From 9d53da37901ac984803fab566df964816b1043e6 Mon Sep 17 00:00:00 2001
From: David Smith <smitdave@gmail.com>
Date: Sat, 20 Jan 2024 09:43:07 -0800
Subject: [PATCH] xde_setup_cohort bug fixes

---
 .README.md.swp            | Bin 16384 -> 0 bytes
 R/adult-GeRM.R            |   4 ++--
 R/adult-RM.R              |   5 ++++-
 R/compute_terms.R         |   4 ++--
 R/diffeqn.R               |   4 ++--
 R/plot-terms.R            |   2 +-
 R/setup.R                 |  18 +++++++++++++-----
 _pkgdown.yml              |   4 ++++
 man/xDE_diffeqn_cohort.Rd |   2 +-
 man/xde_setup_cohort.Rd   |   9 ++++++---
 vignettes/human_hmoi.Rmd  |  23 +++++++----------------
 vignettes/human_sip.Rmd   |  16 ++++++----------
 vignettes/human_sis.Rmd   |  18 ++++++------------
 13 files changed, 54 insertions(+), 55 deletions(-)
 delete mode 100644 .README.md.swp

diff --git a/.README.md.swp b/.README.md.swp
deleted file mode 100644
index ec69c3c980f90b17982581827742142f7b20d31d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 16384
zcmeHN%a0sK9qteU5-0@m5*MWMT7sR`&STfcu{StovX6L3)-1bgTgXCoO?ORCvE5zc
zuI?F+4}>F#a0nMTa|t(c<00`MaDWR3g1GVc3*ZKPU-e^V*K3ea5IOWJ<;_ml<5%DB
z`#pPxy*q<_ajnzy@bhuc`|SFcgLfYP@rBzz^E?~tERa*hNB{08h-_PrW7XEN^gEI9
zWpwWJZ&e$1L!EWiqn+LE;ckCtf436{=PqbIY!GM=cn=YH-n+E9;Y|JF$_4SsPuzYF
z_inao5NHr+5NHr+5NHr+5NHr+5NHs1zax-Mp7q{<kRK=oZI!>DIrICU<<A$&&)3d8
z|3~@!qvhvcJM+B!v-#B^&>+wt&>+wt&>+wt&>+wt&>+wt&>+wt&>--CKtSTn``2;q
zr&;jh{eM;ezw?6U{S@Oz7@x!V;m17hIgGcT_q-oqyoK>?j5jde{D|j$599R@dERRn
z<~h&%!v{U@U5xKO>v`Y7xPkF9MhByf@mn+;euMFAj9+5Bh4FoiH!<FYEWgM29mcOP
zeu43GjGth<jqw=_%KIsd|IN>yNrg^ECXHpLO(Nvb<e3<onaGUrO_HU0m}iQAWn(1*
zHC2(B#45>z83}%~VO>ljC9M*vl7TRJDrA~zKT-nQJ-Lz0#Dl306P0CZb!EFcK_}r#
z>%j%#c^5B=<xf5D!Gi~$PHZNls56oNi42upUE$FyE%(stN0~|!TmZt&*TvlA!j}o|
z<raxRr^?TwxfrD;7WcLf`?tQaI?l3*-RgGzR3@FYJxR?sF{xwHuv;E-okz69YI(h(
z5^^R}KrzN02*y;UmYCr`?kQq97m3LPX7X_)Gi9^oS+DBsW<G3f6?X!bnK6;w+A0OT
zk1vai^Wo}B5VXfKowzTK;Es_VrZSzcRtw5oADjAy=N#wmS{%48(mZh@jZ74o8L$?S
zPL!nzeG@3`BY@YTu*&jA9jAps0iWZA=N;ol76|deD|>n3{?D$6!1y`oV1<(YSd7Xi
zpvJ_cnF_>k?v5@&#nz{G>K9zWMq_D3Y=Ey$+JTy6V{9Q~fN$6Fkssv&<%XE*QKpgr
zJI`cvg1u9dhhtu)B%4*4$S0T?xO+?N8mNeOTq2%&bpMN&E`xIGLW(fg0O35k;wiRq
zhdNn!48TmBD2t8B6fuMLoN%CGBw$iLXXOwTCQ;7C^1<;fu?me7OP}XvFdPB}ldvr@
zgee6eji13XodKG&vQPc{kpkwx8yD!nW~hIizz9atS3J5<22RVy2Bztocw!Q#rBxZ^
zQ3i4B!(3;E=*ovVl<c4W4A&m#u}o~Mz`zn+DXflj5Zk#5X9XH(VJC7_=dqZ|C|4FT
zft?`~0ShDxYA1mkSzJ1G-h%j869ak*3i~R_Kwa_gAT<*ZY?g?LOjKm)ou&%%!1=(>
z+?%PP)tOotb7?r8!jL-J6yLpSbp%OwsUk4Anm9J$9Jrto8*o`!AO23^I7)(xriI?D
z&}1Tc4w*{|n^ETcfz+|3f5f^`9>L9kZ(O=1bhcP$;U@F24LY?a5gY|ol4k{yRG1XQ
z)WCuIk+jY*mymV@wv~89&7m_-WUPIl0$o*10g{z!+ZkLNzlcV1O(d8QssyUpFT~T?
z+}YevDOkTh)^P0sHZIIbQoy06Q>BN)t_m9jcFP@ISvl@aXIR{Y(IM4SteC>J<e(i`
z?^YGF0&O9MKc?TIMpKEWU_zuVyhlx1ZsxcuW@8PHqTODQjPZz=72cIlL!T}T1$s16
zDU}1m0~?*t_9Z83Z5G85!^oIGjFc+9Ngz}RZz$(PmEL`*O=LoiZ}vfxuuMt^+dvQ$
zsSb63PXjfA_jD44Ij#Z2Q*i#!34<tBQX3ZQRN~KHDm(~|NJDy1C$J0xO<?IKVElOs
zOvd>BAvgqO)Lg?E&Z+ni4EF`^v87W8zz9?(bwpSeLM)wI96L4Iabpx|KZEXR29@%}
z1G=rPE&OxeA^0$PP(e(^DiNkK&^VF$2OczLpg)zVmP7dEBAyl=rsTX^UwRrxOSn$h
z1;|idh1;q}zKSC5YfZ!;N_)Q-s3ZPW7&8JhjFEpMHiH@=e=o;qcqJH(!FDO)`#I`g
z-utkFGvT3`6hN9(g)(ITLBydvv>lz~Cb#WO!yA!iG9m8)E+>GwehRJv0OKQ0kr4Ox
zwV#^yzIkQgeoD84_1!9jyIGjj0$AYt%%mp>fle9_+g3irnNh8GnDl8r)oY!ZfJAgd
z2y%4IGMYceU!|7@WPDV5jAd^yG-*Q5R`>xCoaa3Nh@FGCaA;U+QWyym4<d~S3a520
z(iN?$`_W>dJmz@LMw~2ywomgcos!El7DA9<3)x6|P(s$0RxJ)pEOqiyy_xc9taHcp
ziJ4T9slMCN{Xy4qTc^=-BlU<*5t^^#HPV$COp?4JflmkG!kA+TW7g6=ubeH77Wt0z
zJcXInx|NYN!sZh`M-+HM%q3-6pp)s525>I;F3moj1%=LCLB2r624*^es}!JSg50<`
zo<QMJKCT87YGIZWcxGJA;glCzcV3S0EcnJbG<|;R%ZVH!(q|fA!ZZrS7B*Pn@U)=g
zGRnIQ7GMYIf5Y>>bfMiwz7s&^Ek<O~Zoll^yKp8!pUq~p{gcq;=Ed}GnR>hM-dY&o
ze@f=Ld#r-PM|!$gq~ow-5&ojUGGlNjbjw-o&EDo_XJez&d$F^*xp{T7clmM~nNB#)
z!W6!G>1@i0RVns%lG3Zd$8|S)Sl`>|p0m?*qeY3Bg8ODkqVfYu6OL<FLe#pb1QLJT
zrFOec?}fY_I}LAS=0qjekFMO^-o1JG^{cNe2`49$&eL~wQXICo_jlR|&;H2*n{zyx
z6N7$igi^wGmzFI=SvvV?JIJDdXq{$(OBWpvyo-g;UfpH7Z#4pr*jaY;yH%WbKC$NC
z88_!R3S((`tp9(EI{nWWtpBU`_kTxS|2K>jA3Vh9qQ387Jo919!}u%a|D{~_C$4RN
z8Uz{y8U)^_2%tCPY8zJ~xNhB2f^nA}saqPp^o~xE8emeHnTVS*O%a>7O`f1KJjjPA
z8N^K#K<H}BkOiP@V9s2&b8a2&F@0vC?5YD%Cg<y7ZEf3?Y0OZVHN2ux;jgWU)q}xx
z@fDdED~=v#8X2~kYIHn`bfsMGPO3KL>TQ!C)+0wlU!(7%ZcxaOkdI<M!e7j@IqjB9
zypUcV`6yU0cMsPH+=uH38|?oXEG&8>$I2fkE^%BJg9Kuf^O)});6e#XlChpxv3fi>
zKm+g|FN?_EyK?oaSj0vK{KSqrp_z8s84RqFDPl7_C4K&Vqknhj{$S^NwY23j#^v4q
zo6R;ZUA}r{6ZH@9d=k!eaR=8>De|;T+)hx6qeq#|TPQkqp6uN^xJv@CNrRM;;3E-4
zPR;TUHJWQA664!P3z*p()ER4WD4>sGE)AI!62U<-a&1DeYexeT^c2PFtwDdV(<0qS
zBj)-=zZGmbDhq>S7Rauy;V%6^PS{8gcZyCJc#x&&gt1L<h~gs1q3q+L!BNx_T(w_j
z=DU%OtKJ3fbUPiQ^6QUM6z7RJD#|BIP9F9)M1Qbx<<g~VSBa>&E_UP;HS_D@2%VEL
zU@p24%!6y7P$5PUdQnW)Q6;(>y`=hy5d#}NO_qa#wH<Lr7btg@iou~u&|zTL#$ivy
zs&xM;2RnF6eXXsPr_@*>se(y>>v5b{yg$m*snWOwjpg&~2`RLML#nd^k-&wxiG=AM
z4vzL)1Z?y6#<l*SclFwp7cUbq3&dV^JlQd+Rp`DiNXN~#(LjOD5|m3vz<!VEE2?Qz
zR8sqBPFnGrjOUW3_#|<lYG+jN151e4TA^QB_7(&7K#QIg=&_CTo81M7v0Jtra9Lcd
zx?#Qh>R@|!|FBhg6}D85*q1CSoVrCbLz4;X?F0_Rc|tY@a!0?Sx^%v%N<{^eWMUek
zrABWO6^o#r5&G;P^6?mDDBPiMvaCfh5Bmp$ogL7!x;BY)VBm@I@&XH<gh=d^bv*p&
zS7GdsfNv+z##nd4RCacTQ)FwN%+PX5DPa`@cwBM6g4qy>Gb4J=y^h$8&<zv&{%b0E
ztZ~4eK_dmh;yl>laQ67R1uh<2`e^9GR45a6sD!Eu(1m5e@i@0rH<uVdP=7j$B1J*R
zS0Ro)<>43a2UdYTI(5p2?xT4N{-vfi0j%9hMS;?<klKS=cSP?}?@F(Co+mg<?7I>%
zA_+5-lo6~hv3bEVEFSjv51>sm%pp{tts1nBT(6<#V4+<wnn3$}|KVCXMIW(fpB6oi
zp`xbB`W;MK3f;1DmT~F-SbM@-7NOM%Q9)iHMOO{7?H{yn-xZlc93^S!<Lih)Ixg;5
zzLtRP9HBXqA%9prD>_eHUF=x+47Y3XG6Sn%;uFXQ5Z%+tt3oO`TS`-7Q&ADu<Cb+`
zKcg_jmZ|2us&%oi6ZBfyrW%#`N_7nF_!yhu2+5}<c*GHw?b`db)(B_uZlmZg*F7XM
zuf&skRMy=-U1-9~ussal1J&@IhU+9sSU#3-_IlSUgm+`cN=R@}cH%6|rwpcNIkp#J
z(?E8_0NOF;M8r87;*mj@#~C``+JPv@rFbfXE1?*7gmYdHnr2sameB!#C&e^qgB@J<
zye2NmbEb~2kz0ft5_TDdI652i%|^<1N<+MO<q1W%r$()MAB#m`kn@iT(hM~9C0+!M
znNzTH?w%5r08PZ0-4iiKCmg+4_F5yfRs*rRraEC~4f^aK-GogI5|}YqY$wP7z%g;6
l@YZCEW|YGHUFLGCnO~fQS1t?+d=1Ncm<0WL^rOLqe*yink{AF0

diff --git a/R/adult-GeRM.R b/R/adult-GeRM.R
index d2ee336a..7f07b8b0 100644
--- a/R/adult-GeRM.R
+++ b/R/adult-GeRM.R
@@ -67,7 +67,7 @@ dMYZdt.GeRM_ode <- function(t, y, pars, s) {
     with(pars$MYZpar[[s]],{
 
       Omega <- make_Omega(g, sigma, calK, nPatches)
-      Upsilon <- expm(-Omega*eip)
+      Upsilon <- expm::expm(-Omega*eip)
 
       dMdt <- Lambda - (Omega %*% M)
       dGdt <-  f*(M - G) - nu*G  - (Omega %*% G)
@@ -121,7 +121,7 @@ dMYZdt.GeRM_dde <- function(t, y, pars, s){
       dGdt <-  f*(M - G) - nu*G  - (Omega %*% G)
       dYdt <- f*q*kappa*(M - Y) - (Omega %*% Y)
       dZdt <- Upsilon %*% (fqkappa_eip * (M_eip - Y_eip)) - (Omega %*% Z)
-      dUdt <- as.vector(((1-dEIPdt(t,pars))*Omega_eip - Omega) %*% Upsilon)
+      dUdt <- as.vector(((1-dEIPdt(t,EIPmod))*Omega_eip - Omega) %*% Upsilon)
 
       return(c(dMdt, dGdt, dYdt, dZdt, dUdt, f*q*kappa, g, sigma))
     })
diff --git a/R/adult-RM.R b/R/adult-RM.R
index 5d6adea3..1cf1aaf2 100644
--- a/R/adult-RM.R
+++ b/R/adult-RM.R
@@ -63,6 +63,9 @@ dMYZdt.RM_ode <- function(t, y, pars, s) {
     Z <- y[Z_ix]
 
     with(pars$MYZpar[[s]],{
+      Omega <- make_Omega(g, sigma, calK, nPatches)
+      Upsilon <- expm::expm(-Omega*eip)
+
       dM <- Lambda - (Omega %*% M)
       dP <- f*(M - P) - (Omega %*% P)
       dY <- f*q*kappa*(M - Y) - (Omega %*% Y)
@@ -350,7 +353,7 @@ make_parameters_MYZ_RM <- function(pars, g, sigma, f, q, nu, eggsPerBatch, eip,
 
   Omega   <- make_Omega(g, sigma, calK, pars$nPatches)
   MYZpar$Omega <- Omega
-  MYZpar$Upsilon <- expm(-Omega*eip)
+  MYZpar$Upsilon <- expm::expm(-Omega*eip)
   MYZpar$EIPmod <- setup_eip_static(eip=eip)
   MYZpar$eip <- eip
   MYZpar$calK <- calK
diff --git a/R/compute_terms.R b/R/compute_terms.R
index 50656dc7..7a950f3b 100644
--- a/R/compute_terms.R
+++ b/R/compute_terms.R
@@ -66,8 +66,8 @@ compute_terms.xde <- function(varslist, deout, pars, s, i) {
 compute_terms.cohort <- function(varslist, deout, pars, s, i) {
   time = deout[,1]
   d1 = length(time)
-
-  eir = matrix(pars$F_eir(time, pars), d1, pars$Hpar[[i]]$nStrata)
+  eir = as.matrix(with(pars$EIRpar, sapply(time, pars$F_eir, bday=bday, scale=scale)))
+  eir = shapeIt(eir, d1, pars$Hpar[[i]]$nStrata)
   ni = compute_NI(deout, pars, i)
   pr = F_pr(varslist, pars, i)
   return(list(time=time,eir=eir,pr=pr,ni=ni))
diff --git a/R/diffeqn.R b/R/diffeqn.R
index 881a91ad..71076f25 100644
--- a/R/diffeqn.R
+++ b/R/diffeqn.R
@@ -138,13 +138,13 @@ xDE_diffeqn_mosy <- function(t, y, pars) {
 #' @param a age of a cohort
 #' @param y state vector
 #' @param pars a [list]
-#' @param F_eir a trace function that returns the eir
+#' @param F_eir a trace function that returns the eir as a function of time
 #' @return a [list] containing the vector of all state derivatives
 #' @export
 xDE_diffeqn_cohort <- function(a, y, pars, F_eir) {
 
   # EIR: entomological inoculation rate trace
-  pars$EIR[[1]] <- F_eir(a, pars)*pars$BFpar$relativeBitingRate[[1]][[1]]
+  pars$EIR[[1]] <- with(pars$EIRpar, F_eir(a, bday, scale))*pars$BFpar$relativeBitingRate[[1]][[1]]
 
   # FoI: force of infection
   pars <- Exposure(a, y, pars)
diff --git a/R/plot-terms.R b/R/plot-terms.R
index 1fcca019..f940bc43 100644
--- a/R/plot-terms.R
+++ b/R/plot-terms.R
@@ -101,7 +101,7 @@ xde_plot_PR = function(pars, i=1, clrs="black", llty=1, stable=FALSE, add_axes=T
               ylab = "Prevalence", xlab = "Time")
   }
 
-  xde_lines_PR(tm, vars$terms$PR[[i]], pars$Hpar[[i]]$nStrata, clrs, llty)
+  xde_lines_PR(tm, vars$terms$pr[[i]], pars$Hpar[[i]]$nStrata, clrs, llty)
 }
 
 #' Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity
diff --git a/R/setup.R b/R/setup.R
index b44eb97c..94c14c8f 100644
--- a/R/setup.R
+++ b/R/setup.R
@@ -301,15 +301,16 @@ xde_setup_human = function(modelName = "unnamed",
 
 #' @title Set up a model for xde_diffeqn_cohort
 #' @param F_eir is a function F_eir(t, pars) that returns the daily FoI
+#' @param bday the birthday of a cohort
+#' @param scale the birthday of a cohort
 #' @param modelName is a name for the model (arbitrary)
 #' @param Xname is a character string defining a X model
 #' @param HPop is the number of humans in each patch
 #' @param searchB is a vector of search weights for blood feeding
-#' @param residence is a vector that describes the patch where each human stratum lives
 #' @param Xopts a list to configure the X model
 #' @return a [list]
 #' @export
-xde_setup_cohort = function(F_eir,
+xde_setup_cohort = function(F_eir, bday=0, scale=1,
                            modelName = "unnamed",
 
                            # Dynamical Components
@@ -318,7 +319,6 @@ xde_setup_cohort = function(F_eir,
                            # Model Structure
                            HPop=1000,
                            searchB = 1,
-                           residence = 1,
 
                            # Human Strata / Options
                            Xopts = list()
@@ -329,18 +329,26 @@ xde_setup_cohort = function(F_eir,
   class(pars$xde) <- "cohort"
   class(pars$compute) = "cohort"
 
+  pars$nVectors = 1
+  pars$nHosts = 1
+  pars$nPatches = 1
+
   pars$modelName = modelName
   pars$Xname = Xname
 
   pars$F_eir = F_eir
+  pars$EIRpar = list()
+  pars$EIRpar$bday = bday
+  pars$EIRpar$scale = scale
 
   # Structure
   nStrata = length(HPop)
-  pars$nPatches = as.integer(nStrata)
-  pars$nHosts = 1
+  residence = rep(1, nStrata)
 
   pars = setup_Hpar_static(pars, 1, HPop)
   pars = setup_BloodFeeding(pars, 1, 1, list(), residence, searchB, NULL)
+  pars$BFpar$TimeSpent[[1]] = make_TimeSpent_athome(1, residence)
+  pars = make_TaR(0, pars, 1, 1)
 
   # Dynamics
   pars = setup_Xpar(Xname, pars, 1, Xopts)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2e6ea213..2ac0767c 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -809,6 +809,10 @@ reference:
   - compute_terms.human
   - compute_terms.na
   - compute_terms_steady
+  - compute_fqZ
+  - compute_fqZ_ix
+  - compute_fqM
+  - compute_fqM_ix
   - compute_NI
   - compute_NI_ix
   - compute_vars_full
diff --git a/man/xDE_diffeqn_cohort.Rd b/man/xDE_diffeqn_cohort.Rd
index a19811ee..5ebd9d96 100644
--- a/man/xDE_diffeqn_cohort.Rd
+++ b/man/xDE_diffeqn_cohort.Rd
@@ -13,7 +13,7 @@ xDE_diffeqn_cohort(a, y, pars, F_eir)
 
 \item{pars}{a \link{list}}
 
-\item{F_eir}{a trace function that returns the eir}
+\item{F_eir}{a trace function that returns the eir as a function of time}
 }
 \value{
 a \link{list} containing the vector of all state derivatives
diff --git a/man/xde_setup_cohort.Rd b/man/xde_setup_cohort.Rd
index 32837257..fac9c86e 100644
--- a/man/xde_setup_cohort.Rd
+++ b/man/xde_setup_cohort.Rd
@@ -6,17 +6,22 @@
 \usage{
 xde_setup_cohort(
   F_eir,
+  bday = 0,
+  scale = 1,
   modelName = "unnamed",
   Xname = "SIS",
   HPop = 1000,
   searchB = 1,
-  residence = 1,
   Xopts = list()
 )
 }
 \arguments{
 \item{F_eir}{is a function F_eir(t, pars) that returns the daily FoI}
 
+\item{bday}{the birthday of a cohort}
+
+\item{scale}{the birthday of a cohort}
+
 \item{modelName}{is a name for the model (arbitrary)}
 
 \item{Xname}{is a character string defining a X model}
@@ -25,8 +30,6 @@ xde_setup_cohort(
 
 \item{searchB}{is a vector of search weights for blood feeding}
 
-\item{residence}{is a vector that describes the patch where each human stratum lives}
-
 \item{Xopts}{a list to configure the X model}
 }
 \value{
diff --git a/vignettes/human_hmoi.Rmd b/vignettes/human_hmoi.Rmd
index 4b02e84d..2c318667 100644
--- a/vignettes/human_hmoi.Rmd
+++ b/vignettes/human_hmoi.Rmd
@@ -92,7 +92,7 @@ m20 <- 1.5
 h <- r2*m20
 m10 <- h/r1
 
-EIR <- h/b
+EIR <- rep(h/b, 3) 
 ```
 
 ```{r}
@@ -101,12 +101,13 @@ params$nStrata = nStrata
 params$nVectors = 1 
 params$nHosts = 1
 params$nPatches = 1 
-params$eir = rep(EIR, 3)
 params$EIR = list()
 
-F_eir = function(t, pars){
-  pars$EIR[[1]] = pars$eir
-}
+fF_eir = function(EIR){
+  EIR = as.vector(EIR) 
+  return(function(t, bday=0, scale=1){EIR})
+} 
+F_eir = fF_eir(EIR)
 
 params = make_parameters_demography_null(pars = params, H=H) 
 
@@ -152,17 +153,7 @@ Hpop = c(100, 500, 250)
 ```
 
 ```{r}
-h/b
-```
-
-
-```{r}
-fF_eir1 = function(EIR){return(function(t, pars){EIR})} 
-F_eir1 = fF_eir1(EIR)
-```
-
-```{r}
-xde_setup_cohort(F_eir1, Xname="hMoI", HPop=Hpop, Xopts = Xo) ->test_hMoI
+xde_setup_cohort(F_eir, Xname="hMoI", HPop=Hpop, Xopts = Xo) ->test_hMoI
 ```
 
 ```{r}
diff --git a/vignettes/human_sip.Rmd b/vignettes/human_sip.Rmd
index 2d4e111e..011f9f1e 100644
--- a/vignettes/human_sip.Rmd
+++ b/vignettes/human_sip.Rmd
@@ -91,9 +91,11 @@ params$nHosts = 1
 params$eir = EIR
 params$EIR = list()
 
-F_eir = function(t, pars){
-  pars$EIR[[1]] = params$eir
-}
+fF_eir = function(EIR){
+  EIR = as.vector(EIR) 
+  return(function(t, bday=0, scale=1){EIR})
+} 
+F_eir = fF_eir(EIR)
 
 params = make_parameters_demography_null(pars = params, H=H) 
 
@@ -138,15 +140,9 @@ Xo = list(b=0.55, c=0.15, r=1/200,
 Hpop = c(100, 500, 250)
 ```
 
-To use `xde_setup_cohort` we must set up a function `F_eir` returns the value of EIR we computed above:  
 
 ```{r}
-fF_eir1 = function(EIR){return(function(t, pars){EIR})} 
-F_eir1 = fF_eir1(EIR)
-```
-
-```{r}
-xde_setup_cohort(F_eir1, Xname="SIP", HPop=Hpop, Xopts = Xo) -> test_SIP
+xde_setup_cohort(F_eir, Xname="SIP", HPop=Hpop, Xopts = Xo) -> test_SIP
 ```
 
 ```{r}
diff --git a/vignettes/human_sis.Rmd b/vignettes/human_sis.Rmd
index f1323527..3b221341 100644
--- a/vignettes/human_sis.Rmd
+++ b/vignettes/human_sis.Rmd
@@ -102,10 +102,11 @@ params$nHosts = 1
 params$eir = EIR
 params$EIR = list() 
 
-params$eir = as.vector(EIR)
-F_eir = function(t, pars){
-  pars$EIR[[1]] = pars$eir
-}
+fF_eir = function(EIR){
+  EIR = as.vector(EIR) 
+  return(function(t, bday=0, scale=1){EIR})
+} 
+F_eir = fF_eir(EIR)
 
 params = make_parameters_demography_null(pars = params, H=H) 
 
@@ -153,15 +154,8 @@ Hpop = c(100, 500, 250)
 ```
 
 
-To use `xde_setup_cohort` we must set up a function `F_eir` returns the value of EIR we computed above:  
-
-```{r}
-fF_eir1 = function(EIR){return(function(t, pars){EIR})} 
-F_eir1 = fF_eir1(EIR)
-```
-
 ```{r}
-xde_setup_cohort(F_eir1, Xname="SIS", HPop=Hpop, Xopts = Xo) -> test_SIS
+xde_setup_cohort(F_eir, Xname="SIS", HPop=Hpop, Xopts = Xo) -> test_SIS
 ```
 
 ```{r}