_shiny/incidence_difference_calculator_beta/Incdiff_calc.R

In SACEMA/inctools: Incidence Estimation Tools

# Incidence Estimation Tools (Shiny webapps).
# Copyright (C) 2017-2019, Lamin Juwara, individual contributors and 
# Stellenbosch University.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.  This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
# details.  You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

# Incidence difference estimate function

incdiff_calc <- function(case = 1, I1 = 0.05, I2 = 0.03, PrevH1 = 0.20, PrevH2 = 0.20,
                         alpha = 0.05, 
                         Power = 0.8, DE_H_1 = 1, DE_H_2 = 1.1,
                         DE_R_1 = 1, DE_R_2 = 1 ,
                         MDRI = 200, RSE_MDRI = 0.05, FRR = 0.01, RSE_FRR = 0.20,
                         FRR_1 = 0.01, RSE_FRR_1 = 0.20, 
                         FRR_2 = 0.01, RSE_FRR_2 = 0.30,
                         MDRI_1 = 200, MDRI_2 = 200,
                         RSE_MDRI_1 = 0.05, RSE_MDRI_2 = 0.05,
                         CR_1 = 1, CR_2 = 1, BigT = 730) {
  
  #checks if case is correctly specified
  if(!sum(case == c(1, 2, 3))) {stop("Please enter a valid case value")}
  
  #manual dispatching according to case, passing arguments to the appropriate function
  
  if (1 == case) { #Case I: Assumes that the two surveys use a single MDRI and FRRs estimate.
    temp <- incpower( MDRI = MDRI, FRR = FRR, BigT = BigT, RSE_FRR = RSE_FRR,
                         RSE_MDRI = RSE_MDRI, DE_H = c(DE_H_1,DE_H_2), 
                         DE_R = c(DE_R_1,DE_R_2), I1 = I1, I2 = I2,
                         PrevH1 =  PrevH1, PrevH2 =  PrevH2, Power = Power, alpha = alpha,
                         CR = c(CR_1,CR_2),
                         BMest = 'same.test', SS = "out" )
    incdiff<-temp$Inc.Difference.Statistics
  }
  
  if (2 == case) { #Case II: Assumes that the two surveys use a single MDRI estimate, but that the FRRs are independently estimated
    temp <- incpower( MDRI = MDRI, FRR = c(FRR_1,FRR_2), BigT = BigT, 
                         RSE_FRR = c(RSE_FRR_1,RSE_FRR_2),
                         RSE_MDRI = RSE_MDRI, DE_H = c(DE_H_1,DE_H_2), 
                         DE_R = c(DE_R_1,DE_R_2), I1 = I1, I2 = I2,
                         PrevH1 =  PrevH1, PrevH2 =  PrevH2, Power = Power, alpha = alpha,
                         CR = c(CR_1,CR_2),
                         BMest = 'FRR.indep', SS = "out" )
    incdiff <- temp$Inc.Difference.Statistics
    
  }
  
  if(3 == case) { #Case III: Assumes that the two surveys use MDRI estimates which arise from different incidence tests, and that the FRRs are independently estimated
    temp <-incpower( MDRI = c(MDRI_1,MDRI_2), FRR = c(FRR_1,FRR_2), BigT = BigT, 
                        RSE_FRR = c(RSE_FRR_1, RSE_FRR_2),
                        RSE_MDRI = c(RSE_MDRI_1,RSE_MDRI_2), 
                        DE_H = c(DE_H_1,DE_H_2), 
                        DE_R = c(DE_R_1,DE_R_2), I1 = I1, I2 = I2,
                        PrevH1 =  PrevH1, PrevH2 =  PrevH2, Power = Power, alpha = alpha,
                        CR = c(CR_1,CR_2),
                        BMest = 'MDRI.FRR.indep', SS = "out" )
    incdiff <- temp$Inc.Difference.Statistics
    
  }
  
  return(incdiff)
}