make lintr happy (#2)

.lintr

@@ -1,5 +1,6 @@
 linters: linters_with_defaults(
     object_usage_linter = NULL,
-    object_name_lintr = NULL
+    object_name_linter = NULL,
+    line_length_linter(length = 100)
     )
 encoding: "UTF-8"

scratch/test-ngm.R

@@ -16,17 +16,17 @@ vlist <- c(V1, V2)
 params <- list(mu = 0, alpha = 0, beta = 5, gamma = .8, sigma = 1.2, N = 1)
 df <- list(S = 1, E = 0, I = 0, R = 0)
 nextgenR0(
-    Istates = istates, Flist = flist,
-    Vlist = vlist, parameters = params, dfe = df
+  Istates = istates, Flist = flist,
+  Vlist = vlist, parameters = params, dfe = df
 )
 params$beta / params$gamma
 
 ###### SIR Model with two risk groups (high and low) #########
 # example from keeling and rohani
 istates <- c("IH", "IL")
 flist <- c(
-    dIHdt = quote(bHH * SH * IH + bHL * SH * IL),
-    dILdt = quote(bLH * SL * IH + bLL * SL * IL)
+  dIHdt = quote(bHH * SH * IH + bHL * SH * IL),
+  dILdt = quote(bLH * SL * IH + bLL * SL * IL)
 )
 Vm1 <- quote(gamma * IH)
 Vm2 <- quote(gamma * IL)
@@ -36,34 +36,34 @@ V1 <- substitute(a - b, list(a = Vm1, b = Vp1))
 V2 <- substitute(a - b, list(a = Vm2, b = Vp2))
 vlist <- c(V1, V2)
 params <- list(
-    bHH = 10, bHL = 0.1,
-    bLH = 0.1, bLL = 1,
-    gamma = 1
+  bHH = 10, bHL = 0.1,
+  bLH = 0.1, bLL = 1,
+  gamma = 1
 )
 df <- list(
-    SH = 0.2, SL = 0.8,
-    IH = 0, IL = 0,
-    RH = 0, RL = 0
+  SH = 0.2, SL = 0.8,
+  IH = 0, IL = 0,
+  RH = 0, RL = 0
 )
 nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df)
 
 J <- matrix(c(
-    params$bHH * df$SH - params$gamma, params$bHL * df$SH,
-    params$bLH * df$SL, params$bLL * df$SL - params$gamma
+  params$bHH * df$SH - params$gamma, params$bHL * df$SH,
+  params$bLH * df$SL, params$bLL * df$SL - params$gamma
 ), nrow = 2)
 # when params$gamma = 1, R0=
 (params$bHH * df$SH + params$bLH * df$SL) * (1 - (norm(eigen(J)$vectors) - 1)) +
-    (params$bHL * df$SH + params$bLL * df$SL) * (norm(eigen(J)$vectors) - 1)
+  (params$bHL * df$SH + params$bLL * df$SL) * (norm(eigen(J)$vectors) - 1)
 (params$bHH * df$SH + params$bLH * df$SL) * .9376 +
-    (params$bHL * df$SH + params$bLL * df$SL) * .0624
+  (params$bHL * df$SH + params$bLL * df$SL) * .0624
 
 ####### SIR Model with 3 classes ######
 # K, C, G: kids, core, general
 istates <- c("IK", "IC", "IG")
 flist <- c(
-    dIKdt = quote(bKK * SK * IK + bKC * SK * IC + bKG * SK * IG),
-    dICdt = quote(bCK * SC * IK + bCC * SC * IC + bCG * SC * IG),
-    dIGdt = quote(bGK * SG * IK + bGC * SG * IC + bGG * SG * IG)
+  dIKdt = quote(bKK * SK * IK + bKC * SK * IC + bKG * SK * IG),
+  dICdt = quote(bCK * SC * IK + bCC * SC * IC + bCG * SC * IG),
+  dIGdt = quote(bGK * SG * IK + bGC * SG * IC + bGG * SG * IG)
 )
 Vm1 <- quote(gamma * IK)
 Vm2 <- quote(gamma * IC)
@@ -76,14 +76,14 @@ V2 <- substitute(a - b, list(a = Vm2, b = Vp2))
 V3 <- substitute(a - b, list(a = Vm3, b = Vp3))
 vlist <- c(V1, V2, V3)
 params <- list(
-    bKK = 10, bKC = 1, bKG = 1,
-    bCK = 1, bCC = 10, bCG = 1,
-    bGK = 1, bGC = 1, bGG = 1,
-    gamma = 1
+  bKK = 10, bKC = 1, bKG = 1,
+  bCK = 1, bCC = 10, bCG = 1,
+  bGK = 1, bGC = 1, bGG = 1,
+  gamma = 1
 )
 df <- list(
-    SK = 0.1, SC = 0.1, SG = 0.8,
-    IK = 0, IC = 0, IG = 0,
-    RK = 0, RC = 0, RG = 0
+  SK = 0.1, SC = 0.1, SG = 0.8,
+  IK = 0, IC = 0, IG = 0,
+  RK = 0, RC = 0, RG = 0
 )
 nextgenR0(Istates = istates, Flist = flist, Vlist = vlist, parameters = params, dfe = df)