0077   -0.0100   -0.0097     0.0550 -0.1200  0.0943
#>  cir=1 * Age'    0.0103    0.0139    0.0117     0.0723 -0.1251  0.1555
#>  EORTC x f(y)    0.0686    0.0800    0.0776     0.0558 -0.0266  0.1880
#>  EORTC^2 x f(y) -0.0003   -0.0004   -0.0004     0.0004 -0.0012  0.0003
#>                 Pr(Beta>0) Symmetry
#>  cir=1          0.4655     1.02    
#>  Age            0.9755     1.08    
#>  Age'           0.0092     0.96    
#>  linf           0.8090     0.98    
#>  RR_PAC5=1      0.0460     1.01    
#>  RR_PAC5=2      0.0217     1.00    
#>  Esquema2       0.4622     0.99    
#>  Estadio3=1     0.5370     1.04    
#>  Estadio3=2     0.2260     1.01    
#>  EORTC          0.9955     1.00    
#>  EORTC^2        0.0190     1.02    
#>  cir=1 * Age    0.4298     0.97    
#>  cir=1 * Age'   0.5700     1.03    
#>  EORTC x f(y)   0.9290     1.12    
#>  EORTC^2 x f(y) 0.1668     0.88    

summary(bsix2) # not working
#> Error in xd %*% beta: argumentos no compatibles
     
plot(summary(bsix2)) # not working
#> Error in xd %*% beta: argumentos no compatibles

´´´

> install.packages("C:/Users/Alberto/Desktop/caterina/rmsb_current.zip", repos = NULL, type = "win.binary")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Alberto/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open compressed file 'rmsb_current/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : no se puede abrir la conexión

> install.packages("C:/Users/Alberto/Desktop/caterina/rmsb.zip", repos = NULL, type = "win.binary")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Alberto/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
package ‘rmsb’ successfully unpacked and MD5 sums checked
> library(rmsb)
Error: package or namespace load failed for ‘rmsb’ in inDL(x, as.logical(local), as.logical(now), ...):
 unable to load shared object 'C:/Users/Alberto/Documents/R/win-library/3.6/rmsb/libs/x64/rmsb.dll':
  LoadLibrary failure:  No se puede encontrar el módulo especificado.
Además: Warning message:
package ‘rmsb’ was built under R version 4.1.0 

getHdata(titanic3)
dd <- datadist(titanic3); options(datadist='dd')
f <- blrm(age~fare, data=titanic3)

#Works
Predict(f, fare=1000)

#Doesn't work
Predict(f, fare=1000, kint=1)

#Works
predict(f, data.frame(fare=1000), kint=1)

#For reference - doesn't work
predict(f, data.frame(fare=1000), kint=1, ycut=1)

...
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o rmsb.dll tmp.def RcppExports.o stanExports_lrmconppo.o stanExports_lrmcppo.o -LC:/PROGRA~1/R/R-4.0.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/Program Files/R/R-4.0.2/library/RcppParallel/lib/x64 -Wl,-rpath,C:/Program Files/R/R-4.0.2/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/PROGRA~1/R/R-4.0.2/bin/x64 -lR
g++.exe: error: Files/R/R-4.0.2/library/RcppParallel/lib/x64: No such file or directory
no DLL was created
ERROR: compilation failed for package 'rmsb'
* removing 'C:/Program Files/R/R-4.0.2/library/rmsb'
Warning in install.packages :
  installation of package ‘rmsb’ had non-zero exit status

set.seed(836)
data<- data.frame(HE6=sample(1:10, 200, replace = TRUE, prob=c(rep(0.1,6),0.01,0.002,0.19,0.198) ), 
                  Age = sample(1:85, 200, replace = TRUE), EORTC = sample(1:100, 200, replace = TRUE), 
                  linf=rbinom(200, 1,.5),
                  cir=rbinom(200, 1,.5),esquema=rbinom(200, 1,.5), riesgo=factor(rbinom(200, 2,.5)), estadio=factor(rbinom(200, 2,.5)))
head(data)
table(data$HE6)
dd<-datadist(data)
options(datadist='dd')

bsx <- blrm(HE6  ~ cir*rcs(Age,3)+ linf+ pol(EORTC)+esquema+estadio+riesgo, 
            ~ rcs(Age,3)+ pol(EORTC), cppo=function(y) y, data=data) 

newdata <- data.frame(cir=0, Age=85, EORTC= 10, linf=0, riesgo=0, esquema=1, estadio=1)
predict(bsx, newdata, type='fitted.ind') #